Receptor
PDB id Resolution Class Description Source Keywords
6N97 1.75 Å EC: 4.1.1.- METHYLMALONYL-COA DECARBOXYLASE IN COMPLEX WITH 2-SULFONATE- AMINO(DETHIA)-COA ESCHERICHIA COLI (STRAIN K12) CROTONASE BETA-KETO ISOSTERE LYASE
Ref.: SULFONATE/NITRO BEARING METHYLMALONYL-THIOESTER ISO APPLIED TO METHYLMALONYL-COA DECARBOXYLASE STRUCTURE-FUNCTION STUDIES. J. AM. CHEM. SOC. V. 141 5121 2019
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
KGP F:302;
C:302;
D:302;
B:302;
E:303;
A:302;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
none;
none;
Ki = 7.1 uM
886.61 C24 H41 N8 O20 P3 S C[C@H...
YZS F:303;
C:303;
D:301;
B:301;
C:301;
A:301;
F:301;
E:304;
E:302;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Atoms found LESS than expected: % Diff = 0;
Atoms found LESS than expected: % Diff = 0;
none;
none;
none;
none;
none;
Atoms found LESS than expected: % Diff = 0;
none;
Ki = 7.1 uM
886.61 C24 H41 N8 O20 P3 S C[C@@...
NI A:303;
E:301;
Part of Protein;
Part of Protein;
none;
none;
submit data
58.693 Ni [Ni+2...
IMD D:303;
Invalid;
none;
submit data
69.085 C3 H5 N2 c1c[n...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
6N96 1.7 Å EC: 4.1.1.- METHYLMALONYL-COA DECARBOXYLASE IN COMPLEX WITH 2-SULFONATE- OXA(DETHIA)-COA ESCHERICHIA COLI (STRAIN K12) CROTONASE BETA-KETO ISOSTERE LYASE
Ref.: SULFONATE/NITRO BEARING METHYLMALONYL-THIOESTER ISO APPLIED TO METHYLMALONYL-COA DECARBOXYLASE STRUCTURE-FUNCTION STUDIES. J. AM. CHEM. SOC. V. 141 5121 2019
Members (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 7 families.
1 6N93 Ki = 20.6 uM KGA C24 H38 N8 O20 P3 CC(=[N+]([....
2 6N95 Ki = 7.5 uM YXR C24 H40 N7 O20 P3 S2 C[C@H](C(=....
3 6N96 Ki = 3.8 uM SO5 C24 H40 N7 O21 P3 S C[C@H](C(=....
4 6N92 Ki = 10.8 uM KFV C24 H38 N8 O19 P3 S CC(=[N+]([....
5 6N97 Ki = 7.1 uM KGP C24 H41 N8 O20 P3 S C[C@H](C(=....
6 6N94 Ki = 19.8 uM KGJ C24 H39 N9 O19 P3 CC(=[N+]([....
70% Homology Family (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 7 families.
1 6N93 Ki = 20.6 uM KGA C24 H38 N8 O20 P3 CC(=[N+]([....
2 6N95 Ki = 7.5 uM YXR C24 H40 N7 O20 P3 S2 C[C@H](C(=....
3 6N96 Ki = 3.8 uM SO5 C24 H40 N7 O21 P3 S C[C@H](C(=....
4 6N92 Ki = 10.8 uM KFV C24 H38 N8 O19 P3 S CC(=[N+]([....
5 6N97 Ki = 7.1 uM KGP C24 H41 N8 O20 P3 S C[C@H](C(=....
6 6N94 Ki = 19.8 uM KGJ C24 H39 N9 O19 P3 CC(=[N+]([....
50% Homology Family (12)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 1DUB Ki = 1.6 uM CAA C25 H40 N7 O18 P3 S CC(=O)CC(=....
2 1EY3 - DAK C32 H47 N8 O17 P3 S CC(C)(CO[P....
3 1MJ3 - HXC C27 H46 N7 O17 P3 S CCCCCC(=O)....
4 2DUB - CO8 C29 H50 N7 O17 P3 S CCCCCCCC(=....
5 6N95 Ki = 7.5 uM YXR C24 H40 N7 O20 P3 S2 C[C@H](C(=....
6 6N96 Ki = 3.8 uM SO5 C24 H40 N7 O21 P3 S C[C@H](C(=....
