Receptor
PDB id Resolution Class Description Source Keywords
4N9Z 1.9 Å EC: 3.2.1.143 CRYSTAL STRUCTURE OF MOUSE POLY(ADP-RIBOSE) GLYCOHYDROLASE ( CATALYTIC DOMAIN MUTANT E749Q MUS MUSCULUS POLY(ADP-RIBOSE) GLYCOHYDROLASE PARG HYDROLASE
Ref.: CRYSTALLOGRAPHIC AND BIOCHEMICAL ANALYSIS OF THE MO POLY(ADP-RIBOSE) GLYCOHYDROLASE. PLOS ONE V. 9 86010 2014
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
SO4 A:1002;
B:1006;
A:1005;
A:1003;
A:1004;
A:1006;
B:1003;
B:1002;
B:1005;
B:1004;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
96.063 O4 S [O-]S...
V3L A:1001;
B:1001;
Valid;
Valid;
none;
none;
submit data
559.316 C15 H23 N5 O14 P2 c1nc(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4N9Z 1.9 Å EC: 3.2.1.143 CRYSTAL STRUCTURE OF MOUSE POLY(ADP-RIBOSE) GLYCOHYDROLASE ( CATALYTIC DOMAIN MUTANT E749Q MUS MUSCULUS POLY(ADP-RIBOSE) GLYCOHYDROLASE PARG HYDROLASE
Ref.: CRYSTALLOGRAPHIC AND BIOCHEMICAL ANALYSIS OF THE MO POLY(ADP-RIBOSE) GLYCOHYDROLASE. PLOS ONE V. 9 86010 2014
Members (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 4NA0 - AR6 C15 H23 N5 O14 P2 c1nc(c2c(n....
2 5A7R - AR6 AR6 n/a n/a
3 4N9Z - V3L C15 H23 N5 O14 P2 c1nc(c2c(n....
4 4NA4 - A1R C15 H24 N6 O12 P2 c1nc(c2c(n....
5 4N9Y - V3L C15 H23 N5 O14 P2 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 3 families.
1 4NA0 - AR6 C15 H23 N5 O14 P2 c1nc(c2c(n....
2 5A7R - AR6 AR6 n/a n/a
3 4N9Z - V3L C15 H23 N5 O14 P2 c1nc(c2c(n....
4 4NA4 - A1R C15 H24 N6 O12 P2 c1nc(c2c(n....
5 4N9Y - V3L C15 H23 N5 O14 P2 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 3 families.
1 4NA0 - AR6 C15 H23 N5 O14 P2 c1nc(c2c(n....
2 5A7R - AR6 AR6 n/a n/a
3 4N9Z - V3L C15 H23 N5 O14 P2 c1nc(c2c(n....
4 4NA4 - A1R C15 H24 N6 O12 P2 c1nc(c2c(n....
5 4N9Y - V3L C15 H23 N5 O14 P2 c1nc(c2c(n....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: V3L; Similar ligands found: 209
No: Ligand ECFP6 Tc MDL keys Tc
1 V3L 1 1
2 AR6 AR6 0.705263 0.944444
3 A2P 0.7 0.957143
4 AMP 0.6375 0.971429
5 A 0.6375 0.971429
6 25A 0.612903 0.971831
7 ATR 0.595506 0.943662
8 7D5 0.580247 0.878378
9 A2R 0.574468 0.985915
10 2AM 0.573171 0.916667
11 A22 0.568421 0.958333
12 A3P 0.563218 0.971429
13 OVE 0.552941 0.88
14 AN2 0.550562 0.958333
15 A2D 0.54023 0.944444
16 ABM 0.54023 0.917808
17 ADP 0.539326 0.971831
18 NA7 0.53 0.932432
19 25L 0.529412 0.958333
20 AMP MG 0.528736 0.891892
21 BA3 0.52809 0.944444
22 AP2 0.52809 0.932432
23 A12 0.52809 0.932432
24 ADQ 0.525253 0.945205
25 B4P 0.522222 0.944444
26 AP5 0.522222 0.944444
27 ATP 0.521739 0.971831
28 SRA 0.517241 0.918919
29 2A5 0.516129 0.893333
