Receptor
PDB id Resolution Class Description Source Keywords
6R5E 1.85 Å EC: 2.7.7.- CRYSTAL STRUCTURE OF THE PRI1 SUBUNIT OF HUMAN PRIMASE BOUND HOMO SAPIENS PRIMASE DNA-DEPENDENT RNA POLYMERASE ATP PRIMING REPLICA
Ref.: STRUCTURAL BASIS FOR INHIBITION OF HUMAN PRIMASE BY ARABINOFURANOSYL NUCLEOSIDE ANALOGUES FLUDARABINE A VIDARABINE. ACS CHEM.BIOL. V. 14 1904 2019
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
EDO A:508;
A:507;
A:510;
A:506;
E:505;
A:505;
E:506;
A:509;
E:508;
E:507;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
62.068 C2 H6 O2 C(CO)...
MN A:502;
A:503;
E:502;
E:503;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
submit data
54.938 Mn [Mn+2...
JSQ E:504;
A:504;
Valid;
Valid;
none;
none;
submit data
525.171 C10 H15 F N5 O13 P3 c1nc2...
ZN A:501;
E:501;
Part of Protein;
Part of Protein;
none;
none;
submit data
65.409 Zn [Zn+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4LIK 1.7 Å EC: 2.7.7.- CRYSTAL STRUCTURE OF THE CATALYTIC SUBUNIT OF HUMAN PRIMASE HOMO SAPIENS PRIM FOLD TRANSFERASE
Ref.: INSIGHTS INTO EUKARYOTIC PRIMER SYNTHESIS FROM STRU THE P48 SUBUNIT OF HUMAN DNA PRIMASE. J.MOL.BIOL. V. 426 558 2014
Members (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 21 families.
1 4LIK - CIT C6 H8 O7 C(C(=O)O)C....
2 6R5D - DTP C10 H16 N5 O12 P3 c1nc(c2c(n....
3 6R5E - JSQ C10 H15 F N5 O13 P3 c1nc2c(nc(....
4 6R4U - HFD C10 H15 F N5 O13 P3 c1nc2c(nc(....
5 6R4T - HEJ C10 H16 N5 O13 P3 c1nc(c2c(n....
70% Homology Family (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 20 families.
1 4LIK - CIT C6 H8 O7 C(C(=O)O)C....
2 6R5D - DTP C10 H16 N5 O12 P3 c1nc(c2c(n....
3 6R5E - JSQ C10 H15 F N5 O13 P3 c1nc2c(nc(....
4 6R4U - HFD C10 H15 F N5 O13 P3 c1nc2c(nc(....
5 6R4T - HEJ C10 H16 N5 O13 P3 c1nc(c2c(n....
50% Homology Family (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 19 families.
1 4LIK - CIT C6 H8 O7 C(C(=O)O)C....
2 6R5D - DTP C10 H16 N5 O12 P3 c1nc(c2c(n....
3 6R5E - JSQ C10 H15 F N5 O13 P3 c1nc2c(nc(....
4 6R4U - HFD C10 H15 F N5 O13 P3 c1nc2c(nc(....
5 6R4T - HEJ C10 H16 N5 O13 P3 c1nc(c2c(n....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: JSQ; Similar ligands found: 189
No: Ligand ECFP6 Tc MDL keys Tc
1 JSQ 1 1
2 HFD 1 1
3 AVV 0.752941 0.948052
4 ATP 0.695122 0.945946
5 HEJ 0.695122 0.945946
6 5FA 0.686747 0.945946
7 AQP 0.686747 0.945946
8 6AD 0.655172 0.864198
9 B4P 0.638554 0.92
10 AP5 0.638554 0.92
11 2FA 0.626667 0.866667
12 BA3 0.626506 0.92
13 ADP 0.619048 0.945946
14 HDV 0.611111 0.946667
15 ITT 0.604651 0.893333
16 6YZ 0.604396 0.921053
17 A2D 0.60241 0.92
18 RGT 0.585859 0.909091
19 SAP 0.58427 0.897436
20 AGS 0.58427 0.897436
21 25L 0.581633 0.933333
22 ACQ 0.571429 0.921053
23 NFD 0.5625 0.935065
24 AN2 0.556818 0.933333
25 AT4 0.556818 0.909091
26 APR 0.555556 0.92
27 AR6 0.555556 0.92
28 T99 0.554348 0.909091
29 TAT 0.554348 0.909091
30 M33 0.550562 0.907895
31 AD9 0.549451 0.921053
32 ACP 0.544444 0.921053
33 7DT 0.538462 0.932432
34 ANP 0.537634 0.921053
35 ADX 0.533333 0.831325
36 CA0 0.533333 0.896104
37 HQG 0.53125 0.933333
38 A 0.529412 0.918919
39 AMP 0.529412 0.918919
40 ATF 0.526316 0.986486
41 A22 0.525773 0.933333
42 APC 0.521739 0.909091
43 HF7 0.520833 0.848101
44 GTP 0.520833 0.873418
45 7D4 0.516484 0.858974
46 A3R 0.515152 0.8625
47 ADQ 0.515152 0.896104
48 KG4 0.51087 0.896104
49 50T 0.51087 0.907895
50 PRX 0.505376 0.848101
51 71V 0.5 0.8625
52 A1R 0.5 0.8625
53 MGP 0.494845 0.841463
54 45A 0.494382 0.87013
55 ABM 0.494382 0.87013
56 G5P 0.490741 0.875
57 9X8 0.490196 0.873418
58 OAD 0.490196 0.896104
59 OZV 0.49 0.92
60 6G0 0.489796 0.841463
61 EO7 0.488889 0.813953
62 GTA 0.486239 0.843373
63 5AL 0.484536 0.883117