7 6N92 Ki = 10.8 uM KFV C24 H38 N8 O19 P3 S CC(=[N+]([....
8 6N97 Ki = 7.1 uM KGP C24 H41 N8 O20 P3 S C[C@H](C(=....
9 6N94 Ki = 19.8 uM KGJ C24 H39 N9 O19 P3 CC(=[N+]([....
10 5ZAI - COA C21 H36 N7 O16 P3 S CC(C)(CO[P....
11 5DTW Kd = 3.5 uM 5F9 C41 H74 N7 O17 P3 S CCCCCCCCCC....
12 5JBX - MLI C3 H2 O4 C(C(=O)[O-....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: KGP; Similar ligands found: 179
No: Ligand ECFP6 Tc MDL keys Tc
1 YZS 1 1
2 KGP 1 1
3 LCV 0.84375 0.989691
4 SO5 0.84375 0.989691
5 SCO 0.83871 0.865979
6 YXS 0.837209 1
7 YXR 0.837209 1
8 0T1 0.836066 0.865979
9 COA 0.836066 0.885417
10 DCA 0.834711 0.865979
11 ETB 0.819672 0.836735
12 AMX 0.816 0.875
13 CAO 0.816 0.916667
14 30N 0.816 0.96875
15 COS 0.816 0.886598
16 CMX 0.809524 0.865979
17 FAM 0.80315 0.848485
18 ACO 0.80315 0.896907
19 FCX 0.80315 0.84
20 MCD 0.79845 0.867347
21 CA6 0.79845 0.939394
22 HAX 0.796875 0.848485
23 3HC 0.793893 0.895833
24 KGJ 0.793893 0.817308
25 CO6 0.792308 0.90625
26 3KK 0.790698 0.90625
27 FYN 0.790698 0.885417
28 YE1 0.787879 0.857143
29 OXK 0.784615 0.886598
30 SOP 0.784615 0.886598
31 COK 0.784615 0.886598
32 A1S 0.780303 0.867347
33 IVC 0.780303 0.895833
34 BCO 0.780303 0.886598
35 CMC 0.778626 0.867347
36 NMX 0.778626 0.807692
37 1VU 0.778626 0.896907
38 MCA 0.774436 0.896907
39 CAJ 0.772727 0.867347
40 2MC 0.772727 0.87
41 SCD 0.772727 0.865979
42 2CP 0.768657 0.877551
43 MLC 0.766917 0.886598
44 1HE 0.766917 0.868687
45 S0N 0.766423 0.848485
46 3CP 0.762963 0.867347
47 COW 0.762963 0.877551
48 IRC 0.762963 0.895833
49 1GZ 0.762963 0.877551
50 KGA 0.762963 0.809524
51 BYC 0.762963 0.886598
52 CA8 0.762963 0.939394
53 CAA 0.761194 0.895833
54 COO 0.761194 0.886598
55 BCA 0.757353 0.877551
56 FAQ 0.757353 0.886598
57 SCA 0.755556 0.886598
58 MC4 0.755556 0.861386
59 COF 0.75 0.85
60 2KQ 0.75 0.887755
61 HGG 0.75 0.886598
62 KFV 0.75 0.836538
63 4CA 0.744526 0.858586
64 2NE 0.741007 0.868687
65 1CZ 0.741007 0.896907
66 HXC 0.73913 0.887755
67 GRA 0.73913 0.886598
68 TGC 0.733813 0.877551
69 0ET 0.730496 0.868687
70 01A 0.730496 0.833333
71 CO8 0.728571 0.887755
72 CIC 0.728571 0.867347
73 1CV 0.725352 0.886598
74 4CO 0.723404 0.858586
75 UCC 0.723404 0.887755
76 5F9 0.723404 0.887755
77 MYA 0.723404 0.887755
78 DCC 0.723404 0.887755
79 0FQ 0.723404 0.867347
80 MFK 0.723404 0.887755
81 ST9 0.723404 0.887755
82 J5H 0.722222 0.886598
83 4KX 0.72028 0.86
84 MRR 0.715278 0.887755
85 MRS 0.715278 0.887755
86 WCA 0.713287 0.868687
87 CS8 0.713287 0.878788
88 DAK 0.710345 0.86
89 YNC 0.710345 0.877551
90 1HA 0.709459 0.868687
91 NHW 0.708333 0.868687
92 UOQ 0.708333 0.868687
93 HDC 0.708333 0.887755
94 NHM 0.708333 0.868687
95 HFQ 0.703448 0.85
96 8Z2 0.693878 0.878788
97 NHQ 0.684564 0.876289
98 F8G 0.677632 0.852941
99 COD 0.676923 0.875
100 01K 0.671053 0.886598
101 COT 0.666667 0.867347
102 CA3 0.658065 0.867347
103 CCQ 0.657534 0.87
104 7L1 0.652174 0.896907
105 93P 0.64375 0.858586
106 CA5 0.6375 0.833333
107 UCA 0.63354 0.887755