30 APC 0.516129 0.932432
31 AQP 0.516129 0.971831
32 5FA 0.516129 0.971831
33 3AM 0.511628 0.929577
34 ADX 0.51087 0.85
35 CA0 0.51087 0.945205
36 M33 0.51087 0.931507
37 AU1 0.51087 0.945205
38 SAP 0.510638 0.92
39 AGS 0.510638 0.92
40 XYA 0.506329 0.819444
41 ADN 0.506329 0.819444
42 RAB 0.506329 0.819444
43 ACP 0.505376 0.945205
44 50T 0.505376 0.931507
45 PRX 0.5 0.893333
46 7D3 0.5 0.88
47 ADP BMA 0.5 0.918919
48 ACQ 0.5 0.945205
49 TAT 0.5 0.932432
50 APR 0.5 0.971831
51 PO4 PO4 A A A A PO4 0.5 0.902778
52 AR6 0.5 0.971831
53 AD9 0.494737 0.945205
54 ADV 0.494737 0.932432
55 RBY 0.494737 0.932432
56 PAP 0.494737 0.957747
57 7D4 0.494624 0.88
58 ADP MG 0.494624 0.905405
59 ATF 0.489796 0.932432
60 ADP BEF 0.489362 0.881579
61 BEF ADP 0.489362 0.881579
62 ANP 0.484536 0.945205
63 SON 0.483871 0.958904
64 PPS 0.479592 0.85
65 5AL 0.479592 0.958333
66 ADP PO3 0.479167 0.943662
67 DA 0.477778 0.878378
68 D5M 0.477778 0.878378
69 PTJ 0.47619 0.921053
70 5N5 0.47561 0.794521
71 ATP MG 0.474227 0.905405
72 OAD 0.471154 0.945205
73 OOB 0.470588 0.958333
74 5SV 0.470588 0.848101
75 SRP 0.47 0.932432
76 GAP 0.469388 0.918919
77 ODP 0.466102 0.884615
78 PAJ 0.466019 0.884615
79 4AD 0.466019 0.92
80 FYA 0.462264 0.905405
81 NDP 0.461538 0.896104
82 NPW 0.461538 0.8625
83 DLL 0.461538 0.958333
84 MAP 0.460784 0.92
85 ALF ADP 0.46 0.87013
86 ADP ALF 0.46 0.87013
87 AV2 0.46 0.891892
88 TXP 0.457627 0.896104
89 NZQ 0.457627 0.884615
90 5AS 0.457447 0.77907
91 3UK 0.457143 0.945205
92 7D7 0.45679 0.743243
93 8QN 0.456311 0.958333
94 VO4 ADP 0.455446 0.931507
95 ADP VO4 0.455446 0.931507
96 ANP MG 0.455446 0.894737
97 NJP 0.453782 0.92
98 EP4 0.453488 0.753247
99 LAD 0.45283 0.884615
100 5CD 0.452381 0.805556
101 A4D 0.452381 0.794521
102 AMO 0.451923 0.932432
103 A1R 0.451923 0.883117
104 XNP 0.45 0.85
105 TXA 0.448598 0.932432
106 1ZZ 0.448598 0.8625
107 3OD 0.448598 0.945205
108 ME8 0.448598 0.8625
109 BIS 0.448598 0.907895
110 DTA 0.448276 0.786667
111 00A 0.447619 0.907895
112 AHX 0.447619 0.871795
113 DAL AMP 0.446602 0.931507
114 AOC 0.445652 0.821918
115 DSH 0.445652 0.725
116 A3G 0.445652 0.776316
117 G5A 0.444444 0.77907
118 5X8 0.443299 0.786667
119 MTA 0.443182 0.773333
120 3AT 0.44 0.944444
121 PR8 0.439252 0.873418
122 WAQ 0.439252 0.907895
123 A A 0.439252 0.944444
124 FA5 0.436364 0.932432
125 JB6 0.435185 0.883117
126 NB8 0.435185 0.896104
127 6RE 0.434783 0.759494
128 3DH 0.433333 0.773333
129 XAH 0.432432 0.839506
130 M2T 0.431818 0.734177
131 TM1 0.431193 0.795181
132 MYR AMP 0.431193 0.839506
133 VRT 0.43 0.746835
