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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: 142
No: Ligand ECFP6 Tc MDL keys Tc
1 DA 1 1
2 D5M 1 1
3 DAT 0.816901 0.971831
4 AS 0.808824 0.945205
5 DTP 0.773333 0.971831
6 3L1 0.707692 0.833333
7 3D1 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 6OG 0.580247 0.932432
14 103 0.578947 0.849315
15 AMP 0.558442 0.902778
16 A 0.558442 0.902778
17 A3P 0.54321 0.902778
18 DDS 0.528736 0.916667
19 A2P 0.52439 0.915493
20 DG 0.511905 0.894737
21 DGP 0.511905 0.894737
22 HF7 0.511111 0.958333
23 ZDA 0.505747 0.826667
24 ABM 0.5 0.853333
25 3AT 0.494382 0.90411
26 7D3 0.493976 0.866667
27 DA DT DA DA 0.491379 0.82716
28 ADP 0.482353 0.878378
29 A2D 0.481928 0.853333
30 V3L 0.477778 0.878378
31 DI 0.476744 0.893333
32 2AM 0.475 0.902778
33 PPS 0.472527 0.792683
34 PAP 0.47191 0.890411
35 7D4 0.471264 0.866667
36 ADX 0.471264 0.771084
37 BA3 0.470588 0.853333
38 A12 0.470588 0.893333
39 AP2 0.470588 0.893333
40 3AM 0.469136 0.888889
41 MDR 0.467532 0.780822
42 HEJ 0.465909 0.878378
43 ATP 0.465909 0.878378
44 AP5 0.465116 0.853333
45 B4P 0.465116 0.853333
46 PRX 0.460674 0.855263
47 APC 0.460674 0.893333
48 5FA 0.460674 0.878378
49 2A5 0.460674 0.905405
50 AQP 0.460674 0.878378
51 3AD 0.460526 0.791667
52 AN2 0.45977 0.866667
53 AT4 0.45977 0.844156
54 SRA 0.457831 0.855263
55 OVE 0.457831 0.866667
56 ATR 0.455556 0.902778
57 M33 0.454545 0.842105
58 AU1 0.454545 0.855263
59 CA0 0.454545 0.831169
60 2FD 0.45 0.802632
61 ACP 0.449438 0.88
62 50T 0.449438 0.866667
63 25A 0.447917 0.878378
64 7D7 0.445946 0.753425
65 ACQ 0.445652 0.88
66 T99 0.445652 0.844156
67 TAT 0.445652 0.844156
68 AR6 0.444444 0.853333
69 APR 0.444444 0.853333
70 A1R 0.443299 0.894737
71 A3R 0.443299 0.894737
72 RAB 0.44 0.756757
73 XYA 0.44 0.756757
74 ADN 0.44 0.756757
75 AGS 0.43956 0.833333
76 RBY 0.43956 0.868421
77 SAP 0.43956 0.833333
78 AD9 0.43956 0.855263
79 ADV 0.43956 0.868421
80 CL9 0.4375 0.802632
81 AV2 0.43617 0.853333
82 NA7 0.434343 0.918919
83 6YZ 0.431579 0.88
84 ANP 0.430108 0.855263
85 ADS THS THS THS 0.42735 0.767442
86 A2R 0.427083 0.866667
87 SON 0.426966 0.893333
88 5AL 0.425532 0.842105
89 ANZ 0.424528 0.7875
90 ADP PO3 0.423913 0.851351
91 GGZ 0.42268 0.768293
92 A22 0.42268 0.866667
93 3DH 0.421687 0.714286
94 TM1 0.421569 0.741176
95 DG DA DC DG 0.421053 0.819277
96 ALF ADP 0.421053 0.7875
97 ATF 0.421053 0.844156
98 ADP ALF 0.421053 0.7875
99 A A A 0.42 0.891892
100 5SV 0.418367 0.835443
101 ARJ 0.417722 0.712329
102 SRP 0.416667 0.868421
103 GAP 0.414894 0.807692
104 DGI 0.414894 0.883117
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 LMS 0.411765 0.75
110 PTJ 0.411765 0.8125
111 QQY 0.411765 0.802632
112 FYA 0.411765 0.917808
113 NB8 0.411765 0.835443
114 ACK 0.411765 0.847222
