Receptor
PDB id Resolution Class Description Source Keywords
2IRX 1.8 Å EC: 2.7.7.- CRYSTAL STRUCTURE OF THE POLYMERASE DOMAIN FROM MYCOBACTERIU TUBERCULOSIS LIGASE D WITH GTP AND MANGANESE. MYCOBACTERIUM TUBERCULOSIS POLYMERASE PRIMASE LIGASE NHEJ GTP 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
GTP A:305;
Valid;
none;
submit data
523.18 C10 H16 N5 O14 P3 c1nc2...
MN A:304;
Part of Protein;
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: GTP; Similar ligands found: 147
No: Ligand ECFP6 Tc MDL keys Tc
1 GTP 1 1
2 GP3 0.921053 0.973684
3 GDP 0.909091 1
4 GSP 0.853659 0.948718
5 GNH 0.82716 0.986667
6 G1R 0.819277 0.986667
7 GAV 0.811765 0.961039
8 GNP 0.809524 0.973684
9 GCP 0.797619 0.973684
10 5GP 0.797468 0.986486
11 G 0.797468 0.986486
12 GMV 0.764706 0.973684
13 G2R 0.764045 0.961039
14 G5P 0.755319 0.973684
15 GTG 0.752688 0.936709
16 G2P 0.747126 0.961039
17 G3A 0.744681 0.973684
18 GDD 0.741935 0.961039
19 GKE 0.741935 0.961039
20 GDC 0.741935 0.961039
21 0O2 0.736264 0.986486
22 GP2 0.729412 0.961039
23 6CK 0.726316 0.936709
24 Y9Z 0.723404 0.902439
25 GPG 0.717391 0.961039
26 GFB 0.715789 0.961039
27 GDR 0.715789 0.961039
28 GDP MG 0.712644 0.923077
29 GDP BEF 0.704545 0.9
30 GPD 0.704082 0.925
31 JB2 0.693878 0.961039
32 GKD 0.693878 0.961039
33 GCP G 0.692308 0.935065
34 GDX 0.686869 0.973684
35 ALF 5GP 0.685393 0.888889
36 GTP MG 0.681319 0.923077
37 BEF GDP 0.681319 0.888889
38 GH3 0.681319 0.973333
39 YGP 0.677083 0.901235
40 G3D 0.67033 0.986486
41 GDP AF3 0.659574 0.888889
42 GDP ALF 0.659574 0.888889
43 DGT 0.659341 0.923077
44 GMP 0.658228 0.88
45 G4P 0.655914 0.986486
46 JB3 0.653846 0.948718
47 NGD 0.647619 0.961039
48 CAG 0.642202 0.880952
49 2MD 0.62963 0.891566
50 G G 0.622449 0.935065
51 MGP 0.619565 0.961039
52 U2G 0.616822 0.936709
53 6G0 0.612903 0.961039
54 MGD 0.612613 0.891566
55 TPG 0.608696 0.840909
56 CG2 0.605505 0.936709
57 GDP 7MG 0.601942 0.911392
58 FEG 0.601852 0.879518
59 ZGP 0.59633 0.869048
60 MD1 0.591304 0.891566
61 PGD 0.591304 0.925
62 3GP 0.590909 0.946667
63 GPX 0.581633 0.946667
64 DGI 0.580645 0.923077
65 IDP 0.576087 0.972973
66 DBG 0.567797 0.948718
67 FE9 0.555556 0.776596
68 2GP 0.555556 0.96
69 G4M 0.547619 0.880952
70 BGO 0.544643 0.924051
71 I2C FE2 CMO CMO 0.538462 0.808989
72 ATP 0.537634 0.92
73 G1G 0.533898 0.925
74 AQP 0.531915 0.92
75 5FA 0.531915 0.92
76 G A A A 0.525862 0.923077
77 U A G G 0.521368 0.935065
78 01G 0.518868 0.902439
79 ITT 0.510638 0.868421
80 P2G 0.510638 0.883117
81 GGM 0.504274 0.901235
82 G1R G1R 0.504065 0.924051
83 DGP 0.5 0.910256
84 PGD O 0.5 0.850575
85 MGO 0.5 0.864198
86 P1G 0.5 0.871795
87 DG 0.5 0.910256
88 GTA 0.495495 0.936709
89 B4P 0.489362 0.894737
90 AP5 0.489362 0.894737
91 IMP 0.489362 0.959459
92 7DT 0.484536 0.906667
93 G G U 0.482143 0.935065
94 GPC 0.479339 0.879518
95 G C 0.478992 0.9
96 BA3 0.478723 0.894737
97 ADP 0.473684 0.92
98 G2Q 0.471698 0.961039
99 G7M 0.46875 0.948052
100 25L 0.458716 0.907895
101 A2D 0.457447 0.894737
102 RGT 0.45045 0.909091
103 AGS 0.45 0.873418
104 SAP 0.45 0.873418
105 SGP 0.44898 0.82716
106 U G A 0.448529 0.888889
107 A4P 0.445378 0.869048
108 G G G RPC 0.442623 0.875
109 ACQ 0.441176 0.896104
110 ANP 0.441176 0.896104
111 8GT 0.441176 0.875
112 APC G U 0.44 0.886076
113 G U34 0.438017 0.888889
114 6AD 0.436893 0.841463
115 G G G C 0.433071 0.9125
116 UP5 0.432203 0.873418
117 35G 0.431373 0.933333
118 C2E 0.431373 0.921053
119 PCG 0.431373 0.933333
120 A G C C 0.429688 0.911392
121 5GP 5GP 0.427184 0.883117
122 TAT 0.427184 0.884615
123 APR 0.425743 0.894737
124 AR6 0.425743 0.894737
125 AN2 0.424242 0.907895
126 7DD 0.424242 0.906667
127 DG DG 0.423423 0.865854
128 AD9 0.421569 0.896104
129 M33 0.42 0.883117
130 7D4 0.42 0.835443
131 UCG 0.419847 0.911392
132 H6Y 0.419048 0.946667
133 G C C C 0.416667 0.924051
134 ACP 0.415842 0.896104
135 T5A 0.414634 0.802326
136 MGQ 0.412844 0.935897
137 ADQ 0.412844 0.871795
138 A1R 0.412844 0.839506
139 MGT 0.411215 0.823529
140 A G U 0.410072 0.888889
141 93A 0.41 0.833333
142 A22 0.407407 0.907895
143 CA0 0.405941 0.896104
144 ATF 0.40566 0.884615
145 AGO 0.404762 0.888889
146 MGV 0.401786 0.890244
147 CGP 0.4 0.86747
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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