Receptor
PDB id Resolution Class Description Source Keywords
5IHE 2.5 Å EC: 2.7.7.7 D-FAMILY DNA POLYMERASE - DP1 SUBUNIT (3'-5' PROOF-READING EXONUCLEASE) PYROCOCCUS ABYSSI (STRAIN GE5 / ORSAY)ORGANISM_TAXID: 272844 DNA POLYMERASE D-FAMILY EXONUCLEASE TRANSFERASE
Ref.: SHARED ACTIVE SITE ARCHITECTURE BETWEEN ARCHAEAL PO MULTI-SUBUNIT RNA POLYMERASES REVEALED BY X-RAY CRYSTALLOGRAPHY. NAT COMMUN V. 7 12227 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ZN B:703;
A:703;
Part of Protein;
Part of Protein;
none;
none;
submit data
65.409 Zn [Zn+2...
ACT A:705;
B:705;
Invalid;
Invalid;
none;
none;
submit data
59.044 C2 H3 O2 CC(=O...
D5M A:701;
B:701;
Valid;
Valid;
none;
none;
submit data
331.222 C10 H14 N5 O6 P c1nc(...
CA A:706;
B:704;
A:704;
Invalid;
Part of Protein;
Invalid;
none;
none;
none;
submit data
40.078 Ca [Ca+2...
FE A:702;
B:702;
Part of Protein;
Part of Protein;
none;
none;
submit data
55.845 Fe [Fe+3...
EDO B:706;
Invalid;
none;
submit data
62.068 C2 H6 O2 C(CO)...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5IHE 2.5 Å EC: 2.7.7.7 D-FAMILY DNA POLYMERASE - DP1 SUBUNIT (3'-5' PROOF-READING EXONUCLEASE) PYROCOCCUS ABYSSI (STRAIN GE5 / ORSAY)ORGANISM_TAXID: 272844 DNA POLYMERASE D-FAMILY EXONUCLEASE TRANSFERASE
Ref.: SHARED ACTIVE SITE ARCHITECTURE BETWEEN ARCHAEAL PO MULTI-SUBUNIT RNA POLYMERASES REVEALED BY X-RAY CRYSTALLOGRAPHY. NAT COMMUN V. 7 12227 2016
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 16 families.
1 5IHE - D5M C10 H14 N5 O6 P c1nc(c2c(n....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 15 families.
1 5IHE - D5M C10 H14 N5 O6 P c1nc(c2c(n....
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 15 families.
1 5IHE - D5M C10 H14 N5 O6 P c1nc(c2c(n....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: D5M; Similar ligands found: 137
No: Ligand ECFP6 Tc MDL keys Tc
1 D5M 1 1
2 DA 1 1
3 DAT 0.816901 0.971831
4 AS 0.808824 0.945205
5 DTP 0.773333 0.971831
6 3D1 0.707692 0.833333
7 3L1 0.707692 0.833333
8 DOI 0.68 0.916667
9 5F1 0.661765 0.816901
10 101 0.613333 0.943662
11 CPA 0.585859 0.860759
12 7D5 0.581081 0.890411
13 103 0.578947 0.849315
14 AMP 0.558442 0.902778
15 A 0.558442 0.902778
16 A3P 0.54321 0.902778
17 DDS 0.528736 0.916667
18 A2P 0.52439 0.915493
19 DG 0.511905 0.894737
20 DGP 0.511905 0.894737
21 ZDA 0.505747 0.826667
22 ABM 0.5 0.853333
23 3AT 0.494382 0.90411
24 7D3 0.493976 0.866667
25 DA DT DA DA 0.491379 0.82716
26 ADP 0.482353 0.878378
27 A2D 0.481928 0.853333
28 V3L 0.477778 0.878378
29 DI 0.476744 0.893333
30 2AM 0.475 0.902778
31 PPS 0.472527 0.792683
32 PAP 0.47191 0.890411
33 ADX 0.471264 0.771084
34 7D4 0.471264 0.866667
35 A12 0.470588 0.893333
36 BA3 0.470588 0.853333
37 AP2 0.470588 0.893333
38 AMP MG 0.46988 0.828947
39 3AM 0.469136 0.888889
40 MDR 0.467532 0.780822
41 DU DU DU DU BRU DA DU 0.467213 0.807229
42 ATP 0.465909 0.878378
43 AP5 0.465116 0.853333
44 B4P 0.465116 0.853333
45 PRX 0.460674 0.855263
46 2A5 0.460674 0.905405
47 5FA 0.460674 0.878378
48 APC 0.460674 0.893333
49 AQP 0.460674 0.878378
50 3AD 0.460526 0.791667
51 AN2 0.45977 0.866667
52 SRA 0.457831 0.855263
53 OVE 0.457831 0.866667
54 ATR 0.455556 0.902778