115 5N5 0.410256 0.733333
116 DLL 0.41 0.842105
117 MAP 0.408163 0.833333
118 CC5 0.407895 0.777778
119 3UK 0.405941 0.831169
120 DA DC DG DA 0.405797 0.851852
121 A4D 0.405063 0.733333
122 5CD 0.405063 0.743243
123 8QN 0.40404 0.842105
124 9ZD 0.40404 0.822785
125 OOB 0.40404 0.842105
126 9ZA 0.40404 0.822785
127 9SN 0.403846 0.790123
128 DTA 0.402439 0.75
129 A3G 0.402299 0.763158
130 NEC 0.402299 0.688312
131 2VA 0.402174 0.717949
132 5X8 0.402174 0.75
133 ADP VO4 0.402062 0.842105
134 VO4 ADP 0.402062 0.842105
135 B5V 0.401961 0.820513
136 WAQ 0.401961 0.87013
137 PR8 0.401961 0.860759
138 QQX 0.4 0.792208
139 PAJ 0.4 0.780488
140 AFX 0.4 0.625
141 5AS 0.4 0.727273
142 AMO 0.4 0.868421
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5IHE; Ligand: D5M; Similar sites found with APoc: 37
This union binding pocket(no: 1) in the query (biounit: 5ihe.bio2) has 14 residues
No: Leader PDB Ligand Sequence Similarity
1 1HP1 ATP 2.10526
2 3AY6 NAI 2.23048
3 3AY6 BGC 2.23048
4 4JWH SAH 2.23642
5 2WSB NAD 2.3622
6 5GUD NDP 2.52632
7 5GUD 2IT 2.52632
8 5KAS PC 2.8103
9 5I85 PC 2.91595
10 3IB8 AMP 3.0303
11 4PEG 5GP 3.33333
12 5FCB AMP 3.4642
13 4H2F ADN 3.57895
14 1O2D NAP 4.58221
15 4DHL 0K7 4.92958
16 5B4T NAD 5
17 5B4T 3HR 5
18 4R38 RBF 5.71429
19 2RH4 EMO 5.77617
20 4PIO SAH 6.19195
21 1U7T TDT 6.51341
22 3RL3 5GP 6.75676
23 3WSJ MK1 8.62069
24 5OO5 UUA 8.87097
25 2ZO9 MLI 9.12409
26 4OIT MAN 9.73451
27 3WCA FPS 11.2329
28 5MIL DUP 11.3861
29 1II7 DA 12.6126
30 1N9L FMN 12.844
31 5MYD DUP 13.5266
32 1QPR PPC 15.493
33 4J6O CIT 17.803
34 2FXD DR7 18.1818
35 5B4B LP5 22.9839
36 3T50 FMN 25
37 4ZX2 4TE 27.9279
Pocket No.: 2; Query (leader) PDB : 5IHE; Ligand: D5M; Similar sites found with APoc: 44
This union binding pocket(no: 2) in the query (biounit: 5ihe.bio1) has 14 residues
No: Leader PDB Ligand Sequence Similarity
1 2WL5 COA 1.78571
2 2CHN NGT 2.10526
3 1KBJ FMN 2.18447
4 6C5B SAH 2.34604
5 1G0N NDP 2.4735
6 1ZQ5 E04 2.47678
7 1ZQ5 NAP 2.47678
8 4M73 M72 2.67062
9 2NAD NAD 2.79898
10 5M1T C2E 2.84698
11 5JNN 6LM 3.15789
12 2VCH UDP 3.36842
13 4WUJ FMN 3.40136
14 5GWT SIN 3.59712
15 4GCZ FMN 3.63636
16 4MSG 2C6 3.68664
17 4LED XXR 3.73134
18 1G2N EPH 3.78788
19 5OC1 FAD 3.78947
20 5LIA 6XN 4
21 2R40 EPH 4.13534
22 2AE2 PTO 4.23077
23 1EC9 XYH 4.26009
24 5M7S NHT 4.42105
25 2Q3O FMN 4.60358
26 2NYA MGD 4.63158
27 5FLJ QUE 4.83871
28 3NWQ 2NC 5.05051
29 1PN4 HDC 5.71429
30 2CJF RP4 6.36943
31 1ZB6 GST 6.84039
32 1ZB6 DIN 6.84039
33 3TMK T5A 6.94444
34 3HLX PQQ 7.75194
35 2Z6C FMN 9.30233
36 3EM0 CHD 9.42029
37 1MT1 AG2 9.73451
38 1N13 AG2 9.73451
39 2QQC AG2 9.82143
40 1E6W NAD 10.3846
41 2GJ5 VD3 10.4938
42 3AIH BMA MAN MAN 11.2903
43 5ZM4 9FU 11.4379
44 3WBG 2AN 12.4183
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