134 2VA 0.428571 0.776316
135 DAT 0.428571 0.88
136 4UV 0.428571 0.92
137 OMR 0.42735 0.851852
138 9SN 0.427273 0.896104
139 NMN AMP PO4 0.42623 0.87013
140 LAQ 0.426087 0.8625
141 DTP 0.425743 0.88
142 IMO 0.425532 0.929577
143 G3A 0.424779 0.896104
144 ZAS 0.423913 0.766234
145 UPA 0.423729 0.883117
146 YAP 0.423423 0.92
147 ATP A A A 0.423423 0.930556
148 A3S 0.42268 0.786667
149 NAP 0.421875 0.945205
150 S4M 0.421053 0.666667
151 G5P 0.421053 0.896104
152 AFH 0.421053 0.884615
153 7MD 0.421053 0.8625
154 101 0.419355 0.878378
155 GGZ 0.419048 0.802469
156 TSB 0.419048 0.797619
157 DG1 0.418605 0.896104
158 1DG 0.418605 0.896104
159 TAP 0.418605 0.907895
160 A5A 0.417476 0.807229
161 TAD 0.417391 0.860759
162 MAO 0.416667 0.759036
163 A A A 0.416667 0.905405
164 71V 0.416667 0.883117
165 N01 0.416 0.905405
166 AMP DBH 0.415929 0.893333
167 SO8 0.415842 0.766234
168 NA0 0.415385 0.932432
169 TYM 0.415254 0.932432
170 SSA 0.413462 0.77907
171 NSS 0.411215 0.77907
172 LSS 0.411215 0.761364
173 J7C 0.410526 0.769231
174 LPA AMP 0.410256 0.839506
175 5AD 0.409639 0.746479
176 VMS 0.409524 0.788235
177 54H 0.409524 0.788235
178 52H 0.409524 0.77907
179 4UU 0.408696 0.92
180 ANZ 0.408696 0.8
181 ACK 0.408602 0.861111
182 QQY 0.408602 0.815789
183 N6P 0.407407 0.915493
184 TYR AMP 0.40708 0.906667
185 4UW 0.40678 0.884615
186 6V0 0.40678 0.871795
187 NAX 0.40678 0.85
188 AMZ 0.406593 0.890411
189 C2R 0.406593 0.90411
190 GJV 0.40625 0.75
191 8BR 0.40625 0.906667
192 A5D 0.405941 0.786667
193 NVA 2AD 0.405941 0.721519
194 5CA 0.40566 0.77907
195 53H 0.40566 0.77907
196 GTA 0.405172 0.8625
197 LEU LMS 0.40367 0.761364
198 V1N 0.403509 0.944444
199 3AD 0.402299 0.805556
200 ARG AMP 0.401709 0.851852
201 CO7 0.40146 0.784091
202 SFG 0.4 0.773333
203 YLC 0.4 0.8625
204 NEC 0.4 0.723684
205 7MC 0.4 0.841463
206 KAA 0.4 0.752809
207 P5A 0.4 0.744444
208 AP0 0.4 0.871795
209 A3T 0.4 0.797297
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4N9Z; Ligand: V3L; Similar sites found: 128
This union binding pocket(no: 1) in the query (biounit: 4n9z.bio2) has 8 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1ON3 MCA 0.009719 0.42693 0.766284
2 5UAO FAD 0.03854 0.40789 1.14943
3 2J0W ADP 0.006596 0.4049 1.3363
4 3U4C NDP 0.007047 0.44258 1.42349
5 5MW8 ATP 0.008557 0.44585 1.4862
6 4IZC 1GZ 0.01579 0.43669 1.81818
7 5UIU 8CG 0.02377 0.43137 1.85759
8 1FWM CB3 0.04017 0.40128 1.89394
9 5JBX COA 0.009752 0.44088 1.91571
10 2W62 BGC BGC BGC BGC BGC 0.04452 0.40717 1.91571
11 3CZ7 ACO 0.03164 0.41911 1.92308
12 4NBW NAD 0.005415 0.45276 1.94553
