Receptor
PDB id Resolution Class Description Source Keywords
3K8T 2.1 Å EC: 1.17.4.1 STRUCTURE OF EUKARYOTIC RNR LARGE SUBUNIT R1 COMPLEXED WITH ADP ANALOG COMPOUND SACCHAROMYCES CEREVISIAE EUKARYOTIC RIBONUCLEOTIDE REDUCTASE NUCLEOTIDE ANALOGS ALLENZYME ATP-BINDING DNA REPLICATION NUCLEOTIDE-BINDING OXIDOREDUCTASE PHOSPHOPROTEIN ALLOSTERIC ENZYME ATP-BINDNUCLEOTIDE-BINDING OXIDOREDUCTASE
Ref.: STRUCTURE-BASED DESIGN, SYNTHESIS, AND EVALUATION O 2'-(2-HYDROXYETHYL)-2'-DEOXYADENOSINE AND THE 5'-DI DERIVATIVE AS RIBONUCLEOTIDE REDUCTASE INHIBITORS CHEMMEDCHEM V. 4 1649 2009
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
2A5 A:891;
Valid;
none;
submit data
455.254 C12 H19 N5 O10 P2 c1nc(...
DGT A:890;
Valid;
none;
submit data
507.181 C10 H16 N5 O13 P3 c1nc2...
GOL A:892;
Invalid;
none;
submit data
92.094 C3 H8 O3 C(C(C...
MG A:889;
Invalid;
none;
submit data
24.305 Mg [Mg+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3RSR 2.3 Å EC: 1.17.4.1 CRYSTAL STRUCTURE OF 5-NITP INHIBITION OF YEAST RIBONUCLEOTI REDUCTASE SACCHAROMYCES CEREVISIAE 10-STRANDED ALPHA/BETA BARREL NUCLEOTIDE REDUCTION OXIDIZEOXIDOREDUCTASE
Ref.: EVALUATING THE THERAPEUTIC POTENTIAL OF A NON-NATUR NUCLEOTIDE THAT INHIBITS HUMAN RIBONUCLEOTIDE REDUC MOL.CANCER THER. V. 11 2077 2012
Members (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 9 families.
1 3RSR Kd = 44 uM N5P C13 H17 N2 O14 P3 c1cc2c(ccn....
2 3K8T - DGT C10 H16 N5 O13 P3 c1nc2c(n1[....
3 2CVY - TTP C10 H17 N2 O14 P3 CC1=CN(C(=....
4 2CVW - TTP C10 H17 N2 O14 P3 CC1=CN(C(=....
5 2CVX - DGT C10 H16 N5 O13 P3 c1nc2c(n1[....
6 2EUD - GCQ C9 H13 F2 N3 O10 P2 C1=CN(C(=O....
70% Homology Family (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 8 families.
1 3RSR Kd = 44 uM N5P C13 H17 N2 O14 P3 c1cc2c(ccn....
2 3K8T - DGT C10 H16 N5 O13 P3 c1nc2c(n1[....
3 2CVY - TTP C10 H17 N2 O14 P3 CC1=CN(C(=....
4 2CVW - TTP C10 H17 N2 O14 P3 CC1=CN(C(=....
5 2CVX - DGT C10 H16 N5 O13 P3 c1nc2c(n1[....
6 2EUD - GCQ C9 H13 F2 N3 O10 P2 C1=CN(C(=O....
7 3HNC - TTP C10 H17 N2 O14 P3 CC1=CN(C(=....
50% Homology Family (8)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 7 families.
1 3RSR Kd = 44 uM N5P C13 H17 N2 O14 P3 c1cc2c(ccn....
2 3K8T - DGT C10 H16 N5 O13 P3 c1nc2c(n1[....
3 2CVY - TTP C10 H17 N2 O14 P3 CC1=CN(C(=....
4 2CVW - TTP C10 H17 N2 O14 P3 CC1=CN(C(=....
5 2CVX - DGT C10 H16 N5 O13 P3 c1nc2c(n1[....
6 2EUD - GCQ C9 H13 F2 N3 O10 P2 C1=CN(C(=O....
