Receptor
PDB id Resolution Class Description Source Keywords
6IPJ 1.98 Å EC: 2.7.7.7 BINARY COMPLEX OF HUMAN DNA POLYMERASE MU WITH MNDTTP 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:505;
A:507;
A:506;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
submit data
96.063 O4 S [O-]S...
MN A:501;
A:502;
Part of Protein;
Part of Protein;
none;
none;
submit data
54.938 Mn [Mn+2...
TTP A:503;
Valid;
none;
Kd = 1.62 uM
482.168 C10 H17 N2 O14 P3 CC1=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: TTP; Similar ligands found: 84
No: Ligand ECFP6 Tc MDL keys Tc
1 TTP 1 1
2 TYD 0.884058 1
3 TMP 0.760563 0.985714
4 TLO 0.722892 0.945205
5 DAU 0.701149 0.932432
6 TRH 0.689655 0.932432
7 1JB 0.689655 0.932432
8 TDX 0.689655 0.945205
9 3R2 0.689655 0.92
10 18T 0.689655 0.932432
11 T3Q 0.674157 0.907895
12 3YN 0.674157 0.932432
13 DWN 0.674157 0.907895
14 T3F 0.674157 0.907895
15 0N2 0.666667 0.896104
16 T46 0.666667 0.932432
17 0FX 0.659341 0.907895
18 MMF 0.659341 0.907895
19 TTP MG 0.646341 0.943662
20 QDM 0.645161 0.896104
21 FNF 0.638298 0.92
22 JHZ 0.638298 0.884615
23 1YF 0.638298 0.92
24 AKM 0.638298 0.886076
25 9RC 0.636364 0.829268
26 4TG 0.631579 0.92
27 DUT 0.62963 0.957143
28 TBD 0.62963 0.958904
29 D3T 0.62963 0.971831
30 T5A 0.61165 0.841463
31 LLT 0.605634 0.873239
32 THM 0.605634 0.873239
33 ATY 0.6 0.945205
34 FUH 0.588235 0.907895
35 QUH 0.588235 0.907895
36 AZD 0.586207 0.907895
37 UFP 0.56962 0.905405
38 0DN 0.567568 0.833333
39 DCP 0.55814 0.891892
40 BRU 0.54321 0.905405
41 5HU 0.54321 0.971831
42 DUD 0.542169 0.957143
43 NYM 0.536585 0.958333
44 FDM 0.536585 0.918919
45 5IU 0.536585 0.905405
46 F6G 0.534091 0.855263
47 ABT 0.531915 0.884615
48 T3P 0.531646 0.943662
49 THP 0.53012 0.971429
50 D4T 0.528736 0.928571
51 6U4 0.521277 0.848101
52 ATM 0.517241 0.894737
53 TQP 0.512605 0.864198
54 7SG 0.512605 0.864198
55 TXS 0.512195 0.789474
56 TPE 0.510204 0.894737
57 T4K 0.508333 0.853659
58 T5K 0.508333 0.853659
59 3DR DT DT DT DT DT 0.504854 0.905405
60 BVP 0.5 0.944444
61 T3S 0.5 0.789474
62 8DG 0.489583 0.829268
63 BUP 0.477778 0.842105
64 YYY 0.477273 0.891892
65 2DT 0.47561 0.957747
66 4TA 0.469565 0.807229
67 DT ME6 DT 0.468468 0.87013
68 D4D 0.449438 0.928571
69 DU 0.447059 0.942857
70 UMP 0.447059 0.942857
71 AZZ 0.447059 0.779221
72 523 0.442105 0.921053
73 5CM 0.438202 0.918919
74 DUP 0.430108 0.930556
75 ADS THS THS THS 0.429752 0.758621
76 UTP 0.428571 0.875
77 8DD 0.424242 0.8125
78 U5F 0.423913 0.875
79 WMJ 0.42 0.761905
80 DDN 0.418605 0.942857
81 8GD 0.418367 0.829268
82 DGT 0.415842 0.759036
83 UC5 0.406593 0.943662
84 ID2 0.402439 0.8
Similar Ligands (3D)
Ligand no: 1; Ligand: TTP; Similar ligands found: 28
No: Ligand Similarity coefficient
1 DTP 0.9873
2 DZ4 0.9766
3 MG TTP 0.9753
4 HF7 0.9630
5 HEJ 0.9540
6 HDV 0.9485
7 HF4 0.9432
8 DUT MG 0.9338
9 HFD 0.9332
10 JSQ 0.9100
11 GTF 0.9093
12 ACP 0.9066
13 ANP 0.9060
14 CTP 0.8971
15 AGS 0.8934
16 ATP 0.8917
17 3AT 0.8877
18 GTP 0.8866
19 2KH 0.8825
20 0RC 0.8807
21 DCT 0.8752
22 APC 0.8740
23 MGT 0.8701
24 SAM 0.8585
25 UDP 0.8581
26 ADP BEF 0.8567
27 GNP 0.8526
28 ADP ALF 0.8523
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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