Receptor
PDB id Resolution Class Description Source Keywords
6N93 1.7 Å EC: 4.1.1.- METHYLMALONYL-COA DECARBOXYLASE IN COMPLEX WITH 2-NITRONATE- 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
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
PG4 C:304;
Invalid;
none;
submit data
194.226 C8 H18 O5 C(COC...
KGA E:302;
B:301;
A:301;
F:301;
C:301;
E:301;
F:303;
C:303;
D:302;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Atoms found LESS than expected: % Diff = 0;
Atoms found LESS than expected: % Diff = 0;
Atoms found LESS than expected: % Diff = 0;
none;
Atoms found LESS than expected: % Diff = 0;
none;
Atoms found LESS than expected: % Diff = 0;
Atoms found LESS than expected: % Diff = 0;
Atoms found LESS than expected: % Diff = 0;
Ki = 20.6 uM
851.521 C24 H38 N8 O20 P3 CC(=[...
NI A:302;
F:302;
D:301;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
submit data
58.693 Ni [Ni+2...
IMD F:305;
A:303;
D:303;
Invalid;
Invalid;
Invalid;
none;
none;
none;
submit data
69.085 C3 H5 N2 c1c[n...
K C:302;
Part of Protein;
none;
submit data
39.098 K [K+]
KG7 F:304;
Valid;
none;
submit data
103.077 C3 H5 N O3 C/C(=...
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 (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 6N93 Ki = 20.6 uM KGA C24 H38 N8 O20 P3 CC(=[N+]([....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: KGA; Similar ligands found: 165
No: Ligand ECFP6 Tc MDL keys Tc
1 KGA 1 1
2 KGJ 0.825758 0.989362
3 KFV 0.807407 0.96875
4 LCV 0.80597 0.819048
5 SO5 0.80597 0.819048
6 0T1 0.796875 0.884211
7 COA 0.796875 0.884211
8 DCA 0.795276 0.884211
9 AMX 0.792308 0.893617
10 NMX 0.783582 0.957895
11 ETB 0.78125 0.854167
12 FCX 0.780303 0.876289
13 ACO 0.780303 0.876289
14 FAM 0.780303 0.865979
15 30N 0.778626 0.815534
16 COS 0.778626 0.865979
17 CAO 0.778626 0.857143
18 SCO 0.772727 0.904255
19 CMX 0.772727 0.904255
20 3KK 0.768657 0.885417
21 SOP 0.762963 0.885417
22 YZS 0.762963 0.809524
23 KGP 0.762963 0.809524
24 HAX 0.761194 0.925532
25 FYN 0.755556 0.884211
26 SCD 0.751825 0.904255
27 CAJ 0.751825 0.905263
28 2MC 0.751825 0.85
29 OXK 0.75 0.885417
30 MCD 0.75 0.905263
31 COK 0.75 0.865979
32 CA6 0.75 0.809524
33 MC4 0.748201 0.86
34 BCO 0.746377 0.865979
35 1VU 0.744526 0.876289
36 CMC 0.744526 0.885417
37 CO6 0.744526 0.885417
38 YE1 0.741007 0.875
39 CAA 0.741007 0.875
40 YXS 0.735714 0.809524
41 2CP 0.735714 0.895833
42 YXR 0.735714 0.809524
43 1HE 0.733813 0.848485
44 3HC 0.733813 0.875
45 IVC 0.733813 0.875
46 A1S 0.733813 0.865979
47 MLC 0.733813 0.885417
48 2KQ 0.730496 0.886598
49 COO 0.728571 0.865979
50 MCA 0.728571 0.895833
51 4CA 0.725352 0.857143
52 FAQ 0.725352 0.865979
53 SCA 0.723404 0.885417
54 COW 0.71831 0.857143
55 3CP 0.71831 0.885417
56 1GZ 0.71831 0.857143
57 COF 0.71831 0.848485
58 BYC 0.71831 0.865979
59 IRC 0.71831 0.875
60 HGG 0.71831 0.885417
61 CA8 0.71831 0.792453
