Receptor
PDB id Resolution Class Description Source Keywords
2IRY 1.78 Å EC: 2.7.7.- CRYSTAL STRUCTURE OF THE POLYMERASE DOMAIN FROM MYCOBACTERIU TUBERCULOSIS LIGASE D WITH DGTP AND MANGANESE. MYCOBACTERIUM TUBERCULOSIS POLYMERASE PRIMASE LIGASE NHEJ DGTP TRANSFERASE
Ref.: STRUCTURE AND FUNCTION OF A MYCOBACTERIAL NHEJ DNA POLYMERASE. J.MOL.BIOL. V. 366 391 2007
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
DGT A:1102;
B:1103;
Valid;
Valid;
none;
none;
submit data
507.181 C10 H16 N5 O13 P3 c1nc2...
MN A:1100;
B:1101;
Part of Protein;
Part of Protein;
none;
none;
submit data
54.938 Mn [Mn+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2IRY 1.78 Å EC: 2.7.7.- CRYSTAL STRUCTURE OF THE POLYMERASE DOMAIN FROM MYCOBACTERIU TUBERCULOSIS LIGASE D WITH DGTP AND MANGANESE. MYCOBACTERIUM TUBERCULOSIS POLYMERASE PRIMASE LIGASE NHEJ DGTP TRANSFERASE
Ref.: STRUCTURE AND FUNCTION OF A MYCOBACTERIAL NHEJ DNA POLYMERASE. J.MOL.BIOL. V. 366 391 2007
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 18 families.
1 2IRY - DGT C10 H16 N5 O13 P3 c1nc2c(n1[....
2 2IRX - GTP C10 H16 N5 O14 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 2IRY - DGT C10 H16 N5 O13 P3 c1nc2c(n1[....
2 2IRX - GTP C10 H16 N5 O14 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 2IRY - DGT C10 H16 N5 O13 P3 c1nc2c(n1[....
2 2IRX - GTP C10 H16 N5 O14 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 : 2IRY; Ligand: DGT; Similar sites found: 35
This union binding pocket(no: 1) in the query (biounit: 2iry.bio1) has 20 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2YMZ LAT 0.005419 0.40833 None
2 1A78 TDG 0.01756 0.40103 None
3 3NZ1 3NY 0.003002 0.44752 1.91571
4 5N9X THR 0.02249 0.40103 1.9802
5 5DG2 GAL GLC 0.004566 0.41072 2.22222
6 4WCX ALA 0.007297 0.44446 2.9703
7 3B6R CRN 0.01664 0.40773 2.9703
8 2CDO GAL AAL GAL AAL GAL AAL 0.009797 0.42792 3.125
9 3WV6 GAL GLC 0.005017 0.4119 3.37838
10 3WV6 GAL BGC 0.01239 0.40509 3.37838
11 1DJX I3P 0.002065 0.44285 3.63036
12 4RF7 ARG 0.007251 0.42018 3.9604
13 3F5A SIA GAL NAG 0.02018 0.40084 4.06504
14 1Q11 TYE 0.02124 0.40235 4.29043
15 2D6M LBT 0.01388 0.40063 4.40252
16 2WZ5 MET 0.006587 0.43953 4.57516
17 5HV7 RBL 0.0149 0.44219 4.62046
18 5A67 3PO 0.01863 0.40525 4.71698
19 4K55 H6P 0.01757 0.40243 4.83871
20 3IT7 TLA 0.01521 0.41729 4.94506
21 3HZL 6PC 0.01611 0.41094 4.9505
22 3M3E GAL A2G NPO 0.007543 0.42891 4.96894
23 1M5W DXP 0.01129 0.41632 5.34979
24 4LIT AKG 0.009772 0.4224 5.61056
25 3FIU POP 0.02391 0.40095 5.62249
26 3VV1 GAL FUC 0.0159 0.40472 5.625
27 2FOJ GLY ALA ARG ALA HIS SER SER 0.01637 0.40812 7.74194
28 4CP9 GAL CN8 0.02108 0.40252 8.26446
29 5F6U 5VK 0.02121 0.40731 8.28025
30 3HQP OXL 0.01999 0.40509 13.2013
31 5V3D FCN 0.02041 0.40408 13.7931
32 1C3M MAN MAN 0.00801 0.41343 15.6463
33 4M1U A2G MBG 0.01239 0.41606 15.7143
34 3IWD M2T 0.02245 0.40113 16.129
35 2FAR DTP 0.0000000002772 0.772 39.2739
Pocket No.: 2; Query (leader) PDB : 2IRY; Ligand: DGT; 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: 2iry.bio2) has 10 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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