13 3UBM COA 0.003846 0.44847 2.19298
14 1EKO I84 0.01779 0.41742 2.22222
15 1EKO NAP 0.01726 0.41742 2.22222
16 4MOB COA 0.005942 0.40521 2.40964
17 5K6A NAP 0.006584 0.44052 2.43056
18 5JDI NAP 0.008717 0.43721 2.43056
19 4J7U NAP 0.04772 0.40549 2.43056
20 4J7U YTZ 0.04772 0.40549 2.43056
21 1Z6Z NAP 0.0204 0.42583 2.48227
22 5CEO 50D 0.018 0.41005 2.49042
23 3QWI NAP 0.009348 0.4208 2.59259
24 3QWI CUE 0.01302 0.4208 2.59259
25 1NZY BCA 0.03658 0.40559 2.60223
26 1JXZ BCA 0.03591 0.40538 2.60223
27 2WD7 NAP 0.009655 0.43601 2.61194
28 3AFN NAP 0.007066 0.4408 2.71318
29 3DNT ATP 0.007412 0.40531 2.72727
30 4C8E C5P 0.03245 0.41677 2.74725
31 4USR FAD 0.0168 0.40461 2.77008
32 5CCM SAM 0.02371 0.43856 2.80374
33 5CCM 4ZX 0.02756 0.43856 2.80374
34 5THZ SAH 0.002792 0.46455 2.96296
35 2DTX BMA 0.004636 0.46087 3.0303
36 1SR7 MOF 0.02252 0.41095 3.0888
37 1BXK NAD 0.008112 0.40445 3.09859
38 5E9W SAH 0.03481 0.40333 3.20513
39 1JA9 NDP 0.002755 0.475 3.28467
40 1W6U NAP 0.01422 0.41384 3.31126
41 2GDZ NAD 0.009534 0.42886 3.37079
42 3NBC LAT 0.0122 0.4091 3.37838
43 3F7Z 34O 0.004879 0.41556 3.42857
44 4PIV NDP 0.002711 0.47978 3.44828
45 2DKH 3HB 0.02172 0.4182 3.44828
46 2DKH FAD 0.01752 0.4182 3.44828
47 2WTX UDP 0.0007841 0.50656 3.5865
48 2WTX VDO 0.0163 0.42082 3.5865
49 1VL0 NAI 0.008008 0.44143 3.63985
50 1HEX NAD 0.006842 0.4513 3.76812
51 1VAY AZA 0.006145 0.4268 3.83275
52 1XA4 COA 0.004083 0.4558 3.89016
53 3V8S 0HD 0.009907 0.41031 3.90244
54 2IW1 U2F 0.003638 0.43325 4.01069
55 3O0G 3O0 0.009665 0.41065 4.02685
56 1PR9 NAP 0.01254 0.43969 4.09836
57 1ZEM NAD 0.002647 0.44289 4.19847
58 2ZE7 AMP 0.02698 0.40616 4.34783
59 2ZE7 DST 0.02836 0.40616 4.34783
60 5O4J PJL 0.04065 0.40737 4.37956
61 5O4J 9KH 0.04343 0.40538 4.37956
62 5O4J SAH 0.04343 0.40538 4.37956
63 2AMT 1AA 0.0356 0.41325 4.40252
64 3O03 NAP 0.002045 0.46985 4.46735
65 3T7S SAM 0.001801 0.44356 4.47761
66 3H4V DVP 0.006526 0.46112 4.51389
67 3H4V NAP 0.01064 0.44723 4.51389
68 1W55 C 0.01511 0.42067 4.58221
69 3OJF IMJ 0.03364 0.40754 4.66926
70 2VJM COA 0.02117 0.44117 4.6729
71 1F06 2NP 0.006856 0.42518 4.6875
72 1F06 NDP 0.006856 0.42518 4.6875
73 4AT0 FAD 0.0277 0.42864 4.70588
74 4HXY NDP 0.002784 0.45205 4.79452
75 2XVM SAH 0.004867 0.43826 5.02513
76 1Q7E MET 0.02596 0.42221 5.14019
77 3AKK ADP 0.007791 0.41398 5.23077
78 4D42 W0I 0.01801 0.42806 5.31915
79 4D42 NAP 0.01801 0.42806 5.31915
80 2D4V NAD 0.01495 0.43441 5.36131
81 1N62 MCN 0.007002 0.43082 5.42169
82 5TVI O8N 0.002326 0.43591 5.43478
83 3UDZ ADP 0.00284 0.46143 5.47667
84 5THQ NDP 0.001259 0.46217 5.51471
