Receptor
PDB id Resolution Class Description Source Keywords
6N92 1.7 Å EC: 4.1.1.- METHYLMALONYL-COA DECARBOXYLASE IN COMPLEX WITH 2-NITRONATE- 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
KFV F:303;
C:301;
D:302;
A:301;
B:301;
E:302;
F:301;
C:303;
E:301;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
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;
Atoms found LESS than expected: % Diff = 0;
none;
Ki = 10.8 uM
867.587 C24 H38 N8 O19 P3 S CC(=[...
PG4 C:304;
Invalid;
none;
submit data
194.226 C8 H18 O5 C(COC...
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;
D:303;
Invalid;
Invalid;
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 (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: KFV; Similar ligands found: 149
No: Ligand ECFP6 Tc MDL keys Tc
1 KFV 1 1
2 3KK 0.866142 0.915789
3 ACO 0.865079 0.90625
4 2MC 0.860465 0.878788
5 OXK 0.859375 0.895833
6 COS 0.834646 0.876289
7 CAO 0.834646 0.867347
8 MC4 0.827068 0.888889
9 KGJ 0.825758 0.978947
10 1VU 0.824427 0.90625
11 CO6 0.824427 0.915789
12 COO 0.819549 0.895833
13 CAA 0.819549 0.905263
14 SOP 0.816794 0.895833
15 MLC 0.81203 0.895833
16 BCO 0.81203 0.895833
17 1HE 0.81203 0.877551
18 3HC 0.81203 0.905263
19 IVC 0.81203 0.905263
20 FYN 0.80916 0.894737
21 KGA 0.807407 0.96875
22 MCA 0.80597 0.90625
23 COK 0.80303 0.876289
24 YXR 0.8 0.836538
25 SCA 0.8 0.895833
26 YXS 0.8 0.836538
27 CMC 0.796992 0.876289
28 COA 0.796875 0.894737
29 0T1 0.796875 0.875
30 DCA 0.795276 0.875
31 IRC 0.794118 0.905263
32 1GZ 0.794118 0.886598
33 BYC 0.794118 0.895833
34 HGG 0.794118 0.895833
35 COW 0.794118 0.886598
36 AMX 0.792308 0.884211
37 30N 0.792308 0.825243
38 FAQ 0.788321 0.895833
39 BCA 0.788321 0.886598
40 A1S 0.785185 0.876289
41 NMX 0.783582 0.947917
42 HXC 0.782609 0.896907
43 GRA 0.782609 0.895833
44 ETB 0.78125 0.845361
45 COF 0.781022 0.858586
46 TGC 0.776978 0.886598
47 2CP 0.773723 0.886598
48 CMX 0.772727 0.875
49 SCO 0.772727 0.875
50 2NE 0.771429 0.877551
51 1CZ 0.771429 0.886598
52 CO8 0.771429 0.896907
53 3CP 0.768116 0.876289
54 2KQ 0.768116 0.896907
55 CS8 0.767606 0.887755
56 FAM 0.766917 0.857143
57 FCX 0.766917 0.848485
58 5F9 0.765957 0.896907
59 MFK 0.765957 0.896907
60 MYA 0.765957 0.896907
61 DCC 0.765957 0.896907
62 ST9 0.765957 0.896907
63 UCC 0.765957 0.896907
64 SCD 0.764706 0.875
65 4CA 0.76259 0.867347
66 HAX 0.761194 0.915789
67 WCA 0.755245 0.877551
68 DAK 0.751724 0.868687
69 YZS 0.75 0.836538
70 4KX 0.75 0.868687
71 KGP 0.75 0.836538
72 CA6 0.75 0.819048
73 MCD 0.75 0.876289
74 HDC 0.75 0.896907
75 01A 0.748252 0.841584
76 8Z2 0.746575 0.887755
77 CIC 0.746479 0.876289
78 MRS 0.744828 0.896907
79 MRR 0.744828 0.896907
80 0FQ 0.741259 0.876289
81 4CO 0.741259 0.867347
82 J5H 0.739726 0.895833
83 YNC 0.739726 0.886598
84 CAJ 0.73913 0.876289
85 0ET 0.736111 0.877551
86 1CV 0.731034 0.895833
87 SO5 0.728571 0.828571
88 YE1 0.728571 0.865979
89 LCV 0.728571 0.828571
90 UOQ 0.726027 0.877551
91 NHM 0.726027 0.877551
92 NHW 0.726027 0.877551
93 HFQ 0.721088 0.858586
94 CA8 0.71831 0.819048
95 F8G 0.717105 0.861386
96 1HA 0.715232 0.877551
97 CCQ 0.710345 0.897959
98 7L1 0.708029 0.90625
99 NHQ 0.701987 0.885417
100 01K 0.699346 0.895833
101 S0N 0.69863 0.857143
102 COT 0.683871 0.876289
103 CO7 0.680556 0.895833
104 CA3 0.675159 0.876289
105 UCA 0.670807 0.896907
106 CA5 0.654321 0.841584
107 93P 0.650307 0.867347
108 COD 0.647059 0.884211
109 N9V 0.631579 0.848485
110 93M 0.630952 0.867347
111 4BN 0.613636 0.861386
112 5TW 0.613636 0.861386
113 HMG 0.61039 0.885417
114 COA FLC 0.604167 0.884211
115 OXT 0.602273 0.88
116 COA PLM 0.592357 0.886598
117 PLM COA 0.592357 0.886598
118 JBT 0.587912 0.881188
119 BSJ 0.573034 0.887755
120 PAP 0.548387 0.726316
121 ASP ASP ASP ILE CMC NH2 0.546512 0.857143
122 191 0.5125 0.872549
123 RFC 0.502959 0.916667
124 SFC 0.502959 0.916667
125 ACE SER ASP ALY THR NH2 COA 0.502674 0.876289
126 PPS 0.5 0.679612
127 A3P 0.488 0.715789
128 0WD 0.473684 0.71
129 3AM 0.44 0.705263
130 PTJ 0.433566 0.78125
131 3OD 0.423611 0.739583
132 PUA 0.42236 0.737374
133 ATR 0.422222 0.715789
134 A22 0.421429 0.729167
135 ADP 0.416667 0.736842
136 PAJ 0.415493 0.791667
137 A2D 0.415385 0.71875
138 HQG 0.414286 0.729167
139 8LE 0.413043 0.760417
140 SAP 0.411765 0.742268
141 AGS 0.411765 0.742268
142 9BG 0.411392 0.744898
143 OAD 0.409722 0.739583
144 2A5 0.404412 0.757895
145 A2R 0.404255 0.729167
146 F2R 0.402516 0.814433
147 9X8 0.4 0.742268
148 A A A 0.4 0.747368
149 NA7 0.4 0.768421
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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