7 2WGH - DTP C10 H16 N5 O12 P3 c1nc(c2c(n....
8 3HNC - TTP C10 H17 N2 O14 P3 CC1=CN(C(=....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 2A5; Similar ligands found: 287
No: Ligand ECFP6 Tc MDL keys Tc
1 2A5 1 1
2 ADP 0.717949 0.918919
3 7D3 0.714286 0.906667
4 ATR 0.695122 0.917808
5 PAP 0.674699 0.931507
6 7D4 0.658537 0.906667
7 ATP 0.650602 0.918919
8 5FA 0.642857 0.918919
9 AQP 0.642857 0.918919
10 A2D 0.6375 0.893333
11 B4P 0.634146 0.893333
12 AP5 0.634146 0.893333
13 AN2 0.626506 0.906667
14 BA3 0.621951 0.893333
15 7D5 0.602564 0.88
16 ACQ 0.602273 0.92
17 M33 0.6 0.881579
18 ACP 0.593023 0.92
19 AV2 0.588889 0.868421
20 APR 0.586207 0.893333
21 AR6 0.586207 0.893333
22 ANP 0.58427 0.894737
23 AMP 0.580247 0.891892
24 A 0.580247 0.891892
25 AD9 0.579545 0.894737
26 SAP 0.579545 0.871795
27 AGS 0.579545 0.871795
28 A2R 0.576087 0.906667
29 DAT 0.574713 0.932432
30 A22 0.569892 0.906667
31 TAT 0.566667 0.883117
32 A3P 0.564706 0.917808
33 A2P 0.564706 0.90411
34 CA0 0.563218 0.87013
35 ADX 0.563218 0.807229
36 25L 0.561224 0.906667
37 5AL 0.56044 0.857143
38 50T 0.556818 0.881579
39 ATF 0.554348 0.883117
40 APC 0.550562 0.907895
41 PRX 0.550562 0.87013
42 3AT 0.549451 0.945205
43 AMP MG 0.547619 0.820513
44 NA7 0.546392 0.933333
45 PPS 0.543478 0.829268
46 A1R 0.541667 0.909091
47 ADQ 0.541667 0.894737
48 ABM 0.541176 0.844156
49 ADP BEF 0.539326 0.8125
50 BEF ADP 0.539326 0.8125
51 2AM 0.536585 0.917808
52 DTP 0.532609 0.932432
53 SRP 0.531915 0.883117
54 25A 0.53125 0.893333
55 8QN 0.53125 0.857143
56 3AM 0.53012 0.90411
57 AP2 0.528736 0.907895
58 A12 0.528736 0.907895
59 ADP MG 0.52809 0.833333
60 3OD 0.52 0.87013
61 SRA 0.517647 0.846154
62 OVE 0.517647 0.881579
63 V3L 0.516129 0.893333
64 OAD 0.515152 0.87013
65 7D7 0.513158 0.746667
66 AU1 0.511111 0.894737
67 ADP PO3 0.51087 0.866667
68 PAJ 0.510204 0.839506
69 AMO 0.510204 0.883117
70 ATP MG 0.505376 0.833333
71 AHX 0.50505 0.873418
72 00A 0.50505 0.814815
73 BIS 0.504951 0.884615
74 OOB 0.5 0.857143
75 DDS 0.5 0.905405
76 5SV 0.5 0.82716
77 128 0.495413 0.738636
78 LAD 0.49505 0.8625
79 4AD 0.494949 0.871795
80 6AD 0.494737 0.839506
81 RBY 0.494624 0.883117
82 ADV 0.494624 0.883117
83 12D 0.490741 0.747126
84 PTJ 0.490196 0.82716
85 FYA 0.490196 0.881579
86 NB8 0.490196 0.85
87 ME8 0.490196 0.819277
88 DLL 0.49 0.857143
89 MAP 0.489796 0.871795
90 ALF ADP 0.489583 0.802469
91 ADP ALF 0.489583 0.802469
92 XYA 0.487179 0.797297
93 RAB 0.487179 0.797297
94 ADN 0.487179 0.797297
95 G5P 0.485981 0.85
96 3UK 0.485149 0.846154
97 ADP VO4 0.484536 0.857143
