Receptor
PDB id Resolution Class Description Source Keywords
6IPM 1.72 Å EC: 2.7.7.7 BINARY COMPLEX OF HUMAN DNA POLYMERASE MU WITH MGDCTP HOMO SAPIENS DNA POLYMERASE MU DNA BREAK REPAIR TRANSFERASE-DNTP COMPLETRANSFERASE
Ref.: HUMAN DNA POLYMERASE MU CAN USE A NONCANONICAL MECH MULTIPLE MN2+-MEDIATED FUNCTIONS. J.AM.CHEM.SOC. V. 141 8489 2019
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
SO4 A:504;
A:506;
A:508;
A:505;
A:509;
A:507;
A:503;
 Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
none;
none;
none;
 submit data
96.063 O4 S [O-]S...
MG A:502;
 Part of Protein;
 none;
 submit data
24.305 Mg [Mg+2...
DCP A:501;
 Valid;
 Atoms found MORE than expected: % Diff = 2;
 Kd = 206 uM
467.157 C9 H16 N3 O13 P3 C1[C@...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
6IPH 1.65 Å EC: 2.7.7.7 BINARY COMPLEX OF HUMAN DNA POLYMERASE MU WITH MNDATP HOMO SAPIENS DNA POLYMERASE MU DNA BREAK REPAIR TRANSFERASE-DNTP COMPLETRANSFERASE
Ref.: HUMAN DNA POLYMERASE MU CAN USE A NONCANONICAL MECH MULTIPLE MN2+-MEDIATED FUNCTIONS. J.AM.CHEM.SOC. V. 141 8489 2019
Members (12)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 21 families.
1 6IPN Kd = 140 uM DGT C10 H16 N5 O13 P3 c1nc2c(n1[....
2 6IPK Kd = 6.7 uM 8DG C10 H16 N5 O14 P3 C1[C@@H]([....
3 6IPI Kd = 1.95 uM DCP C9 H16 N3 O13 P3 C1[C@@H]([....
4 6IPH Kd = 0.22 uM DTP C10 H16 N5 O12 P3 c1nc(c2c(n....
5 5ZLC Kd = 0.95 uM DGT C10 H16 N5 O13 P3 c1nc2c(n1[....
6 6AEC Kd = 0.71 uM ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
7 6IPJ Kd = 1.62 uM TTP C10 H17 N2 O14 P3 CC1=CN(C(=....
8 6AK5 Kd = 0.75 uM GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
9 6IPM Kd = 206 uM DCP C9 H16 N3 O13 P3 C1[C@@H]([....
10 6AEH Kd = 1.77 uM UTP C9 H15 N2 O15 P3 C1=CN(C(=O....
11 6AK6 Kd = 2.76 uM CTP C9 H16 N3 O14 P3 C1=CN(C(=O....
12 6IPL Kd = 153 uM DTP C10 H16 N5 O12 P3 c1nc(c2c(n....
70% Homology Family (12)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 20 families.
1 6IPN Kd = 140 uM DGT C10 H16 N5 O13 P3 c1nc2c(n1[....
2 6IPK Kd = 6.7 uM 8DG C10 H16 N5 O14 P3 C1[C@@H]([....
3 6IPI Kd = 1.95 uM DCP C9 H16 N3 O13 P3 C1[C@@H]([....
4 6IPH Kd = 0.22 uM DTP C10 H16 N5 O12 P3 c1nc(c2c(n....
5 5ZLC Kd = 0.95 uM DGT C10 H16 N5 O13 P3 c1nc2c(n1[....
6 6AEC Kd = 0.71 uM ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
7 6IPJ Kd = 1.62 uM TTP C10 H17 N2 O14 P3 CC1=CN(C(=....
8 6AK5 Kd = 0.75 uM GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
9 6IPM Kd = 206 uM DCP C9 H16 N3 O13 P3 C1[C@@H]([....
10 6AEH Kd = 1.77 uM UTP C9 H15 N2 O15 P3 C1=CN(C(=O....
11 6AK6 Kd = 2.76 uM CTP C9 H16 N3 O14 P3 C1=CN(C(=O....
12 6IPL Kd = 153 uM DTP C10 H16 N5 O12 P3 c1nc(c2c(n....
50% Homology Family (16)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 20 families.
1 6IPN Kd = 140 uM DGT C10 H16 N5 O13 P3 c1nc2c(n1[....
2 6IPK Kd = 6.7 uM 8DG C10 H16 N5 O14 P3 C1[C@@H]([....