108 CO7 0.627586 0.886598
109 93M 0.624242 0.858586
110 COA FLC 0.618705 0.85567
111 N9V 0.613333 0.84
112 5TW 0.597701 0.852941
113 4BN 0.597701 0.852941
114 OXT 0.586207 0.852941
115 JBT 0.572222 0.836538
116 BSJ 0.565714 0.841584
117 PAP 0.563025 0.71875
118 HMG 0.56129 0.857143
119 PLM COA 0.544304 0.858586
120 COA PLM 0.544304 0.858586
121 PPS 0.536585 0.8125
122 ASP ASP ASP ILE CMC NH2 0.520468 0.83
123 A3P 0.512605 0.708333
124 0WD 0.493151 0.70297
125 RFC 0.48503 0.887755
126 SFC 0.48503 0.887755
127 ACE SER ASP ALY THR NH2 COA 0.470588 0.848485
128 191 0.465839 0.811321
129 PTJ 0.452555 0.773196
130 3AM 0.45 0.697917
131 A22 0.440298 0.721649
132 PUA 0.43871 0.73
133 A2D 0.435484 0.71134
134 PAJ 0.433824 0.783505
135 HQG 0.432836 0.721649
136 3OD 0.431655 0.731959
137 AGS 0.430769 0.770833
138 ATR 0.430769 0.708333
139 SAP 0.430769 0.770833
140 9BG 0.427632 0.70297
141 ADP 0.425197 0.729167
142 A2R 0.422222 0.721649
143 48N 0.421769 0.737374
144 8LE 0.421053 0.752577
145 5AL 0.421053 0.721649
146 8LQ 0.419118 0.742268
147 BA3 0.417323 0.71134
148 OAD 0.417266 0.731959
149 9X8 0.417266 0.752577
150 NA7 0.417266 0.760417
151 ATP 0.415385 0.729167
152 HEJ 0.415385 0.729167
153 8LH 0.414815 0.742268
154 B4P 0.414062 0.71134
155 AP5 0.414062 0.71134
156 YLB 0.413333 0.806122
157 AQP 0.412214 0.729167
158 APR 0.412214 0.71134
159 AR6 0.412214 0.71134
160 2A5 0.412214 0.75
161 5FA 0.412214 0.729167
162 AN2 0.410853 0.721649
163 APU 0.410596 0.7
164 F2R 0.409091 0.77
165 M33 0.407692 0.721649
166 ATF 0.407407 0.707071
167 8QN 0.405797 0.721649
168 SRP 0.404412 0.742268
169 J4G 0.404255 0.752577
170 ANP 0.402985 0.714286
171 ADQ 0.402878 0.714286
172 YLP 0.402685 0.806122
173 FYA 0.401408 0.721649
174 TXA 0.401408 0.72449
175 PAX 0.401235 0.708738
176 NJP 0.4 0.717172
177 AT4 0.4 0.760417
178 00A 0.4 0.676471
179 DLL 0.4 0.704082
Ligand no: 2; Ligand: YZS; Similar ligands found: 179
No: Ligand ECFP6 Tc MDL keys Tc
1 YZS 1 1
2 KGP 1 1
3 LCV 0.84375 0.989691
4 SO5 0.84375 0.989691
5 SCO 0.83871 0.865979
6 YXS 0.837209 1
7 YXR 0.837209 1
8 0T1 0.836066 0.865979
9 COA 0.836066 0.885417
10 DCA 0.834711 0.865979
11 ETB 0.819672 0.836735
12 AMX 0.816 0.875
13 CAO 0.816 0.916667
14 30N 0.816 0.96875
15 COS 0.816 0.886598
16 CMX 0.809524 0.865979
17 FAM 0.80315 0.848485
18 ACO 0.80315 0.896907
19 FCX 0.80315 0.84
20 MCD 0.79845 0.867347
21 CA6 0.79845 0.939394
22 HAX 0.796875 0.848485
23 3HC 0.793893 0.895833
24 KGJ 0.793893 0.817308
25 CO6 0.792308 0.90625
26 3KK 0.790698 0.90625
27 FYN 0.790698 0.885417
28 YE1 0.787879 0.857143
29 OXK 0.784615 0.886598
30 SOP 0.784615 0.886598
31 COK 0.784615 0.886598
32 A1S 0.780303 0.867347
33 IVC 0.780303 0.895833
34 BCO 0.780303 0.886598
35 CMC 0.778626 0.867347
36 NMX 0.778626 0.807692
37 1VU 0.778626 0.896907
38 MCA 0.774436 0.896907
39 CAJ 0.772727 0.867347
40 2MC 0.772727 0.87
41 SCD 0.772727 0.865979
42 2CP 0.768657 0.877551
43 MLC 0.766917 0.886598
44 1HE 0.766917 0.868687
45 S0N 0.766423 0.848485