85 2XVD AS6 0.01897 0.42918 5.62914
86 2AG5 NAD 0.01785 0.41312 5.69106
87 1VLH PNS 0.01625 0.41237 5.78035
88 1UCD URA 0.008425 0.43086 5.78947
89 1UCD U5P 0.004327 0.43086 5.78947
90 1TZD ADP 0.01563 0.40748 5.81818
91 1AE1 NAP 0.0007046 0.4777 5.86081
92 2RFI SAH 0.01081 0.41896 5.96491
93 2Q4H AMP 0.01247 0.42289 5.98291
94 1RJD SAM 0.002323 0.46695 5.98802
95 5CUQ NSC 0.03595 0.41333 5.99251
96 4Q9N NAI 0.03635 0.40626 6.04027
97 4QED NAP 0.004715 0.46136 6.04839
98 2UZH CDP 0.03394 0.41764 6.06061
99 5VYR B62 0.00909 0.43859 6.13027
100 5VYR GMP 0.00909 0.43859 6.13027
101 3OID NDP 0.01112 0.41448 6.20155
102 2V6G NAP 0.00009779 0.55608 6.31868
103 4J36 FAD 0.02649 0.40195 6.32184
104 1I2B NAD 0.01628 0.42156 6.43564
105 4EJN 0R4 0.01849 0.42024 6.50224
106 2WA2 SAM 0.009428 0.44011 6.52174
107 1WMA AB3 0.01819 0.42389 6.52174
108 2AE2 NAP 0.0003847 0.52242 6.53846
109 2VSU ACO 0.0128 0.41864 6.54545
110 4XSU UDP 0.02076 0.40798 7.2165
111 4XSU GLC 0.02076 0.40798 7.2165
112 2A14 SAH 0.0006696 0.49364 7.22433
113 2VSS ACO 0.0161 0.40991 7.66284
114 3FRH SAH 0.02624 0.40246 7.90514
115 2J9D ADP 0.04185 0.40041 8.40336
116 5L4S 6KX 0.03073 0.40366 8.80503
117 5L4S NAP 0.03073 0.40366 8.80503
118 3DZ6 M8E 0.004918 0.42634 9.3633
119 4N9I PCG 0.03056 0.42019 9.52381
120 4FC7 COA 0.009259 0.43455 9.74729
121 4FC7 NAP 0.009259 0.43455 9.74729
122 1IV2 CDP 0.03922 0.40483 9.86842
123 3GCZ SAM 0.01989 0.41315 9.92908
124 2PD4 DCN 0.01164 0.43334 10.1818
125 2PD4 NAD 0.01252 0.43068 10.1818
126 4J1Q NDP 0.01702 0.40877 10.5603
127 5FBN 5WF 0.04396 0.41558 12.5461
128 3O7J 2AL 0.01762 0.40776 14.8148
Pocket No.: 2; Query (leader) PDB : 4N9Z; Ligand: V3L; Similar sites found: 20
This union binding pocket(no: 2) in the query (biounit: 4n9z.bio1) has 8 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4O8A FAD 0.0482 0.40373 1.4556
2 4N49 SAM 0.008781 0.40615 1.86916
3 2PK3 A2R 0.01328 0.40513 1.86916
4 1IID NHM 0.01914 0.42016 2.60664
5 5L4L 7OX 0.04628 0.40724 2.63158
6 2BNE U5P 0.0153 0.40253 3.3195
7 3CH6 311 0.01977 0.42122 3.4965
8 3CH6 NAP 0.01977 0.42122 3.4965
9 1PUJ GNP 0.02642 0.41117 3.5461
10 2BGM NAJ 0.02106 0.40182 3.59712
11 5DWQ SFG 0.02386 0.40162 4.01146
12 4EUE NAI 0.02128 0.41187 4.30622
13 1KAO GDP 0.03928 0.40409 4.79042
14 3TN7 NJP 0.01224 0.43694 5.44747
15 2J0B UDP 0.02037 0.40413 5.71429
16 3HRD MCN 0.005716 0.43402 5.88235
17 5TUZ 7L6 0.03169 0.40747 6.51341
18 5TUZ SAM 0.03169 0.40747 6.51341
19 1YXM ADE 0.002013 0.40813 6.93069
20 5UR1 YY9 0.0215 0.40041 7.07396
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