Receptor
PDB id Resolution Class Description Source Keywords
6N95 1.8 Å EC: 4.1.1.- METHYLMALONYL-COA DECARBOXYLASE IN COMPLEX WITH 2-SULFONATE- 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
YXR F:302;
C:302;
A:302;
B:302;
D:303;
E:302;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
none;
none;
Ki = 7.5 uM
903.661 C24 H40 N7 O20 P3 S2 C[C@H...
PG4 C:304;
Invalid;
none;
submit data
194.226 C8 H18 O5 C(COC...
PGE F:304;
Invalid;
none;
submit data
150.173 C6 H14 O4 C(COC...
YXS B:301;
A:301;
E:301;
D:302;
F:301;
C:301;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
none;
none;
Ki = 7.5 uM
903.661 C24 H40 N7 O20 P3 S2 C[C@@...
K C:303;
F:303;
Part of Protein;
Invalid;
none;
none;
submit data
39.098 K [K+]
PEG C:305;
F:305;
Invalid;
Invalid;
none;
none;
submit data
106.12 C4 H10 O3 C(COC...
NI A:303;
D:301;
Part of Protein;
Part of Protein;
none;
none;
submit data
58.693 Ni [Ni+2...
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: YXR; Similar ligands found: 154
No: Ligand ECFP6 Tc MDL keys Tc
1 YXR 1 1
2 YXS 1 1
3 CO6 0.888889 0.90625
4 MCA 0.868217 0.896907
5 ACO 0.857143 0.896907
6 IRC 0.854962 0.895833
7 3HC 0.846154 0.895833
8 3KK 0.84375 0.90625
9 CAO 0.84127 0.916667
10 COS 0.84127 0.886598
11 KGP 0.837209 1
12 OXK 0.837209 0.886598
13 YZS 0.837209 1
14 IVC 0.832061 0.895833
15 BCO 0.832061 0.886598
16 1VU 0.830769 0.896907
17 1GZ 0.827068 0.877551
18 LCV 0.825758 0.989691
19 SO5 0.825758 0.989691
20 2MC 0.824427 0.87
21 1HE 0.818182 0.868687
22 MLC 0.818182 0.886598
23 FYN 0.815385 0.885417
24 CAA 0.81203 0.895833
25 COO 0.81203 0.886598
26 COK 0.80916 0.886598
27 SOP 0.80916 0.886598
28 MC4 0.80597 0.861386
29 SCA 0.80597 0.886598
30 A1S 0.804511 0.867347
31 COA 0.80315 0.885417
32 0T1 0.80315 0.865979
33 CMC 0.80303 0.867347
34 DCA 0.801587 0.865979
35 ETB 0.801587 0.836735
36 MRS 0.8 0.887755
37 MRR 0.8 0.887755
38 HGG 0.8 0.886598
39 KFV 0.8 0.836538
40 BYC 0.8 0.886598
41 COW 0.8 0.877551
42 30N 0.79845 0.96875
43 BCA 0.794118 0.877551
44 FAQ 0.794118 0.886598
45 2CP 0.792593 0.877551
46 SCO 0.792308 0.865979
47 GRA 0.788321 0.886598
48 HXC 0.788321 0.887755
49 AMX 0.784615 0.875
50 TGC 0.782609 0.877551
51 CMX 0.778626 0.865979
52 2NE 0.776978 0.868687
53 CO8 0.776978 0.887755
54 1CZ 0.776978 0.896907
55 2KQ 0.773723 0.887755
56 3CP 0.773723 0.867347
57 COF 0.773723 0.85
58 FCX 0.772727 0.84
59 FAM 0.772727 0.848485
60 ST9 0.771429 0.887755
61 MYA 0.771429 0.887755
62 MFK 0.771429 0.887755
63 5F9 0.771429 0.887755
64 DCC 0.771429 0.887755
65 UCC 0.771429 0.887755
66 CA6 0.768657 0.939394
67 MCD 0.768657 0.867347
68 4CA 0.768116 0.858586
69 4KX 0.767606 0.86
70 HAX 0.766917 0.848485
71 WCA 0.760563 0.868687
72 CS8 0.760563 0.878788
73 SCD 0.757353 0.865979
74 YNC 0.756944 0.877551
75 DAK 0.756944 0.86
76 HDC 0.755245 0.887755
77 01A 0.753521 0.833333
78 CIC 0.751773 0.867347
79 NMX 0.75 0.807692
80 1CV 0.748252 0.886598
81 0FQ 0.746479 0.867347