46 3CP 0.762963 0.867347
47 COW 0.762963 0.877551
48 IRC 0.762963 0.895833
49 1GZ 0.762963 0.877551
50 KGA 0.762963 0.809524
51 BYC 0.762963 0.886598
52 CA8 0.762963 0.939394
53 CAA 0.761194 0.895833
54 COO 0.761194 0.886598
55 BCA 0.757353 0.877551
56 FAQ 0.757353 0.886598
57 SCA 0.755556 0.886598
58 MC4 0.755556 0.861386
59 COF 0.75 0.85
60 2KQ 0.75 0.887755
61 HGG 0.75 0.886598
62 KFV 0.75 0.836538
63 4CA 0.744526 0.858586
64 2NE 0.741007 0.868687
65 1CZ 0.741007 0.896907
66 HXC 0.73913 0.887755
67 GRA 0.73913 0.886598
68 TGC 0.733813 0.877551
69 0ET 0.730496 0.868687
70 01A 0.730496 0.833333
71 CO8 0.728571 0.887755
72 CIC 0.728571 0.867347
73 1CV 0.725352 0.886598
74 4CO 0.723404 0.858586
75 UCC 0.723404 0.887755
76 5F9 0.723404 0.887755
77 MYA 0.723404 0.887755
78 DCC 0.723404 0.887755
79 0FQ 0.723404 0.867347
80 MFK 0.723404 0.887755
81 ST9 0.723404 0.887755
82 J5H 0.722222 0.886598
83 4KX 0.72028 0.86
84 MRR 0.715278 0.887755
85 MRS 0.715278 0.887755
86 WCA 0.713287 0.868687
87 CS8 0.713287 0.878788
88 DAK 0.710345 0.86
89 YNC 0.710345 0.877551
90 1HA 0.709459 0.868687
91 NHW 0.708333 0.868687
92 UOQ 0.708333 0.868687
93 HDC 0.708333 0.887755
94 NHM 0.708333 0.868687
95 HFQ 0.703448 0.85
96 8Z2 0.693878 0.878788
97 NHQ 0.684564 0.876289
98 F8G 0.677632 0.852941
99 COD 0.676923 0.875
100 01K 0.671053 0.886598
101 COT 0.666667 0.867347
102 CA3 0.658065 0.867347
103 CCQ 0.657534 0.87
104 7L1 0.652174 0.896907
105 93P 0.64375 0.858586
106 CA5 0.6375 0.833333
107 UCA 0.63354 0.887755
108 CO7 0.627586 0.886598
109 93M 0.624242 0.858586
110 COA FLC 0.618705 0.85567
111 N9V 0.613333 0.84
112 5TW 0.597701 0.852941
113 4BN 0.597701 0.852941
114 OXT 0.586207 0.852941
115 JBT 0.572222 0.836538
116 BSJ 0.565714 0.841584
117 PAP 0.563025 0.71875
118 HMG 0.56129 0.857143
119 PLM COA 0.544304 0.858586
120 COA PLM 0.544304 0.858586
121 PPS 0.536585 0.8125
122 ASP ASP ASP ILE CMC NH2 0.520468 0.83
123 A3P 0.512605 0.708333
124 0WD 0.493151 0.70297
125 RFC 0.48503 0.887755
126 SFC 0.48503 0.887755
127 ACE SER ASP ALY THR NH2 COA 0.470588 0.848485
128 191 0.465839 0.811321
129 PTJ 0.452555 0.773196
130 3AM 0.45 0.697917
131 A22 0.440298 0.721649
132 PUA 0.43871 0.73
133 A2D 0.435484 0.71134
134 PAJ 0.433824 0.783505
135 HQG 0.432836 0.721649
136 3OD 0.431655 0.731959
137 AGS 0.430769 0.770833
138 ATR 0.430769 0.708333
139 SAP 0.430769 0.770833
140 9BG 0.427632 0.70297
141 ADP 0.425197 0.729167
142 A2R 0.422222 0.721649
143 48N 0.421769 0.737374
144 8LE 0.421053 0.752577
145 5AL 0.421053 0.721649
146 8LQ 0.419118 0.742268
147 BA3 0.417323 0.71134
148 OAD 0.417266 0.731959
149 9X8 0.417266 0.752577
150 NA7 0.417266 0.760417
151 ATP 0.415385 0.729167
152 HEJ 0.415385 0.729167
153 8LH 0.414815 0.742268
154 B4P 0.414062 0.71134
155 AP5 0.414062 0.71134
156 YLB 0.413333 0.806122
157 AQP 0.412214 0.729167
158 APR 0.412214 0.71134
159 AR6 0.412214 0.71134
160 2A5 0.412214 0.75
161 5FA 0.412214 0.729167
162 AN2 0.410853 0.721649
163 APU 0.410596 0.7
