Receptor
PDB id Resolution Class Description Source Keywords
3B0Y 1.45 Å EC: 2.7.7.7 K263D MUTANT OF POLX FROM THERMUS THERMOPHILUS HB8 COMPLEXED DGTP THERMUS THERMOPHILUS STRUCTURAL GENOMICS RIKEN STRUCTURAL GENOMICS/PROTEOMICS INRSGI POLXC PHP DNA POLYMERASE DRP LYASE 3-prime -5-prime EXONUCLEENDONUCLEASE DNA REPAIR NUCLEOTIDE DNA TRANSFERASE
Ref.: THE STRUCTURAL BASIS OF THE KINETIC MECHANISM OF A GAP-FILLING X-FAMILY DNA POLYMERASE THAT BINDS MG(2 BEFORE BINDING TO DNA. J.MOL.BIOL. V. 417 179 2012
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CA A:578;
A:579;
A:580;
A:581;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
submit data
40.078 Ca [Ca+2...
CL A:582;
Invalid;
none;
submit data
35.453 Cl [Cl-]
DGT A:576;
Valid;
none;
submit data
507.181 C10 H16 N5 O13 P3 c1nc2...
ZN A:577;
Part of Protein;
none;
submit data
65.409 Zn [Zn+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3B0X 1.36 Å EC: 2.7.7.7 K263A MUTANT OF POLX FROM THERMUS THERMOPHILUS HB8 COMPLEXED DGTP THERMUS THERMOPHILUS STRUCTURAL GENOMICS RIKEN STRUCTURAL GENOMICS/PROTEOMICS INRSGI POLXC PHP DNA POLYMERASE DRP LYASE 3-prime -5-prime EXONUCLEENDONUCLEASE DNA REPAIR NUCLEOTIDE DNA TRANSFERASE
Ref.: THE STRUCTURAL BASIS OF THE KINETIC MECHANISM OF A GAP-FILLING X-FAMILY DNA POLYMERASE THAT BINDS MG(2 BEFORE BINDING TO DNA. J.MOL.BIOL. V. 417 179 2012
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 16 families.
1 3B0X - DGT C10 H16 N5 O13 P3 c1nc2c(n1[....
2 3B0Y - DGT C10 H16 N5 O13 P3 c1nc2c(n1[....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 15 families.
1 3B0X - DGT C10 H16 N5 O13 P3 c1nc2c(n1[....
2 3B0Y - DGT C10 H16 N5 O13 P3 c1nc2c(n1[....
50% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 15 families.
1 3B0X - DGT C10 H16 N5 O13 P3 c1nc2c(n1[....
2 3B0Y - DGT C10 H16 N5 O13 P3 c1nc2c(n1[....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: DGT; Similar ligands found: 103
No: Ligand ECFP6 Tc MDL keys Tc
1 DGT 1 1
2 DGI 0.897436 1
3 DGP 0.775 0.986842
4 DG 0.775 0.986842
5 GH3 0.673913 0.948052
6 GTP 0.659341 0.923077
7 DG DG 0.639175 0.91358
8 0O2 0.622449 0.935065
9 CGP 0.6 0.914634
10 GP3 0.597826 0.9
11 GDP 0.591398 0.923077
12 G3D 0.561224 0.935065
13 GSP 0.561224 0.878049
14 DTP 0.557895 0.909091
15 GAV 0.55 0.888889
16 G4P 0.55 0.935065
17 DC DG 0.53913 0.891566
18 GNH 0.536082 0.911392
19 G1R 0.535354 0.911392
20 G2R 0.533981 0.961538
21 GNP 0.53 0.9
22 5GP 0.521277 0.910256
23 G 0.521277 0.910256
24 GCP 0.52 0.924051
25 GPX 0.514563 0.922078
26 GPD 0.513514 0.902439
27 G5P 0.509091 0.9
28 GTG 0.504587 0.86747
29 G3A 0.5 0.9
30 G2P 0.5 0.936709
31 GDC 0.495413 0.888889
32 GKE 0.495413 0.888889
33 GDD 0.495413 0.888889
34 GMV 0.49505 0.9
35 DI 0.494737 0.960526