3 6IPI Kd = 1.95 uM DCP C9 H16 N3 O13 P3 C1[C@@H]([....
4 6IPH Kd = 0.22 uM DTP C10 H16 N5 O12 P3 c1nc(c2c(n....
5 5ZLC Kd = 0.95 uM DGT C10 H16 N5 O13 P3 c1nc2c(n1[....
6 6AEC Kd = 0.71 uM ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
7 6IPJ Kd = 1.62 uM TTP C10 H17 N2 O14 P3 CC1=CN(C(=....
8 6AK5 Kd = 0.75 uM GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
9 6IPM Kd = 206 uM DCP C9 H16 N3 O13 P3 C1[C@@H]([....
10 6AEH Kd = 1.77 uM UTP C9 H15 N2 O15 P3 C1=CN(C(=O....
11 6AK6 Kd = 2.76 uM CTP C9 H16 N3 O14 P3 C1=CN(C(=O....
12 6IPL Kd = 153 uM DTP C10 H16 N5 O12 P3 c1nc(c2c(n....
13 6GO4 - DCT C9 H16 N3 O12 P3 C1C[C@@H](....
14 4I2D - APC C11 H18 N5 O12 P3 c1nc(c2c(n....
15 4IQU - 1FQ C17 H12 F N O5 c1cc(ccc1C....
16 4I2I - AP5 C20 H29 N10 O22 P5 c1nc(c2c(n....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: DCP; Similar ligands found: 55
No: Ligand ECFP6 Tc MDL keys Tc
1 DCP 1 1
2 YYY 0.884058 1
3 DC 0.760563 0.985714
4 DCM 0.760563 0.985714
5 0KX 0.708861 0.972222
6 DCP MG 0.646341 0.943662
7 DCT 0.621951 0.971831
8 CTP 0.609756 0.90411
9 DUT 0.609756 0.929577
10 HF4 0.609756 0.90411
11 DCZ 0.605634 0.847222
12 LDC 0.605634 0.847222
13 GTF 0.581395 0.891892
14 TTP 0.55814 0.891892
15 6U4 0.554348 0.921053
16 CDP 0.535714 0.90411
17 DUD 0.52381 0.929577
18 F6G 0.516854 0.905405
19 GCQ 0.511364 0.891892
20 8DG 0.505263 0.875
21 TYD 0.477273 0.891892
22 5CM 0.471264 0.945205
23 CPA 0.468468 0.85
24 DOC 0.464286 0.957747
25 7XL 0.462366 0.88
26 0RC 0.462366 0.881579
27 CXY 0.46 0.88
28 CGP 0.452174 0.841463
29 C2G 0.447917 0.891892
30 C5P 0.447059 0.890411
31 C 0.447059 0.890411
32 CAR 0.447059 0.890411
33 2TM 0.44086 0.918919
34 CDM 0.44 0.858974
35 C5G 0.435644 0.855263
36 8GD 0.43299 0.875
37 DTP 0.43299 0.831169
38 UMP 0.430233 0.915493
39 DU 0.430233 0.915493
40 DGT 0.43 0.848101
41 CDC 0.43 0.77381
42 TLO 0.415842 0.844156
43 DUP 0.414894 0.90411
44 UTP 0.413043 0.849315
45 523 0.412371 0.921053
46 0FX 0.411215 0.835443
47 8DD 0.41 0.835443
48 U5F 0.408602 0.849315
49 HF7 0.405941 0.820513
50 T3F 0.40566 0.835443
51 T3Q 0.40566 0.835443
52 C3P 0.402299 0.876712
53 DDN 0.402299 0.915493
54 C2P 0.402299 0.916667
55 CDP MG 0.402174 0.851351
Similar Ligands (3D)
Ligand no: 1; Ligand: DCP; Similar ligands found: 16
No: Ligand Similarity coefficient
1 HEJ 0.9343
2 DZ4 0.9320
3 2KH 0.9268
4 D3T 0.9176
5 ATP 0.9141
6 AGS 0.9032
7 HDV 0.8991
8 UNP 0.8939
9 APC 0.8885
10 ACP 0.8847
11 ANP 0.8734
12 GTP 0.8670
13 UDP 0.8657
14 ADP BEF 0.8644
15 ALF ADP 0.8568
16 ADP ALF 0.8561
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 6IPH; Ligand: DTP; Similar sites found with APoc: 1
This union binding pocket(no: 1) in the query (biounit: 6iph.bio1) has 23 residues
No: Leader PDB Ligand Sequence Similarity
1 4P4M D3T 44.9438
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