Receptor
PDB id Resolution Class Description Source Keywords
6OXD 2 Å EC: 5.4.99.2 STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS METHYLMALONYL-COA MU ADENOSYL COBALAMIN MYCOBACTERIUM TUBERCULOSIS METHYLMALONYL COA MUTASE METHYLMALONYL COA MUTASE DEFICIENCMETABOLIC DISEASE COBALAMIN COBALT DISEASE MUTATION ISOMETAL-BINDING ITACONYL COA RADICAL MYCOBACTERIUM TUBERCUIMMUNOMETABOLITE B12 METHYLMALONIC ACIDURIA
Ref.: ITACONYL-COA FORMS A STABLE BIRADICAL IN METHYLMALO MUTASE AND DERAILS ITS ACTIVITY AND REPAIR. SCIENCE V. 366 589 2019
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
K A:1003;
 Part of Protein;
 none;
 submit data
39.098 K [K+]
B12 A:1000;
 Part of Protein;
 none;
 submit data
1330.36 C62 H89 Co N13 O14 P Cc1cc...
5AD NJS A:1001;
 Valid;
 none;
 submit data
1126.84 n/a S(C(=...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
6OXC 1.9 Å EC: 5.4.99.2 STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS METHYLMALONYL-COA MU ADENOSYL COBALAMIN MYCOBACTERIUM TUBERCULOSIS METHYLMALONYL COA MUTASE METHYLMALONYL COA MUTASE DEFICIENCMETABOLIC DISEASE COBALAMIN COBALT DISEASE MUTATION ISOMETAL-BINDING ITACONYL COA RADICAL MYCOBACTERIUM TUBERCUIMMUNOMETABOLITE B12 METHYLMALONIC ACIDURIA
Ref.: ITACONYL-COA FORMS A STABLE BIRADICAL IN METHYLMALO MUTASE AND DERAILS ITS ACTIVITY AND REPAIR. SCIENCE V. 366 589 2019
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 6OXD - 5AD NJS n/a n/a
2 6OXC - 5AD C10 H13 N5 O3 C[C@@H]1[C....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 6OXD - 5AD NJS n/a n/a
2 6OXC - 5AD C10 H13 N5 O3 C[C@@H]1[C....
50% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 6OXD - 5AD NJS n/a n/a
2 6OXC - 5AD C10 H13 N5 O3 C[C@@H]1[C....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: 5AD NJS; Similar ligands found: 133
No: Ligand ECFP6 Tc MDL keys Tc
1 5AD NJS 1 1
2 COA FLC 0.638158 0.923077
3 BUA COA 0.614907 0.923913
4 HMG 0.612121 0.945055
5 6NA COA 0.596386 0.904255
6 MYR COA 0.585799 0.904255
7 PLM COA 0.585799 0.904255
8 DAO COA 0.585799 0.904255
9 EO3 COA 0.585799 0.904255
10 DKA COA 0.585799 0.904255
11 DCR COA 0.585799 0.904255
12 X90 COA 0.585799 0.904255
13 ASP ASP ASP ILE NH2 CMC 0.543478 0.913979
14 ACE SER ASP ALY THR NH2 COA 0.533333 0.913979
15 MET VAL ASN ALA CMC 0.507614 0.893617
16 CCQ 0.502825 0.895833
17 ACE MET LEU GLY PRO NH2 COA 0.490385 0.893617
18 WCA 0.486188 0.935484
19 COO 0.485714 0.934783
20 30N 0.485207 0.84
21 MC4 0.482955 0.946809
22 FYN 0.482558 0.913043
23 DCA 0.481928 0.87234
24 1GZ 0.480226 0.924731
25 ACO 0.479532 0.904255
26 FAM 0.479532 0.873684
27 DAK 0.478261 0.925532
28 1VU 0.477012 0.904255
29 CO6 0.477012 0.913979
30 CAO 0.476471 0.884211
31 COS 0.476471 0.893617
32 COA 0.47619 0.913043
33 2CP 0.474576 0.904255
34 2MC 0.474286 0.93617
35 3KK 0.473988 0.913979
