Receptor
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
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:583;
Valid;
none;
submit data
507.181 C10 H16 N5 O13 P3 c1nc2...
ZN A:576;
A:577;
Part of Protein;
Part of Protein;
none;
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 18 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 17 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 17 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 DG 0.775 0.986842
4 DGP 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 HF7 0.556701 0.897436
16 GAV 0.55 0.888889
17 G4P 0.55 0.935065
18 DC DG 0.53913 0.891566
19 GNH 0.536082 0.911392
20 G1R 0.535354 0.911392
21 G2R 0.533981 0.961538
22 9GM 0.53 0.9
23 GNP 0.53 0.9
24 G 0.521277 0.910256
25 5GP 0.521277 0.910256
26 GCP 0.52 0.924051
27 GPX 0.514563 0.922078
28 GPD 0.513514 0.902439
29 G5P 0.509091 0.9
30 GTG 0.504587 0.86747
31 G2P 0.5 0.936709
32 G3A 0.5 0.9
33 GKE 0.495413 0.888889
34 GDD 0.495413 0.888889
35 GDC 0.495413 0.888889
36 GMV 0.49505 0.9
37 DI 0.494737 0.960526
38 6CK 0.486486 0.86747
39 DAT 0.484536 0.909091
40 Y9Z 0.481818 0.880952
41 GP2 0.48 0.936709
42 JB2 0.477876 0.888889
43 GDR 0.477477 0.888889
44 GFB 0.477477 0.888889
45 GPG 0.472222 0.888889
46 3GP 0.46875 0.897436
47 2GP 0.46875 0.935065
48 ALF 5GP 0.466019 0.823529
49 GKD 0.464912 0.888889
50 BGO 0.462185 0.878049
51 8DG 0.461538 0.857143
52 GDX 0.46087 0.9
53 P2G 0.459184 0.860759
54 MGP 0.456311 0.888889
55 JB3 0.453782 0.878049
56 ALF GDP 0.453704 0.823529
57 GDP ALF 0.453704 0.823529
58 6G0 0.451923 0.888889
59 CAG 0.451613 0.818182
60 GMP 0.450549 0.810127
61 NGD 0.45 0.888889
62 P1G 0.45 0.873418
63 YGP 0.446429 0.835294
64 3PD UM3 0.446281 0.86747
65 G1G 0.444444 0.857143
66 DG DC 0.44186 0.925926
67 GCP G 0.441441 0.873418
68 GDP AF3 0.440367 0.823529
69 F6G 0.44 0.8375
70 N5P 0.439252 0.75
71 DUT 0.438776 0.7875
72 DG DA DC DG 0.43662 0.880952
73 01G 0.433628 0.903614
74 C1Z 0.432432 0.935065
75 TPG 0.430769 0.782609
76 DCP 0.43 0.848101
77 CF2 0.428571 0.802326
78 GGM 0.427419 0.857143
79 2MD 0.427419 0.827586
80 U2G 0.42623 0.86747
81 CG2 0.419355 0.86747
82 KB7 0.419048 0.785714
83 MGD 0.417323 0.827586
84 TTP 0.415842 0.759036
85 MD1 0.415385 0.848837
86 PGD 0.415385 0.857143
87 FEG 0.414634 0.858824
88 DA DU DG DA 0.414634 0.835294
89 G G 0.413793 0.876543
90 ZGP 0.41129 0.848837
91 DDS 0.409524 0.858974
92 3AT 0.409524 0.871795
93 DBG 0.409091 0.878049
94 3ZE 0.407767 0.886076
95 6U4 0.407407 0.853659
96 GDP 7MG 0.40678 0.843373
97 GPC 0.40625 0.816092
98 523 0.403846 0.788235
99 DA DC DG DA 0.402685 0.914634
100 7D4 0.401961 0.814815
101 SGP 0.401961 0.807229
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 with APoc: 1
This union binding pocket(no: 1) in the query (biounit: 3b0x.bio1) has 16 residues
No: Leader PDB Ligand Sequence Similarity
1 4P4M D3T 41.5344
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