Receptor
PDB id Resolution Class Description Source Keywords
6N94 1.75 Å EC: 4.1.1.- METHYLMALONYL-COA DECARBOXYLASE IN COMPLEX WITH 2-NITRONATE- 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
PGE F:304;
Invalid;
none;
submit data
150.173 C6 H14 O4 C(COC...
KGJ A:301;
E:302;
E:301;
F:301;
C:301;
C:302;
B:301;
D:302;
F:302;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
none;
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;
Ki = 19.8 uM
850.537 C24 H39 N9 O19 P3 CC(=[...
NI A:302;
D:301;
Part of Protein;
Part of Protein;
none;
none;
submit data
58.693 Ni [Ni+2...
K C:303;
F:303;
Part of Protein;
Invalid;
none;
none;
submit data
39.098 K [K+]
PG4 C:305;
Invalid;
none;
submit data
194.226 C8 H18 O5 C(COC...
PEG B:302;
C:304;
Invalid;
Invalid;
none;
none;
submit data
106.12 C4 H10 O3 C(COC...
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: KGJ; Similar ligands found: 165
No: Ligand ECFP6 Tc MDL keys Tc
1 KGJ 1 1
2 KFV 0.825758 0.978947
3 KGA 0.825758 0.989362
4 SCO 0.818898 0.893617
5 0T1 0.816 0.893617
6 COA 0.816 0.893617
7 DCA 0.814516 0.893617
8 AMX 0.811024 0.903226
9 NMX 0.801527 0.968085
10 ETB 0.8 0.863158
11 ACO 0.79845 0.885417
12 CAO 0.796875 0.865979
13 30N 0.796875 0.823529
14 COS 0.796875 0.875
15 YZS 0.793893 0.817308
16 KGP 0.793893 0.817308
17 CMX 0.790698 0.893617
18 3KK 0.78626 0.894737
19 FAM 0.784615 0.875
20 FCX 0.784615 0.865979
21 SOP 0.780303 0.894737
22 OXK 0.780303 0.875
23 HAX 0.778626 0.935484
24 1VU 0.774436 0.885417
25 CO6 0.774436 0.894737
26 FYN 0.772727 0.893617
27 YE1 0.77037 0.884211
28 SCD 0.768657 0.893617
29 2MC 0.768657 0.858586
30 COK 0.766917 0.875
31 CA6 0.766917 0.817308
32 MCD 0.766917 0.894737
33 MC4 0.764706 0.868687
34 1HE 0.762963 0.857143
35 CMC 0.761194 0.875
36 CAA 0.757353 0.884211
37 CAJ 0.755556 0.894737
38 A1S 0.75 0.875
39 MLC 0.75 0.875
40 3HC 0.75 0.884211
41 IVC 0.75 0.884211
42 BCO 0.75 0.875
43 3CP 0.746377 0.875
44 BYC 0.746377 0.875
45 COW 0.746377 0.865979
46 MCA 0.744526 0.885417
47 COO 0.744526 0.875
48 LCV 0.744526 0.809524
49 SO5 0.744526 0.809524
50 BCA 0.741007 0.865979
51 2CP 0.73913 0.885417
52 SCA 0.73913 0.875
53 YXS 0.73913 0.817308
54 YXR 0.73913 0.817308
55 S0N 0.737589 0.875
56 1GZ 0.733813 0.865979
57 IRC 0.733813 0.884211
58 COF 0.733813 0.857143
59 2KQ 0.733813 0.876289
60 CA8 0.733813 0.8
61 HGG 0.733813 0.875
62 4CA 0.728571 0.865979
63 FAQ 0.728571 0.875
64 2NE 0.725352 0.857143
65 HXC 0.723404 0.876289
66 GRA 0.723404 0.875
67 TGC 0.71831 0.865979
68 4KX 0.717241 0.848485
69 1CZ 0.713287 0.865979
