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 = 0.45;
Atoms found LESS than expected: % Diff = 0.45;
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 44V 1 1
2 B62 1 1
3 2K8 0.54717 0.85
4 ZZZ 0.54717 0.927273
5 H4B 0.526316 0.852459
6 BHS 0.526316 0.852459
Ligand no: 2; Ligand: GMP; Similar ligands found: 114
No: Ligand ECFP6 Tc MDL keys Tc
1 GMP 1 1
2 5GP 0.732394 0.866667
3 G 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 GDP MG 0.64557 0.833333
12 G2P 0.641975 0.846154
13 GSP 0.641975 0.835443
14 GDP BEF 0.6375 0.8125
15 ALF 5GP 0.6375 0.802469
16 GMV 0.6375 0.857143
17 GPG 0.635294 0.87013
18 GCP 0.62963 0.857143
19 G1R 0.62963 0.868421
20 GAV 0.626506 0.846154
21 GKE 0.625 0.87013
22 GDD 0.625 0.87013
23 GDC 0.625 0.87013
24 GNP 0.621951 0.857143
25 BEF GDP 0.614458 0.802469
26 GTP MG 0.614458 0.833333
27 GCP G 0.607143 0.844156
28 GDP ALF 0.593023 0.802469
29 GDP AF3 0.593023 0.802469
30 G G 0.590909 0.844156
31 G4P 0.588235 0.866667
32 G2R 0.586207 0.846154
33 G3D 0.583333 0.866667
34 P2G 0.576923 0.815789
35 SGP 0.576923 0.78481
36 GFB 0.565217 0.846154
37 GDR 0.565217 0.846154
38 GKD 0.56383 0.87013
39 P1G 0.5625 0.805195
40 0O2 0.561798 0.866667
41 YGP 0.56044 0.792683
42 6CK 0.55914 0.825
43 G3A 0.55914 0.857143
44 Y9Z 0.554348 0.817073
45 G5P 0.553191 0.857143
46 NOS 0.549296 0.940298
47 GTG 0.548387 0.825
48 JB2 0.547368 0.846154
49 GPD 0.541667 0.814815
50 GDX 0.541667 0.857143
51 U2G 0.54 0.848101
52 GDP 7MG 0.536842 0.822785
53 C2E 0.53012 0.828947
54 PCG 0.53012 0.84
55 35G 0.53012 0.84
56 CG2 0.529412 0.848101
57 5GP 5GP 0.52381 0.815789
58 MG7 0.520548 0.957143
59 JB3 0.514852 0.835443
60 G A A A 0.504762 0.857143
61 U A G G 0.5 0.844156
62 FEG 0.495146 0.77381
63 NGD 0.495146 0.846154
64 G U34 0.490385 0.825
65 ZGP 0.490385 0.764706
66 GH3 0.488889 0.855263
67 DGP 0.487805 0.797468
68 DG 0.487805 0.797468
69 G G U 0.484848 0.820513
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 CAG 0.46789 0.776471
77 MGD 0.46789 0.785714
78 I2C FE2 CMO CMO 0.463636 0.730337
79 TPG 0.45614 0.741573
80 FE9 0.455357 0.684211
81 4BW 0.454545 0.828947
82 1YD 0.454545 0.828947
83 GGM 0.453704 0.792683
84 G G G RPC 0.453704 0.7875
85 SNI 0.453333 0.898551
86 PGD 0.451327 0.814815
87 MD1 0.451327 0.785714
88 DGT 0.450549 0.810127
89 APC G U 0.45045 0.797468
90 DBG 0.443478 0.835443
91 G1R G1R 0.443478 0.835443
92 13A 0.441558 0.768293
93 GPC 0.441441 0.795181
94 PGD O 0.439655 0.75
95 DG DG 0.43299 0.802469
96 G4M 0.430894 0.797619
97 G G G C 0.429825 0.802469
98 A G C C 0.426087 0.822785
99 U G A 0.424 0.825
100 1YC 0.421569 0.802632
101 AD3 0.421053 0.882353
102 4UR 0.416667 0.828947
103 G C C C 0.411765 0.8125
104 ADN 0.410959 0.882353
105 RAB 0.410959 0.882353
106 XYA 0.410959 0.882353
107 G1G 0.408696 0.814815
108 1DA 0.407895 0.882353
109 AC2 0.407895 0.797297
110 IMP 0.406977 0.84
111 A G U 0.404762 0.825
112 3ZE 0.404494 0.772152
113 MZR 0.402778 0.838235
114 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: 30