164 F2R 0.409091 0.77
165 M33 0.407692 0.721649
166 ATF 0.407407 0.707071
167 8QN 0.405797 0.721649
168 SRP 0.404412 0.742268
169 J4G 0.404255 0.752577
170 ANP 0.402985 0.714286
171 ADQ 0.402878 0.714286
172 YLP 0.402685 0.806122
173 FYA 0.401408 0.721649
174 TXA 0.401408 0.72449
175 PAX 0.401235 0.708738
176 NJP 0.4 0.717172
177 AT4 0.4 0.760417
178 00A 0.4 0.676471
179 DLL 0.4 0.704082
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 6N96; Ligand: SO5; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 6n96.bio1) has 36 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 6N96; Ligand: SO5; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 6n96.bio1) has 37 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 6N96; Ligand: SO5; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 6n96.bio1) has 26 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 6N96; Ligand: LCV; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 6n96.bio1) has 38 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 6N96; Ligand: LCV; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 5) in the query (biounit: 6n96.bio1) has 37 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 6; Query (leader) PDB : 6N96; Ligand: LCV; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 6) in the query (biounit: 6n96.bio1) has 27 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 7; Query (leader) PDB : 6N96; Ligand: SO5; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 7) in the query (biounit: 6n96.bio1) has 38 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 8; Query (leader) PDB : 6N96; Ligand: SO5; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 8) in the query (biounit: 6n96.bio1) has 25 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 9; Query (leader) PDB : 6N96; Ligand: LCV; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 9) in the query (biounit: 6n96.bio1) has 25 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 10; Query (leader) PDB : 6N96; Ligand: LCV; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 10) in the query (biounit: 6n96.bio1) has 36 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 11; Query (leader) PDB : 6N96; Ligand: LCV; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 11) in the query (biounit: 6n96.bio1) has 37 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 12; Query (leader) PDB : 6N96; Ligand: SO5; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 12) in the query (biounit: 6n96.bio1) has 27 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 13; Query (leader) PDB : 6N96; Ligand: LCV; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 13) in the query (biounit: 6n96.bio1) has 26 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 14; Query (leader) PDB : 6N96; Ligand: LCV; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 14) in the query (biounit: 6n96.bio1) has 38 residues
No: Leader PDB Ligand Sequence Similarity
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