Receptor
PDB id Resolution Class Description Source Keywords
6IPK 2.15 Å EC: 2.7.7.7 BINARY COMPLEX OF HUMAN DNA POLYMERASE MU WITH MN8OXODGTP HOMO SAPIENS DNA POLYMERASE MU DNA BREAK REPAIR TRANSFERASE-DNTP COMPLEDGTP TRANSFERASE
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:503;
A:507;
 Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
none;
none;
 submit data
96.063 O4 S [O-]S...
EPE A:509;
 Invalid;
 none;
 submit data
238.305 C8 H18 N2 O4 S C1CN(...
8DG A:502;
 Valid;
 none;
 Kd = 6.7 uM
523.18 C10 H16 N5 O14 P3 C1[C@...
MN A:500;
A:501;
 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
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: 8DG; Similar ligands found: 19
No: Ligand ECFP6 Tc MDL keys Tc
1 8DG 1 1
2 8GD 0.897436 1
3 8OG 0.775 0.9875
4 8HG 0.670886 0.901235
5 8GT 0.644444 0.95
6 G8D 0.586957 0.95
7 F6G 0.548387 0.841463
8 8GM 0.505376 0.9375
9 DCP 0.505263 0.875
10 DUT 0.5 0.8375
11 TTP 0.489583 0.829268
12 6U4 0.475728 0.95
13 8DD 0.470588 0.845238
14 DGT 0.461538 0.857143
15 MGT 0.433962 0.872093
16 YYY 0.43299 0.875
17 DUD 0.427083 0.8375
18 2X3 0.422018 0.879518
19 TYD 0.418367 0.829268
Similar Ligands (3D)
Ligand no: 1; Ligand: 8DG; Similar ligands found: 12
No: Ligand Similarity coefficient
1 QBQ 0.9690
2 GTP 0.9681
3 ANP 0.9119
4 ATP 0.9051
5 GCP 0.8919
6 APC 0.8837
7 MGP 0.8784
8 3AT 0.8673
9 AGS 0.8610
10 GNP 0.8607
11 M7G 0.8565
12 DUP 0.8512
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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