Receptor
PDB id Resolution Class Description Source Keywords
5VYR 1.7 Å EC: 2.1.2.- CRYSTAL STRUCTURE OF THE WBKC FORMYL TRANSFERASE FROM BRUCEL MELITENSIS BRUCELLA MELITENSIS BIOTYPE 1 (STRAIN ATCC 23456 / NCTC 10094) N-FORMYLTRANSFERASE DEOXYSUGAR TRANSFERASE
Ref.: BIOCHEMICAL CHARACTERIZATION OF WBKC, AN N-FORMYLTR FROM BRUCELLA MELITENSIS. BIOCHEMISTRY V. 56 3657 2017
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
B62 B:301;
A:301;
Valid;
Valid;
none;
none;
submit data
181.195 C7 H11 N5 O C[C@@...
GMP B:302;
B:303;
A:304;
Valid;
Valid;
Valid;
none;
Atoms found LESS than expected: % Diff = 0;
Atoms found LESS than expected: % Diff = 0;
submit data
283.241 C10 H13 N5 O5 c1nc2...
CL A:303;
Invalid;
none;
submit data
35.453 Cl [Cl-]
EDO A:302;
Invalid;
none;
submit data
62.068 C2 H6 O2 C(CO)...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5VYR 1.7 Å EC: 2.1.2.- CRYSTAL STRUCTURE OF THE WBKC FORMYL TRANSFERASE FROM BRUCEL MELITENSIS BRUCELLA MELITENSIS BIOTYPE 1 (STRAIN ATCC 23456 / NCTC 10094) N-FORMYLTRANSFERASE DEOXYSUGAR TRANSFERASE
Ref.: BIOCHEMICAL CHARACTERIZATION OF WBKC, AN N-FORMYLTR FROM BRUCELLA MELITENSIS. BIOCHEMISTRY V. 56 3657 2017
Members (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 5VYU - JB2 C16 H26 N6 O14 P2 C[C@@H]1[C....
2 5VYT - FON C20 H23 N7 O7 c1cc(ccc1C....
3 5VYR - GMP C10 H13 N5 O5 c1nc2c(n1[....
4 5VYS - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
70% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 5VYU - JB2 C16 H26 N6 O14 P2 C[C@@H]1[C....
2 5VYT - FON C20 H23 N7 O7 c1cc(ccc1C....
3 5VYR - GMP C10 H13 N5 O5 c1nc2c(n1[....
4 5VYS - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
50% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 5VYU - JB2 C16 H26 N6 O14 P2 C[C@@H]1[C....
2 5VYT - FON C20 H23 N7 O7 c1cc(ccc1C....
3 5VYR - GMP C10 H13 N5 O5 c1nc2c(n1[....
4 5VYS - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: B62; Similar ligands found: 6
No: Ligand ECFP6 Tc MDL keys Tc
1 B62 1 1
2 44V 1 1
3 2K8 0.54717 0.85
4 ZZZ 0.54717 0.927273
5 BHS 0.526316 0.852459
6 H4B 0.526316 0.852459
Ligand no: 2; Ligand: GMP; Similar ligands found: 112
No: Ligand ECFP6 Tc MDL keys Tc
1 GMP 1 1
2 G 0.732394 0.866667
3 5GP 0.732394 0.866667
4 3GP 0.704225 0.853333
5 GDP 0.684211 0.88
6 GNH 0.675325 0.868421
7 GP3 0.671053 0.857143
8 GP2 0.662338 0.846154
9 GTP 0.658228 0.88
10 2GP 0.657534 0.866667
11 GSP 0.641975 0.835443
12 G2P 0.641975 0.846154
13 ALF 5GP 0.6375 0.802469
14 GMV 0.6375 0.857143
15 GPG 0.635294 0.87013
16 G1R 0.62963 0.868421
17 GCP 0.62963 0.857143
18 GAV 0.626506 0.846154
19 GKE 0.625 0.87013
20 GDC 0.625 0.87013
21 GDD 0.625 0.87013
22 GNP 0.621951 0.857143
23 9GM 0.621951 0.857143
24 ALF GDP 0.593023 0.802469
25 GDP AF3 0.593023 0.802469
26 GDP ALF 0.593023 0.802469
27 G4P 0.588235 0.866667
28 G2R 0.586207 0.846154
29 G3D 0.583333 0.866667
30 P2G 0.576923 0.815789
31 SGP 0.576923 0.78481
32 G G 0.565217 0.833333
33 GFB 0.565217 0.846154