98 VO4 ADP 0.484536 0.857143
99 ANP MG 0.484536 0.825
100 GAP 0.484211 0.846154
101 SON 0.483516 0.883117
102 9SN 0.480769 0.804878
103 WAQ 0.480392 0.884615
104 PR8 0.480392 0.875
105 G3A 0.476636 0.85
106 FA5 0.47619 0.858974
107 YAP 0.47619 0.848101
108 1ZZ 0.475728 0.819277
109 TXA 0.475728 0.858974
110 AFH 0.472222 0.8625
111 XAH 0.471698 0.841463
112 PO4 PO4 A A A A PO4 0.470588 0.853333
113 ADP BMA 0.470588 0.87013
114 A A A 0.470588 0.881579
115 TXP 0.469565 0.873418
116 A4P 0.469027 0.802326
117 TXD 0.468468 0.860759
118 UP5 0.468468 0.848101
119 GTA 0.46789 0.819277
120 4UV 0.46729 0.825
121 A A 0.466019 0.868421
122 ODP 0.465517 0.839506
123 NJP 0.465517 0.871795
124 ITT 0.462366 0.866667
125 ATP A A A 0.462264 0.855263
126 0WD 0.461538 0.85
127 NPW 0.46087 0.864198
128 NDP 0.46087 0.85
129 D5M 0.460674 0.905405
130 DA 0.460674 0.905405
131 DAL AMP 0.46 0.833333
132 GGZ 0.46 0.783133
133 48N 0.459459 0.85
134 4UU 0.458716 0.825
135 NZQ 0.456897 0.8625
136 5N5 0.45679 0.773333
137 6V0 0.455357 0.82716
138 NXX 0.455357 0.858974
139 DND 0.455357 0.858974
140 NAI 0.455357 0.8375
141 NAX 0.455357 0.851852
142 J7V 0.451613 0.772727
143 OMR 0.451327 0.831325
144 TYM 0.451327 0.858974
145 TXE 0.451327 0.860759
146 A4D 0.451219 0.773333
147 5CD 0.451219 0.736842
148 LAQ 0.45045 0.819277
149 6RE 0.449438 0.7625
150 XNP 0.449153 0.851852
151 139 0.448276 0.851852
152 ADJ 0.448276 0.831325
153 T5A 0.448276 0.821429
154 4TC 0.447368 0.85
155 AP0 0.447368 0.82716
156 YLP 0.446429 0.843373
157 ETB 0.446281 0.835294
158 DCA 0.446281 0.847059
159 A3G 0.444444 0.779221
160 AOC 0.444444 0.753247
161 4UW 0.442478 0.795181
162 A3T 0.442105 0.776316
163 2VA 0.442105 0.75641
164 5AS 0.44086 0.761364
165 J7C 0.43956 0.772152
166 COA 0.439024 0.847059
167 0T1 0.439024 0.847059
168 NAD 0.436975 0.857143
169 COD 0.436975 0.835294
170 SCO 0.436508 0.847059
171 A3S 0.43617 0.789474
172 7DD 0.43617 0.905405
173 EP4 0.435294 0.691358
174 YLC 0.434783 0.841463
175 YLB 0.434783 0.843373
176 UPA 0.434783 0.860759
177 JB6 0.433962 0.884615
178 101 0.433333 0.905405
179 AR6 AR6 0.432432 0.844156
180 CNA 0.432203 0.858974
181 NAP 0.432 0.87013
182 APU 0.431034 0.871795
183 PUA 0.430894 0.8625
184 DTA 0.430233 0.721519
185 M2T 0.430233 0.674699
186 A5A 0.43 0.747126
187 MYR AMP 0.429907 0.797619
188 TM1 0.429907 0.735632
189 A3D 0.429752 0.846154
190 COS 0.428571 0.827586
191 AMX 0.428571 0.857143
192 TAP 0.428571 0.8375
193 30N 0.428571 0.774194
194 CAO 0.428571 0.818182
195 SO8 0.428571 0.746835
196 NAE 0.427419 0.825
197 5X8 0.427083 0.721519