62 BCA 0.713287 0.857143
63 0ET 0.712329 0.867347
64 CO8 0.710345 0.867347
65 HXC 0.708333 0.867347
66 GRA 0.708333 0.885417
67 DCC 0.705479 0.867347
68 MYA 0.705479 0.867347
69 5F9 0.705479 0.867347
70 MFK 0.705479 0.867347
71 UCC 0.705479 0.867347
72 ST9 0.705479 0.867347
73 TGC 0.703448 0.876289
74 2NE 0.69863 0.848485
75 1CZ 0.69863 0.876289
76 CIC 0.69863 0.885417
77 S0N 0.69863 0.885417
78 CS8 0.695946 0.858586
79 4CO 0.693878 0.857143
80 0FQ 0.693878 0.865979
81 NHM 0.691275 0.867347
82 UOQ 0.691275 0.867347
83 NHW 0.691275 0.867347
84 HDC 0.691275 0.867347
85 01A 0.689189 0.831683
86 8Z2 0.688742 0.858586
87 MRR 0.686667 0.867347
88 MRS 0.686667 0.867347
89 1CV 0.684564 0.885417
90 WCA 0.684564 0.848485
91 YNC 0.682119 0.857143
92 4KX 0.68 0.84
93 HFQ 0.675497 0.848485
94 DAK 0.671053 0.84
95 J5H 0.671053 0.865979
96 NHQ 0.668831 0.875
97 COD 0.659259 0.873684
98 01K 0.656051 0.885417
99 1HA 0.649682 0.848485
100 CCQ 0.642384 0.868687
101 F8G 0.641509 0.851485
102 COT 0.641509 0.865979
103 93P 0.640244 0.876289
104 7L1 0.636364 0.876289
105 CA3 0.63354 0.865979
106 CA5 0.624242 0.831683
107 93M 0.621302 0.876289
108 UCA 0.610778 0.867347
109 COA FLC 0.604167 0.873684
110 CO7 0.602649 0.865979
111 N9V 0.6 0.838384
112 OXT 0.575419 0.851485
113 5TW 0.569061 0.833333
114 4BN 0.569061 0.833333
115 JBT 0.553763 0.871287
116 PAP 0.548387 0.734043
117 BSJ 0.546961 0.896907
118 PLM COA 0.54321 0.857143
119 COA PLM 0.54321 0.857143
120 HMG 0.540373 0.875
121 ASP ASP ASP ILE CMC NH2 0.511364 0.865979
122 PPS 0.48855 0.669903
123 A3P 0.488 0.723404
124 0WD 0.473684 0.717172
125 ACE SER ASP ALY THR NH2 COA 0.471204 0.885417
126 RFC 0.45977 0.886598
127 SFC 0.45977 0.886598
128 191 0.449102 0.84466
129 PTJ 0.443662 0.808511
130 3OD 0.433566 0.765957
131 A22 0.431655 0.736842
132 3AM 0.428571 0.712766
133 ADP 0.427481 0.744681
134 A2D 0.426357 0.726316
135 PAJ 0.425532 0.819149
136 HQG 0.42446 0.755319
137 8LE 0.423358 0.787234
138 PUA 0.42236 0.744898
139 ATR 0.422222 0.723404
140 SAP 0.422222 0.714286
141 AGS 0.422222 0.714286
142 OAD 0.41958 0.765957
143 F2R 0.411392 0.842105
144 9BG 0.411392 0.752577
145 ATF 0.410072 0.721649
146 9X8 0.409722 0.731959
147 BA3 0.409091 0.726316
148 ATP 0.407407 0.744681
149 HEJ 0.407407 0.744681
150 SRP 0.407143 0.776596
151 YLB 0.406452 0.842105
152 B4P 0.406015 0.726316
153 AP5 0.406015 0.726316
154 48N 0.405229 0.808511
155 5FA 0.404412 0.744681
156 2A5 0.404412 0.765957
157 AQP 0.404412 0.744681
158 APR 0.404412 0.744681
159 AR6 0.404412 0.744681
160 A2R 0.404255 0.755319
161 AN2 0.402985 0.755319
162 DLL 0.402778 0.736842
163 8LQ 0.401408 0.776596
164 M33 0.4 0.736842
165 NA7 0.4 0.776596
Ligand no: 2; Ligand: KG7; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 KG7 1 1
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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