34 GDR 0.565217 0.846154
35 GKD 0.56383 0.87013
36 P1G 0.5625 0.805195
37 0O2 0.561798 0.866667
38 YGP 0.56044 0.792683
39 G3A 0.55914 0.857143
40 6CK 0.55914 0.825
41 Y9Z 0.554348 0.817073
42 G5P 0.553191 0.857143
43 NOS 0.549296 0.940298
44 GTG 0.548387 0.825
45 JB2 0.547368 0.846154
46 GDX 0.541667 0.857143
47 GPD 0.541667 0.814815
48 U2G 0.54 0.848101
49 GCP G 0.538462 0.828947
50 GDP 7MG 0.536842 0.822785
51 35G 0.53012 0.84
52 C2E 0.53012 0.828947
53 PCG 0.53012 0.84
54 CG2 0.529412 0.848101
55 5GP 5GP 0.52381 0.815789
56 MG7 0.520548 0.957143
57 JB3 0.514852 0.835443
58 A G 0.504762 0.844156
59 G A A A 0.504762 0.857143
60 U A G G 0.5 0.844156
61 AKW 0.495146 0.783133
62 FEG 0.495146 0.77381
63 NGD 0.495146 0.846154
64 ZGP 0.490385 0.764706
65 G U 0.490385 0.835443
66 G U34 0.490385 0.825
67 GH3 0.488889 0.855263
68 DG 0.487805 0.797468
69 DGP 0.487805 0.797468
70 2MD 0.481132 0.785714
71 G C 0.481132 0.835443
72 BGO 0.480769 0.8125
73 GPX 0.478261 0.828947
74 XTS 0.472973 0.913043
75 DGI 0.471264 0.810127
76 MGD 0.46789 0.785714
77 CAG 0.46789 0.776471
78 TPG 0.45614 0.741573
79 FE9 0.455357 0.684211
80 4BW 0.454545 0.828947
81 1YD 0.454545 0.828947
82 G G G RPC 0.453704 0.7875
83 GGM 0.453704 0.792683
84 SNI 0.453333 0.898551
85 PGD 0.451327 0.814815
86 MD1 0.451327 0.785714
87 DGT 0.450549 0.810127
88 APC G U 0.45045 0.797468
89 DBG 0.443478 0.835443
90 G1R G1R 0.443478 0.835443
91 13A 0.441558 0.768293
92 GPC 0.441441 0.795181
93 PGD O 0.439655 0.75
94 DG DG 0.43299 0.802469
95 G4M 0.430894 0.797619
96 G G G C 0.429825 0.802469
97 A G C C 0.426087 0.822785
98 1YC 0.421569 0.802632
99 AD3 0.421053 0.882353
100 4UR 0.416667 0.828947
101 G C C C 0.411765 0.8125
102 XYA 0.410959 0.882353
103 RAB 0.410959 0.882353
104 ADN 0.410959 0.882353
105 G1G 0.408696 0.814815
106 1DA 0.407895 0.882353
107 AC2 0.407895 0.797297
108 IMP 0.406977 0.84
109 A G U 0.404762 0.825
110 3ZE 0.404494 0.772152
111 MZR 0.402778 0.838235
112 CFE 0.4 0.857143
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5VYR; Ligand: GMP; Similar sites found with APoc: 1
This union binding pocket(no: 1) in the query (biounit: 5vyr.bio1) has 31 residues
No: Leader PDB Ligand Sequence Similarity
1 4YFY 1YJ 20.4724
Pocket No.: 2; Query (leader) PDB : 5VYR; Ligand: GMP; 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: 5vyr.bio1) has 30 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 5VYR; Ligand: B62; Similar sites found with APoc: 1
This union binding pocket(no: 3) in the query (biounit: 5vyr.bio1) has 31 residues
No: Leader PDB Ligand Sequence Similarity
1 4YFY 1YJ 20.4724
Pocket No.: 4; Query (leader) PDB : 5VYR; Ligand: GMP; 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: 5vyr.bio1) has 31 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 5VYR; Ligand: B62; 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: 5vyr.bio1) has 30 residues
No: Leader PDB Ligand Sequence Similarity
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