36 ETB 0.473054 0.842105
37 OXK 0.471264 0.934783
38 FCX 0.47093 0.884211
39 MCA 0.468927 0.924731
40 CAA 0.468927 0.923913
41 0T1 0.467456 0.892473
42 KFV 0.463687 0.86
43 HGG 0.463687 0.934783
44 1HE 0.463277 0.894737
45 MLC 0.463277 0.934783
46 IVC 0.463277 0.923913
47 A1S 0.463277 0.893617
48 BCO 0.463277 0.913979
49 3HC 0.463277 0.923913
50 SOP 0.462857 0.893617
51 COK 0.462857 0.893617
52 NMX 0.460227 0.848485
53 CMC 0.460227 0.913979
54 8Z2 0.459893 0.905263
55 HAX 0.45977 0.873684
56 HDC 0.459459 0.894737
57 4KX 0.459459 0.967391
58 AMX 0.459302 0.902174
59 SCA 0.458101 0.934783
60 YXR 0.458101 0.833333
61 YXS 0.458101 0.833333
62 COD 0.457831 0.902174
63 SCD 0.457627 0.913043
64 MRR 0.456989 0.894737
65 MRS 0.456989 0.894737
66 SCO 0.456647 0.913043
67 CMX 0.456647 0.913043
68 0ET 0.456522 0.875
69 COW 0.455556 0.924731
70 IRC 0.455556 0.923913
71 BYC 0.455556 0.934783
72 COF 0.455556 0.875
73 MCD 0.454545 0.893617
74 FAQ 0.453039 0.934783
75 BCA 0.453039 0.924731
76 4CA 0.453039 0.904255
77 GRA 0.450549 0.934783
78 HXC 0.450549 0.894737
79 TGC 0.448087 0.924731
80 01K 0.447917 0.893617
81 2KQ 0.447514 0.914894
82 3CP 0.447514 0.913979
83 KGJ 0.446927 0.84
84 KGP 0.446328 0.833333
85 YZS 0.446328 0.833333
86 CA6 0.446328 0.815534
87 1CV 0.446237 0.934783
88 2NE 0.445652 0.914894
89 CIC 0.445652 0.913979
90 1CZ 0.445652 0.924731
91 CO8 0.445652 0.894737
92 YE1 0.444444 0.903226
93 LCV 0.444444 0.843137
94 SO5 0.444444 0.843137
95 NHW 0.44385 0.875
96 UOQ 0.44385 0.875
97 NHM 0.44385 0.875
98 UCC 0.443243 0.894737
99 ST9 0.443243 0.894737
100 5F9 0.443243 0.894737
101 DCC 0.443243 0.894737
102 MYA 0.443243 0.894737
103 MFK 0.443243 0.894737
104 93P 0.442211 0.924731
105 CAJ 0.441341 0.893617
106 KGA 0.43956 0.85
107 ATP A 0.43949 0.758242
108 ATP A A A 0.43949 0.758242
109 YNC 0.439153 0.924731
110 J5H 0.439153 0.934783
111 CS8 0.438503 0.885417
112 93M 0.438424 0.924731
113 N9V 0.437838 0.904255
114 0FQ 0.435484 0.913979
115 4CO 0.435484 0.904255
116 HFQ 0.433862 0.894737
117 01A 0.433155 0.876289
118 NHQ 0.432292 0.903226
119 CA8 0.431694 0.851485
120 S0N 0.430108 0.913979
121 RMW 0.43 0.935484
122 UCA 0.427861 0.914894
123 1HA 0.427835 0.914894
124 CA3 0.426396 0.913979
125 COT 0.423469 0.913979
126 F8G 0.423469 0.957447
127 CO7 0.420765 0.934783
128 ADP BMA 0.416667 0.791209
129 7L1 0.407821 0.904255
130 PTJ 0.402516 0.815217
131 CA5 0.401961 0.876289
132 JBT 0.401826 0.878788
133 DAL AMP 0.4 0.78022
Similar Ligands (3D)
Ligand no: 1; Ligand: 5AD NJS; Similar ligands found: 0
No: Ligand Similarity coefficient
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 6OXC; Ligand: 5AD; 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: 6oxc.bio1) has 40 residues
No: Leader PDB Ligand Sequence Similarity
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