This union binding pocket(no: 1) in the query (biounit: 5vyr.bio1) has 31 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2DTJ THR 0.03366 0.4003 2.80899
2 3R4S SIA 0.0006757 0.49621 3.06513
3 1X8X TYR 0.03015 0.40275 3.06513
4 1A8S PPI 0.0231 0.4183 4.21456
5 4YSW URC 0.02781 0.41293 4.21456
6 4LH7 1X8 0.04055 0.40543 5.36398
7 4IN9 SER TRP PHE PRO 0.04087 0.40414 6.0241
8 4N9Z V3L 0.00909 0.43859 6.13027
9 1XE7 GUN 0.02709 0.42326 7.38916
10 1YQC GLV 0.02355 0.42699 8.23529
11 1D8C SOR 0.00648 0.41746 8.42912
12 4LSY FLC 0.01208 0.42111 16.4835
13 4TTS 6DD 0.000001397 0.56391 17.2414
14 2CFI ZZZ 0.00000528 0.60094 18.0077
15 4YFY 1YJ 0.000000007808 0.6937 20.4724
16 4YFY 0FX 0.01072 0.42994 20.4724
17 1GAR U89 0.0001224 0.44895 21.6981
18 5VYQ FON 0.00000004561 0.68615 23.5294
19 5VYQ 0FX 0.0008184 0.47159 23.5294
20 5VYQ TYD 0.03156 0.4104 23.5294
21 3DCJ THH 0.00000004455 0.66761 23.7209
22 4NV1 0FX 0.001674 0.4791 30.0412
23 4NV1 4TG 0.005607 0.44954 30.0412
24 4NV1 TYD 0.007837 0.43501 30.0412
25 5UIJ TYD 0.00000005594 0.59779 31.0345
26 1RC0 KT5 0.000004121 0.50984 31.1005
27 4LXQ FON 0.000000003816 0.58094 40.2299
28 4LXQ TYD 0.000000003816 0.58094 40.2299
29 2BLN FON 0.000000006062 0.60732 45.977
30 2BLN U5P 0.00000001848 0.59819 45.977
Pocket No.: 2; Query (leader) PDB : 5VYR; Ligand: GMP; Similar sites found: 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 P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 5VYR; Ligand: B62; Similar sites found: 30
This union binding pocket(no: 3) in the query (biounit: 5vyr.bio1) has 31 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2DTJ THR 0.03366 0.4003 2.80899
2 3R4S SIA 0.0006757 0.49621 3.06513
3 1X8X TYR 0.03015 0.40275 3.06513
4 1A8S PPI 0.0231 0.4183 4.21456
5 4YSW URC 0.02781 0.41293 4.21456
6 4LH7 1X8 0.04055 0.40543 5.36398
7 4IN9 SER TRP PHE PRO 0.04087 0.40414 6.0241
8 4N9Z V3L 0.00909 0.43859 6.13027
9 1XE7 GUN 0.02709 0.42326 7.38916
10 1YQC GLV 0.02355 0.42699 8.23529
11 1D8C SOR 0.00648 0.41746 8.42912
12 4LSY FLC 0.01208 0.42111 16.4835
13 4TTS 6DD 0.000001397 0.56391 17.2414
14 2CFI ZZZ 0.00000528 0.60094 18.0077
15 4YFY 1YJ 0.000000007808 0.6937 20.4724
16 4YFY 0FX 0.01072 0.42994 20.4724
17 1GAR U89 0.0001224 0.44895 21.6981
18 5VYQ FON 0.00000004561 0.68615 23.5294
19 5VYQ 0FX 0.0008184 0.47159 23.5294
20 5VYQ TYD 0.03156 0.4104 23.5294
21 3DCJ THH 0.00000004455 0.66761 23.7209
22 4NV1 0FX 0.001674 0.4791 30.0412
23 4NV1 4TG 0.005607 0.44954 30.0412
24 4NV1 TYD 0.007837 0.43501 30.0412
25 5UIJ TYD 0.00000005594 0.59779 31.0345
26 1RC0 KT5 0.000004121 0.50984 31.1005
27 4LXQ FON 0.000000003816 0.58094 40.2299
28 4LXQ TYD 0.000000003816 0.58094 40.2299
29 2BLN FON 0.000000006062 0.60732 45.977
30 2BLN U5P 0.00000001848 0.59819 45.977
Pocket No.: 4; Query (leader) PDB : 5VYR; Ligand: GMP; Similar sites found: 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 P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 5VYR; Ligand: B62; Similar sites found: 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 P-value (APoc) PS_Score (APoc) Sequence Similarity
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