36 6CK 0.486486 0.86747
37 DAT 0.484536 0.909091
38 Y9Z 0.481818 0.880952
39 GP2 0.48 0.936709
40 JB2 0.477876 0.888889
41 GDR 0.477477 0.888889
42 GFB 0.477477 0.888889
43 GPG 0.472222 0.888889
44 GDP MG 0.470588 0.853659
45 DU DU DU DU BRU DG DU 0.469697 0.840909
46 3GP 0.46875 0.897436
47 2GP 0.46875 0.935065
48 GDP BEF 0.466019 0.833333
49 ALF 5GP 0.466019 0.823529
50 GKD 0.464912 0.888889
51 GCP G 0.462264 0.864198
52 BGO 0.462185 0.878049
53 8DG 0.461538 0.857143
54 GDX 0.46087 0.9
55 P2G 0.459184 0.860759
56 MGP 0.456311 0.888889
57 JB3 0.453782 0.878049
58 GDP ALF 0.453704 0.823529
59 BEF GDP 0.45283 0.823529
60 GTP MG 0.45283 0.853659
61 6G0 0.451923 0.888889
62 CAG 0.451613 0.818182
63 GMP 0.450549 0.810127
64 P1G 0.45 0.873418
65 NGD 0.45 0.888889
66 YGP 0.446429 0.835294
67 3PD UM3 0.446281 0.86747
68 G1G 0.444444 0.857143
69 DG DC 0.44186 0.925926
70 GDP AF3 0.440367 0.823529
71 N5P 0.439252 0.75
72 DUT 0.438776 0.7875
73 DG DA DC DG 0.43662 0.880952
74 01G 0.433628 0.903614
75 DA DC DG DA 0.433566 0.880952
76 TPG 0.430769 0.782609
77 DCP 0.43 0.848101
78 G G 0.428571 0.864198
79 CF2 0.428571 0.802326
80 GGM 0.427419 0.857143
81 2MD 0.427419 0.827586
82 U2G 0.42623 0.86747
83 CG2 0.419355 0.86747
84 MGD 0.417323 0.827586
85 DG DT DC 0.416667 0.850575
86 TTP 0.415842 0.759036
87 MD1 0.415385 0.848837
88 PGD 0.415385 0.857143
89 G G U 0.415254 0.8875
90 DA DU DG DA 0.414634 0.835294
91 FEG 0.414634 0.858824
92 ZGP 0.41129 0.848837
93 DDS 0.409524 0.858974
94 3AT 0.409524 0.871795
95 DBG 0.409091 0.878049
96 3ZE 0.407767 0.886076
97 6U4 0.407407 0.853659
98 GDP 7MG 0.40678 0.843373
99 GPC 0.40625 0.816092
100 SGP 0.401961 0.807229
101 7D4 0.401961 0.814815
102 AGO 0.401575 0.86747
103 DC DG DA DC 0.401408 0.902439
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3B0X; Ligand: DGT; Similar sites found: 20
This union binding pocket(no: 1) in the query (biounit: 3b0x.bio1) has 16 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2B56 U5P 0.01045 0.42077 2.13675
2 3IES M24 0.0299 0.40735 2.17786
3 1VPE ANP 0.01509 0.40986 2.26131
4 3JYY PPV 0.001305 0.46507 3.48432
5 5VSM MET 0.01007 0.41354 4.40252
6 3ER9 3AT 0.00669 0.41629 4.7138
7 5A2Z GTP 0.008692 0.4085 5.04504
8 1USF FMN 0.02527 0.40421 5.05618
9 1USF NAP 0.0334 0.40162 5.05618
10 4MSG 2C6 0.03791 0.40199 5.06912
11 4A1O JLN 0.0188 0.40513 5.54493
12 4F07 FAD 0.01505 0.40504 5.78947
13 2Q0D ATP 0.009447 0.42839 5.94901
14 2F5Z FAD 0.02893 0.41728 6.25
15 1KNY APC 0.003028 0.41196 8.3004
16 5W0N 2KH 0.01279 0.40283 8.933
17 3UVD MB3 0.003659 0.4298 9.67742
18 4I2D APC 0.0000001197 0.6581 9.75
19 3RNM FAD 0.03544 0.41176 22.4138
20 4P4M D3T 0.0000000000439 0.76915 41.5344
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