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 23 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 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....
50% 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....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: JSQ; Similar ligands found: 198
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 AQP 0.686747 0.945946
7 5FA 0.686747 0.945946
8 6AD 0.655172 0.864198
9 AP5 0.638554 0.92
10 B4P 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 AGS 0.58427 0.897436
20 25L 0.581633 0.933333
21 ACQ 0.571429 0.921053
22 NFD 0.5625 0.935065
23 AT4 0.556818 0.909091
24 AN2 0.556818 0.933333
25 AR6 0.555556 0.92
26 APR 0.555556 0.92
27 TAT 0.554348 0.909091
28 T99 0.554348 0.909091
29 M33 0.550562 0.907895
30 AD9 0.549451 0.921053
31 ACP 0.544444 0.921053
32 7DT 0.538462 0.932432
33 ANP 0.537634 0.921053
34 ADX 0.533333 0.831325
35 CA0 0.533333 0.896104
36 HQG 0.53125 0.933333
37 AMP 0.529412 0.918919
38 A 0.529412 0.918919
39 O02 0.526882 0.875
40 ATF 0.526316 0.986486
41 A22 0.525773 0.933333
42 APC 0.521739 0.909091
43 GTP 0.520833 0.873418
44 HF7 0.520833 0.848101
45 7D4 0.516484 0.858974
46 QBQ 0.515789 0.860759
47 A3R 0.515152 0.8625
48 ADQ 0.515152 0.896104
49 50T 0.51087 0.907895
50 KG4 0.51087 0.896104
51 PRX 0.505376 0.848101
52 A1R 0.5 0.8625
53 71V 0.5 0.8625
54 JNT 0.49505 0.896104
55 MGP 0.494845 0.841463
56 45A 0.494382 0.87013
57 ABM 0.494382 0.87013
58 G5P 0.490741 0.875
59 OAD 0.490196 0.896104
60 9X8 0.490196 0.873418
61 OZV 0.49 0.92
62 6G0 0.489796 0.841463
63 CZF 0.489583 0.883117
64 EO7 0.488889 0.813953
65 AMP MG 0.488636 0.88
66 GTA 0.486239 0.843373
67 8LE 0.484536 0.85
68 5AL 0.484536 0.883117
69 APC MG 0.484211 0.87013
70 AP2 0.483516 0.909091
71 A12 0.483516 0.909091
72 G3A 0.481481 0.875
73 O05 0.480769 0.804598
74 BIS 0.480769 0.960526
75 3OD 0.480769 0.896104
76 8LQ 0.48 0.860759
77 T5A 0.478261 0.802326
78 25A 0.475248 0.92
79 8LH 0.474747 0.860759
80 SRP 0.474747 0.860759
81 DTP 0.474227 0.858974
82 3AT 0.474227 0.92
83 UP5 0.473214 0.873418
84 ADP MG 0.473118 0.893333
85 ADP BEF 0.473118 0.893333
86 7DD 0.473118 0.932432
87 SRA 0.47191 0.871795
88 4AD 0.470588 0.873418
89 NO7 0.47 0.884615
90 ADV 0.46875 0.884615
91 RBY 0.46875 0.884615
92 AU1 0.468085 0.921053
93 KMQ 0.46729 0.884615
94 00A 0.466019 0.910256
95 QA7 0.465347 0.85
96 GP3 0.463918 0.875
97 AFH 0.463636 0.935897
98 A4P 0.46087 0.804598
99 5SV 0.460784 0.807229
100 OOB 0.460784 0.883117
101 8QN 0.460784 0.883117
102 TXD 0.460177 0.8625
103 MGO 0.46 0.819277
104 GDP 0.459184 0.873418
105 2A5 0.458333 0.871795
