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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 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: 100
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 GSP 0.561224 0.878049
13 G3D 0.561224 0.935065
14 DTP 0.557895 0.909091
15 HF7 0.556701 0.897436
16 G4P 0.55 0.935065
17 GAV 0.55 0.888889
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 5GP 0.521277 0.910256
25 G 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 G3A 0.5 0.9
32 G2P 0.5 0.936709
33 GDC 0.495413 0.888889
34 GDD 0.495413 0.888889
35 GKE 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 GFB 0.477477 0.888889
44 GDR 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 GDP ALF 0.453704 0.823529
57 ALF GDP 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 N5P 0.439252 0.75
70 DUT 0.438776 0.7875
71 DG DA DC DG 0.43662 0.880952
72 01G 0.433628 0.903614
73 C1Z 0.432432 0.935065
74 TPG 0.430769 0.782609
75 DCP 0.43 0.848101
76 CF2 0.428571 0.802326
77 2MD 0.427419 0.827586
78 GGM 0.427419 0.857143
79 U2G 0.42623 0.86747
80 CG2 0.419355 0.86747
81 MGD 0.417323 0.827586
82 TTP 0.415842 0.759036
83 MD1 0.415385 0.848837
84 PGD 0.415385 0.857143
85 DA DU DG DA 0.414634 0.835294
86 FEG 0.414634 0.858824
87 G G 0.413793 0.876543
88 ZGP 0.41129 0.848837
89 DDS 0.409524 0.858974
90 3AT 0.409524 0.871795
91 DBG 0.409091 0.878049
92 3ZE 0.407767 0.886076
93 6U4 0.407407 0.853659
94 GDP 7MG 0.40678 0.843373
95 GPC 0.40625 0.816092
96 DA DC DG DA 0.402685 0.914634
97 SGP 0.401961 0.807229
98 7D4 0.401961 0.814815
99 AGO 0.401575 0.86747
100 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: 31
This union binding pocket(no: 1) in the query (biounit: 3b0x.bio1) has 16 residues
No: Leader PDB Ligand Sequence Similarity
1 2B56 UTP 2.13675
2 2B56 U5P 2.13675
3 3IES M24 2.17786
4 1VPE ANP 2.26131
5 1H82 FAD 2.54237
6 3HQP OXL 3.20641
7 1V6A TRE 3.31325
8 3JYY PPV 3.48432
9 3JZ0 APC 3.48432
10 5VSM MET 4.40252
11 3ER9 3AT 4.7138
12 1D4O NAP 4.8913
13 5A2Z GTP 5.04504
14 1USF FMN 5.05618
15 1USF NAP 5.05618
16 4MSG 2C6 5.06912
17 4A1O JLN 5.54493
18 1K0E TRP 5.73951
19 4F07 FAD 5.78947
20 2Q0D ATP 5.94901
21 2F5Z FAD 6.25
22 4RF7 ARG 6.95652
23 1KNY APC 8.3004
24 3ZOD FMN 8.37696
25 3ZOD HQE 8.37696
26 2ZFZ ARG 8.86076
27 5W0N 2KH 8.933
28 3UVD MB3 9.67742
29 4I2D APC 9.75
30 3RNM FAD 22.4138
31 4P4M D3T 41.5344
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