55 AU1 0.454545 0.855263
56 M33 0.454545 0.842105
57 CA0 0.454545 0.831169
58 2FD 0.45 0.802632
59 50T 0.449438 0.866667
60 ACP 0.449438 0.88
61 25A 0.447917 0.878378
62 7D7 0.445946 0.753425
63 ACQ 0.445652 0.88
64 TAT 0.445652 0.844156
65 APR 0.444444 0.853333
66 AR6 0.444444 0.853333
67 A1R 0.443299 0.894737
68 RAB 0.44 0.756757
69 ADN 0.44 0.756757
70 XYA 0.44 0.756757
71 ADV 0.43956 0.868421
72 AD9 0.43956 0.855263
73 RBY 0.43956 0.868421
74 AGS 0.43956 0.833333
75 SAP 0.43956 0.833333
76 ADP MG 0.438202 0.818182
77 CL9 0.4375 0.802632
78 AV2 0.43617 0.853333
79 NA7 0.434343 0.918919
80 ADP BEF 0.433333 0.797468
81 BEF ADP 0.433333 0.797468
82 ANP 0.430108 0.855263
83 DA DC DG DA 0.428571 0.819277
84 A2R 0.427083 0.866667
85 SON 0.426966 0.893333
86 5AL 0.425532 0.842105
87 ANZ 0.424528 0.7875
88 ADP PO3 0.423913 0.851351
89 GGZ 0.42268 0.768293
90 A22 0.42268 0.866667
91 3DH 0.421687 0.714286
92 TM1 0.421569 0.741176
93 ATF 0.421053 0.844156
94 ADP ALF 0.421053 0.7875
95 DG DA DC DG 0.421053 0.819277
96 ALF ADP 0.421053 0.7875
97 A A A 0.42 0.891892
98 ATP MG 0.419355 0.818182
99 5SV 0.418367 0.835443
100 ARJ 0.417722 0.712329
101 SRP 0.416667 0.868421
102 ANP MG 0.416667 0.810127
103 DGI 0.414894 0.883117
104 GAP 0.414894 0.807692
105 MTA 0.414634 0.714286
106 4AD 0.414141 0.857143
107 ADQ 0.414141 0.831169
108 ZZB 0.412281 0.761905
109 ACK 0.411765 0.847222
110 PTJ 0.411765 0.8125
111 NB8 0.411765 0.835443
112 QQY 0.411765 0.802632
113 FYA 0.411765 0.917808
114 5N5 0.410256 0.733333
115 DLL 0.41 0.842105
116 MAP 0.408163 0.833333
117 CC5 0.407895 0.777778
118 3UK 0.405941 0.831169
119 5CD 0.405063 0.743243
120 A4D 0.405063 0.733333
121 OOB 0.40404 0.842105
122 8QN 0.40404 0.842105
123 9SN 0.403846 0.790123
124 DTA 0.402439 0.75
125 NEC 0.402299 0.688312
126 A3G 0.402299 0.763158
127 2VA 0.402174 0.717949
128 5X8 0.402174 0.75
129 VO4 ADP 0.402062 0.842105
130 ADP VO4 0.402062 0.842105
131 WAQ 0.401961 0.87013
132 PR8 0.401961 0.860759
133 QQX 0.4 0.792208
134 5AS 0.4 0.727273
135 AFX 0.4 0.625
136 AMO 0.4 0.868421
137 PAJ 0.4 0.780488
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5IHE; Ligand: D5M; Similar sites found: 12
This union binding pocket(no: 1) in the query (biounit: 5ihe.bio2) has 14 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5KAS PC 0.00000008248 0.656 2.8103
2 5I85 PC 0.000000001762 0.64805 2.91595
3 4PEG 5GP 0.00002426 0.5437 3.33333
4 5FCB AMP 0.0000000931 0.64873 3.4642
5 4DHL 0K7 0.000002316 0.59589 4.92958
6 3RL3 5GP 0.0000002769 0.54822 6.75676
7 2ZO9 MLI 0.0000000139 0.72546 9.12409
8 4OIT MAN 0.02874 0.40191 9.73451
9 3WCA FPS 0.03756 0.40421 11.2329
10 1II7 DA 0.00000000951 0.72198 12.6126
11 4J6O CIT 0.0002396 0.48358 17.803
12 4ZX2 4TE 0.00000953 0.5566 27.9279
Pocket No.: 2; Query (leader) PDB : 5IHE; Ligand: D5M; Similar sites found: 4
This union binding pocket(no: 2) in the query (biounit: 5ihe.bio1) has 14 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5JNN 6LM 0.03282 0.40076 3.15789
2 1N13 AG2 0.007814 0.41344 9.73451
3 2QQC AG2 0.00749 0.41435 9.82143
4 3AIH BMA MAN MAN 0.01234 0.40587 11.2903
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