106 9SN 0.457944 0.923077
107 PAJ 0.456311 0.841463
108 AMO 0.456311 0.884615
109 ATP MG 0.453608 0.893333
110 ADP PO3 0.453608 0.893333
111 ATR 0.453608 0.918919
112 PTJ 0.45283 0.851852
113 TXA 0.45283 0.884615
114 DLL 0.451923 0.883117
115 AHX 0.451923 0.851852
116 MAP 0.45098 0.897436
117 VO4 ADP 0.45 0.896104
118 ALF ADP 0.45 0.897436
119 CNA 0.449153 0.884615
120 BEF ADP 0.44898 0.87013
121 3UK 0.447619 0.871795
122 DND 0.447368 0.884615
123 6V0 0.447368 0.851852
124 DQV 0.446429 0.907895
125 IMO 0.445652 0.88
126 PR8 0.443396 0.809524
127 LAD 0.443396 0.819277
128 WAQ 0.443396 0.839506
129 B5V 0.443396 0.860759
130 7D3 0.44086 0.858974
131 V2G 0.44 0.851852
132 L3W 0.439655 0.884615
133 AP0 0.439655 0.851852
134 1ZZ 0.439252 0.8
135 NB8 0.439252 0.851852
136 FYA 0.439252 0.858974
137 ME8 0.439252 0.8
138 PAP 0.438776 0.932432
139 48N 0.438596 0.851852
140 GSP 0.436893 0.831325
141 XAH 0.436364 0.8
142 ANP MG 0.435644 0.883117
143 NAX 0.434783 0.831325
144 NAI 0.434783 0.8625
145 F2R 0.433333 0.823529
146 9ZA 0.432692 0.8625
147 9ZD 0.432692 0.8625
148 2FD 0.431818 0.797468
149 OMR 0.431034 0.811765
150 TXE 0.431034 0.8625
151 DDS 0.43 0.833333
152 GAP 0.43 0.848101
153 139 0.428571 0.831325
154 LMS 0.428571 0.788235
155 ADJ 0.428571 0.811765
156 4TC 0.42735 0.851852
157 FA5 0.427273 0.860759
158 B5M 0.427273 0.85
159 PRT 0.427273 0.883117
160 B5Y 0.427273 0.85
161 A2R 0.427184 0.933333
162 SON 0.427083 0.884615
163 6MZ 0.425532 0.881579
164 ARU 0.424528 0.864198
165 IDP 0.424242 0.871795
166 DAL AMP 0.423077 0.858974
167 ADP BMA 0.420561 0.871795
168 4UV 0.419643 0.85
169 GAV 0.415094 0.841463
170 GCP 0.413462 0.851852
171 G1R 0.413462 0.8625
172 4UU 0.412281 0.85
173 GA7 0.412281 0.860759
174 GNH 0.411765 0.8625
175 80F 0.41129 0.802326
176 N6P 0.411215 0.866667
177 C2R 0.411111 0.857143
178 AMZ 0.411111 0.868421
179 9GM 0.409524 0.851852
180 GNP 0.409524 0.851852
181 PGS 0.408163 0.839506
182 GTG 0.40708 0.843373
183 NAD 0.406504 0.883117
184 COD 0.406504 0.775281
185 6C6 0.405941 0.8375
186 LAQ 0.405172 0.8
187 CUU 0.40404 0.92
188 DAT 0.40404 0.858974
189 UPA 0.403361 0.8625
190 AIR 0.402299 0.853333
191 NIA 0.402174 0.783133
192 5AS 0.402062 0.744444
193 01G 0.401786 0.793103
194 YLP 0.401709 0.781609
195 AAM 0.4 0.918919
196 7RA 0.4 0.906667
197 JB6 0.4 0.839506
198 A3D 0.4 0.871795
Similar Ligands (3D)
Ligand no: 1; Ligand: JSQ; Similar ligands found: 5
No: Ligand Similarity coefficient
1 DGT 0.9693
2 TTP 0.9100
3 GH3 0.8765
4 ADP ALF 0.8584
5 UTP 0.8556
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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