70 CO8 0.713287 0.876289
71 CIC 0.713287 0.875
72 CS8 0.710345 0.867347
73 4CO 0.708333 0.865979
74 MYA 0.708333 0.876289
75 UCC 0.708333 0.876289
76 MFK 0.708333 0.876289
77 0FQ 0.708333 0.875
78 ST9 0.708333 0.876289
79 5F9 0.708333 0.876289
80 DCC 0.708333 0.876289
81 01A 0.703448 0.84
82 0ET 0.703448 0.876289
83 WCA 0.69863 0.857143
84 1CV 0.69863 0.875
85 J5H 0.695946 0.875
86 NHW 0.693878 0.876289
87 HDC 0.693878 0.876289
88 NHM 0.693878 0.876289
89 UOQ 0.693878 0.876289
90 8Z2 0.691275 0.867347
91 MRS 0.689189 0.876289
92 MRR 0.689189 0.876289
93 HFQ 0.689189 0.857143
94 DAK 0.684564 0.848485
95 YNC 0.684564 0.865979
96 F8G 0.675325 0.841584
97 1HA 0.673203 0.857143
98 NHQ 0.671053 0.884211
99 01K 0.668831 0.894737
100 CCQ 0.666667 0.877551
101 COT 0.664516 0.875
102 COD 0.661654 0.882979
103 CA3 0.656051 0.875
104 7L1 0.65 0.885417
105 CA5 0.635802 0.84
106 93P 0.621951 0.865979
107 UCA 0.621951 0.876289
108 COA FLC 0.617021 0.882979
109 CO7 0.614865 0.875
110 93M 0.60355 0.865979
111 N9V 0.601307 0.828283
112 OXT 0.585227 0.86
113 5TW 0.569832 0.841584
114 4BN 0.569832 0.841584
115 PAP 0.561983 0.741935
116 BSJ 0.55618 0.886598
117 JBT 0.554348 0.861386
118 HMG 0.550633 0.864583
119 COA PLM 0.54375 0.865979
120 PLM COA 0.54375 0.865979
121 ASP ASP ASP ILE CMC NH2 0.520231 0.85567
122 PPS 0.511811 0.676471
123 A3P 0.5 0.731183
124 0WD 0.483221 0.72449
125 ACE SER ASP ALY THR NH2 COA 0.478723 0.875
126 191 0.475309 0.852941
127 SFC 0.467836 0.895833
128 RFC 0.467836 0.895833
129 PTJ 0.442857 0.797872
130 3AM 0.439024 0.72043
131 PAJ 0.434783 0.808511
132 3OD 0.432624 0.755319
133 ATR 0.431818 0.731183
134 A22 0.430657 0.744681
135 PUA 0.43038 0.752577
136 ADP 0.426357 0.752688
137 A2D 0.425197 0.734043
138 HQG 0.423358 0.744681
139 8LE 0.422222 0.776596
140 AGS 0.421053 0.721649
141 SAP 0.421053 0.721649
142 9BG 0.419355 0.760417
143 F2R 0.419355 0.831579
144 OAD 0.41844 0.755319
145 2A5 0.413534 0.774194
146 A2R 0.413043 0.744681
147 PAX 0.411043 0.747475
148 9X8 0.408451 0.721649
149 NA7 0.408451 0.784946
150 BA3 0.407692 0.734043
151 HEJ 0.406015 0.752688
152 ATP 0.406015 0.752688
153 SRP 0.405797 0.765957
154 B4P 0.40458 0.734043
155 AP5 0.40458 0.734043
156 48N 0.403974 0.797872
157 APR 0.402985 0.734043
158 5FA 0.402985 0.752688
159 AQP 0.402985 0.752688
160 AR6 0.402985 0.734043
161 APU 0.402597 0.721649
162 AN2 0.401515 0.763441
163 AHX 0.401408 0.817204
164 7D3 0.4 0.726316
165 8LQ 0.4 0.765957
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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