82 4CO 0.746479 0.858586
83 J5H 0.744828 0.886598
84 CAJ 0.744526 0.867347
85 0ET 0.741259 0.868687
86 8Z2 0.739726 0.878788
87 KGJ 0.73913 0.817308
88 CA8 0.735714 0.939394
89 KGA 0.735714 0.809524
90 YE1 0.733813 0.857143
91 UOQ 0.731034 0.868687
92 NHM 0.731034 0.868687
93 NHW 0.731034 0.868687
94 HFQ 0.726027 0.85
95 1HA 0.72 0.868687
96 S0N 0.715278 0.848485
97 F8G 0.710526 0.852941
98 NHQ 0.706667 0.876289
99 CCQ 0.703448 0.87
100 7L1 0.70073 0.896907
101 01K 0.69281 0.886598
102 COT 0.688312 0.867347
103 UCA 0.685535 0.887755
104 CA3 0.679487 0.867347
105 CO7 0.673611 0.886598
106 N9V 0.668919 0.84
107 4BN 0.664706 0.852941
108 5TW 0.664706 0.852941
109 CA5 0.658385 0.833333
110 93P 0.654321 0.858586
111 COD 0.651852 0.875
112 93M 0.634731 0.858586
113 OXT 0.614943 0.852941
114 JBT 0.608939 0.836538
115 HMG 0.603896 0.857143
116 COA FLC 0.597222 0.85567
117 COA PLM 0.585987 0.858586
118 PLM COA 0.585987 0.858586
119 BSJ 0.567416 0.841584
120 SFC 0.542683 0.887755
121 RFC 0.542683 0.887755
122 ASP ASP ASP ILE CMC NH2 0.540698 0.83
123 PAP 0.540323 0.71875
124 PPS 0.527559 0.8125
125 191 0.50625 0.811321
126 ACE SER ASP ALY THR NH2 COA 0.497326 0.848485
127 A3P 0.491935 0.708333
128 0WD 0.476821 0.70297
129 HQG 0.437956 0.721649
130 PTJ 0.43662 0.773196
131 PUA 0.433962 0.73
132 3AM 0.432 0.697917
133 A22 0.42446 0.721649
134 A2D 0.418605 0.71134
135 PAJ 0.41844 0.783505
136 3OD 0.416667 0.731959
137 AGS 0.414815 0.770833
138 ATR 0.414815 0.708333
139 SAP 0.414815 0.770833
140 9BG 0.414013 0.70297
141 ADP 0.409091 0.729167
142 ADQ 0.408451 0.714286
143 48N 0.407895 0.737374
144 A2R 0.407143 0.721649
145 8LE 0.405797 0.752577
146 F2R 0.405063 0.77
147 8LQ 0.404255 0.742268
148 NA7 0.402778 0.760417
149 OAD 0.402778 0.731959
150 BA3 0.401515 0.71134
151 8LH 0.4 0.742268
152 YLB 0.4 0.806122
153 HEJ 0.4 0.729167
154 ATP 0.4 0.729167
Ligand no: 2; Ligand: YXS; Similar ligands found: 154
No: Ligand ECFP6 Tc MDL keys Tc
1 YXR 1 1
2 YXS 1 1
3 CO6 0.888889 0.90625
4 MCA 0.868217 0.896907
5 ACO 0.857143 0.896907
6 IRC 0.854962 0.895833
7 3HC 0.846154 0.895833
8 3KK 0.84375 0.90625
9 CAO 0.84127 0.916667
10 COS 0.84127 0.886598
11 KGP 0.837209 1
12 OXK 0.837209 0.886598
13 YZS 0.837209 1
14 IVC 0.832061 0.895833
15 BCO 0.832061 0.886598
16 1VU 0.830769 0.896907
17 1GZ 0.827068 0.877551
18 LCV 0.825758 0.989691
19 SO5 0.825758 0.989691
20 2MC 0.824427 0.87
21 1HE 0.818182 0.868687
22 MLC 0.818182 0.886598
23 FYN 0.815385 0.885417
24 CAA 0.81203 0.895833
25 COO 0.81203 0.886598
26 COK 0.80916 0.886598
27 SOP 0.80916 0.886598
28 MC4 0.80597 0.861386
29 SCA 0.80597 0.886598
30 A1S 0.804511 0.867347
31 COA 0.80315 0.885417
32 0T1 0.80315 0.865979
33 CMC 0.80303 0.867347
34 DCA 0.801587 0.865979
35 ETB 0.801587 0.836735
36 MRS 0.8 0.887755
37 MRR 0.8 0.887755
38 HGG 0.8 0.886598
39 KFV 0.8 0.836538
40 BYC 0.8 0.886598
41 COW 0.8 0.877551
42 30N 0.79845 0.96875