64 8LE 0.484536 0.85
65 APC MG 0.484211 0.87013
66 AP2 0.483516 0.909091
67 A12 0.483516 0.909091
68 G3A 0.481481 0.875
69 3OD 0.480769 0.896104
70 BIS 0.480769 0.960526
71 8LQ 0.48 0.860759
72 T5A 0.478261 0.802326
73 25A 0.475248 0.92
74 8LH 0.474747 0.860759
75 SRP 0.474747 0.860759
76 DTP 0.474227 0.858974
77 3AT 0.474227 0.92
78 UP5 0.473214 0.873418
79 ADP MG 0.473118 0.893333
80 7DD 0.473118 0.932432
81 SRA 0.47191 0.871795
82 4AD 0.470588 0.873418
83 NO7 0.47 0.884615
84 RBY 0.46875 0.884615
85 ADV 0.46875 0.884615
86 AU1 0.468085 0.921053
87 00A 0.466019 0.910256
88 GP3 0.463918 0.875
89 AFH 0.463636 0.935897
90 A4P 0.46087 0.804598
91 8QN 0.460784 0.883117
92 5SV 0.460784 0.807229
93 OOB 0.460784 0.883117
94 TXD 0.460177 0.8625
95 MGO 0.46 0.819277
96 GDP 0.459184 0.873418
97 2A5 0.458333 0.871795
98 9SN 0.457944 0.923077
99 PAJ 0.456311 0.841463
100 AMO 0.456311 0.884615
101 ADP PO3 0.453608 0.893333
102 ATR 0.453608 0.918919
103 ATP MG 0.453608 0.893333
104 TXA 0.45283 0.884615
105 PTJ 0.45283 0.851852
106 DLL 0.451923 0.883117
107 AHX 0.451923 0.851852
108 MAP 0.45098 0.897436
109 ADP ALF 0.45 0.897436
110 ALF ADP 0.45 0.897436
111 CNA 0.449153 0.884615
112 3UK 0.447619 0.871795
113 DND 0.447368 0.884615
114 NXX 0.447368 0.884615
115 6V0 0.447368 0.851852
116 DQV 0.446429 0.907895
117 IMO 0.445652 0.88
118 B5V 0.443396 0.860759
119 WAQ 0.443396 0.839506
120 PR8 0.443396 0.809524
121 LAD 0.443396 0.819277
122 7D3 0.44086 0.858974
123 AP0 0.439655 0.851852
124 1ZZ 0.439252 0.8
125 FYA 0.439252 0.858974
126 NB8 0.439252 0.851852
127 ME8 0.439252 0.8
128 PAP 0.438776 0.932432
129 48N 0.438596 0.851852
130 GSP 0.436893 0.831325
131 XAH 0.436364 0.8
132 NAX 0.434783 0.831325
133 NAI 0.434783 0.8625
134 F2R 0.433333 0.823529
135 9ZD 0.432692 0.8625
136 9ZA 0.432692 0.8625
137 2FD 0.431818 0.797468
138 ADP VO4 0.431373 0.883117
139 VO4 ADP 0.431373 0.883117
140 OMR 0.431034 0.811765
141 TXE 0.431034 0.8625
142 GAP 0.43 0.848101
143 DDS 0.43 0.833333
144 ADJ 0.428571 0.811765
145 LMS 0.428571 0.788235
146 139 0.428571 0.831325
147 4TC 0.42735 0.851852
148 B5Y 0.427273 0.85
149 PRT 0.427273 0.883117
150 FA5 0.427273 0.860759
151 YAP 0.427273 0.85
152 B5M 0.427273 0.85
153 A2R 0.427184 0.933333
154 SON 0.427083 0.884615
155 6MZ 0.425532 0.881579
156 ARU 0.424528 0.864198
157 IDP 0.424242 0.871795
158 DAL AMP 0.423077 0.858974
159 ADP BMA 0.420561 0.871795
160 4UV 0.419643 0.85
161 GAV 0.415094 0.841463
162 G1R 0.413462 0.8625
163 GCP 0.413462 0.851852
164 4UU 0.412281 0.85
165 GA7 0.412281 0.860759
166 GNH 0.411765 0.8625
167 80F 0.41129 0.802326
168 N6P 0.411215 0.866667
169 AMZ 0.411111 0.868421
170 C2R 0.411111 0.857143
171 GNP 0.409524 0.851852
172 9GM 0.409524 0.851852
173 PGS 0.408163 0.839506
174 GTG 0.40708 0.843373
175 COD 0.406504 0.775281
176 NAD 0.406504 0.883117
177 6C6 0.405941 0.8375
178 LAQ 0.405172 0.8
179 DAT 0.40404 0.858974
180 UPA 0.403361 0.8625
181 AIR 0.402299 0.853333
182 NIA 0.402174 0.783133
183 5AS 0.402062 0.744444
184 01G 0.401786 0.793103
185 YLP 0.401709 0.781609
186 7RA 0.4 0.906667
187 A3D 0.4 0.871795
188 JB6 0.4 0.839506
189 AAM 0.4 0.918919
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4LIK; Ligand: CIT; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 4lik.bio1) has 4 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 4LIK; Ligand: CIT; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 4lik.bio1) has 17 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 4LIK; Ligand: CIT; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 4lik.bio1) has 6 residues
No: Leader PDB Ligand Sequence Similarity
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