43 BCA 0.794118 0.877551
44 FAQ 0.794118 0.886598
45 2CP 0.792593 0.877551
46 SCO 0.792308 0.865979
47 GRA 0.788321 0.886598
48 HXC 0.788321 0.887755
49 AMX 0.784615 0.875
50 TGC 0.782609 0.877551
51 CMX 0.778626 0.865979
52 2NE 0.776978 0.868687
53 CO8 0.776978 0.887755
54 1CZ 0.776978 0.896907
55 2KQ 0.773723 0.887755
56 3CP 0.773723 0.867347
57 COF 0.773723 0.85
58 FCX 0.772727 0.84
59 FAM 0.772727 0.848485
60 ST9 0.771429 0.887755
61 MYA 0.771429 0.887755
62 MFK 0.771429 0.887755
63 5F9 0.771429 0.887755
64 DCC 0.771429 0.887755
65 UCC 0.771429 0.887755
66 CA6 0.768657 0.939394
67 MCD 0.768657 0.867347
68 4CA 0.768116 0.858586
69 4KX 0.767606 0.86
70 HAX 0.766917 0.848485
71 WCA 0.760563 0.868687
72 CS8 0.760563 0.878788
73 SCD 0.757353 0.865979
74 YNC 0.756944 0.877551
75 DAK 0.756944 0.86
76 HDC 0.755245 0.887755
77 01A 0.753521 0.833333
78 CIC 0.751773 0.867347
79 NMX 0.75 0.807692
80 1CV 0.748252 0.886598
81 0FQ 0.746479 0.867347
82 4CO 0.746479 0.858586
83 J5H 0.744828 0.886598
84 CAJ 0.744526 0.867347
85 0ET 0.741259 0.868687
86 8Z2 0.739726 0.878788
87 KGJ 0.73913 0.817308
88 CA8 0.735714 0.939394
89 KGA 0.735714 0.809524
90 YE1 0.733813 0.857143
91 UOQ 0.731034 0.868687
92 NHM 0.731034 0.868687
93 NHW 0.731034 0.868687
94 HFQ 0.726027 0.85
95 1HA 0.72 0.868687
96 S0N 0.715278 0.848485
97 F8G 0.710526 0.852941
98 NHQ 0.706667 0.876289
99 CCQ 0.703448 0.87
100 7L1 0.70073 0.896907
101 01K 0.69281 0.886598
102 COT 0.688312 0.867347
103 UCA 0.685535 0.887755
104 CA3 0.679487 0.867347
105 CO7 0.673611 0.886598
106 N9V 0.668919 0.84
107 4BN 0.664706 0.852941
108 5TW 0.664706 0.852941
109 CA5 0.658385 0.833333
110 93P 0.654321 0.858586
111 COD 0.651852 0.875
112 93M 0.634731 0.858586
113 OXT 0.614943 0.852941
114 JBT 0.608939 0.836538
115 HMG 0.603896 0.857143
116 COA FLC 0.597222 0.85567
117 COA PLM 0.585987 0.858586
118 PLM COA 0.585987 0.858586
119 BSJ 0.567416 0.841584
120 SFC 0.542683 0.887755
121 RFC 0.542683 0.887755
122 ASP ASP ASP ILE CMC NH2 0.540698 0.83
123 PAP 0.540323 0.71875
124 PPS 0.527559 0.8125
125 191 0.50625 0.811321
126 ACE SER ASP ALY THR NH2 COA 0.497326 0.848485
127 A3P 0.491935 0.708333
128 0WD 0.476821 0.70297
129 HQG 0.437956 0.721649
130 PTJ 0.43662 0.773196
131 PUA 0.433962 0.73
132 3AM 0.432 0.697917
133 A22 0.42446 0.721649
134 A2D 0.418605 0.71134
135 PAJ 0.41844 0.783505
136 3OD 0.416667 0.731959
137 AGS 0.414815 0.770833
138 ATR 0.414815 0.708333
139 SAP 0.414815 0.770833
140 9BG 0.414013 0.70297
141 ADP 0.409091 0.729167
142 ADQ 0.408451 0.714286
143 48N 0.407895 0.737374
144 A2R 0.407143 0.721649
145 8LE 0.405797 0.752577
146 F2R 0.405063 0.77
147 8LQ 0.404255 0.742268
148 NA7 0.402778 0.760417
149 OAD 0.402778 0.731959
150 BA3 0.401515 0.71134
151 8LH 0.4 0.742268
152 YLB 0.4 0.806122
153 HEJ 0.4 0.729167
154 ATP 0.4 0.729167
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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