198 QQX 0.426966 0.78481
199 3KK 0.426357 0.827586
200 FYN 0.426357 0.847059
201 ALF ADP 3PG 0.426087 0.795181
202 LA8 ALF 3PG 0.426087 0.795181
203 MTA 0.425287 0.708861
204 NA0 0.425197 0.858974
205 CMX 0.425197 0.847059
206 5AD 0.425 0.68
207 SAM 0.424242 0.674419
208 YLA 0.423729 0.843373
209 COK 0.423077 0.827586
210 CA6 0.423077 0.75
211 ACK 0.422222 0.837838
212 QQY 0.422222 0.794872
213 ZAS 0.422222 0.703704
214 FCX 0.421875 0.818182
215 ACO 0.421875 0.818182
216 FAM 0.421875 0.827586
217 Y3J 0.421687 0.662338
218 AYB 0.420168 0.833333
219 NMX 0.419847 0.782609
220 7MD 0.419643 0.8875
221 HAX 0.418605 0.827586
222 TYR AMP 0.418182 0.8125
223 TSB 0.417476 0.758621
224 DG1 0.417323 0.85
225 1DG 0.417323 0.85
226 3AD 0.416667 0.808219
227 3DH 0.41573 0.708861
228 IOT 0.415254 0.855422
229 AMP DBH 0.414414 0.822785
230 G5A 0.414141 0.761364
231 VRT 0.414141 0.772152
232 EAD 0.414062 0.807229
233 IVC 0.413534 0.837209
234 BTX 0.413223 0.843373
235 NEC 0.413043 0.705128
236 NAQ 0.412698 0.804878
237 AHZ 0.412281 0.776471
238 OXK 0.412214 0.827586
239 SOP 0.412214 0.827586
240 MCD 0.412214 0.827586
241 SMM 0.411765 0.670455
242 SSA 0.411765 0.781609
243 BT5 0.409836 0.833333
244 ZID 0.409449 0.846154
245 CMC 0.409091 0.827586
246 CO6 0.409091 0.827586
247 1VU 0.409091 0.818182
248 LPA AMP 0.408696 0.797619
249 AS 0.408602 0.858974
250 ZZB 0.408333 0.755814
251 VMS 0.407767 0.730337
252 54H 0.407767 0.730337
253 MC4 0.407407 0.782609
254 ANZ 0.40708 0.759036
255 A U 0.40678 0.825
256 SCD 0.406015 0.847059
257 CAJ 0.406015 0.827586
258 2MC 0.406015 0.791209
259 2KQ 0.404412 0.808989
260 S4M 0.404255 0.689655
261 GJV 0.404255 0.753086
262 ZDA 0.40404 0.842105
263 5CA 0.403846 0.781609
264 53H 0.403846 0.722222
265 TAD 0.403509 0.839506
266 A1S 0.402985 0.827586
267 3HC 0.402985 0.837209
268 1HE 0.402985 0.808989
269 BCO 0.402985 0.827586
270 MLC 0.402985 0.827586
271 1CZ 0.402878 0.818182
272 CC5 0.402439 0.77027
273 AF3 ADP 3PG 0.401709 0.795181
274 G A A A 0.401639 0.82716
275 NDE 0.401515 0.858974
276 P1H 0.401515 0.809524
277 FAQ 0.40146 0.827586
278 CO7 0.4 0.827586
279 8OD 0.4 0.87013
280 ARG AMP 0.4 0.831325
281 3L1 0.4 0.824324
282 YE1 0.4 0.837209
283 MCA 0.4 0.818182
284 CAA 0.4 0.837209
285 3D1 0.4 0.824324
286 MAO 0.4 0.741176
287 COO 0.4 0.827586
Ligand no: 2; Ligand: DGT; Similar ligands found: 103
No: Ligand ECFP6 Tc MDL keys Tc
1 DGT 1 1
2 DGI 0.897436 1
3 DGP 0.775 0.986842
4 DG 0.775 0.986842
5 GH3 0.673913 0.948052
6 GTP 0.659341 0.923077
7 DG DG 0.639175 0.91358
8 0O2 0.622449 0.935065
9 CGP 0.6 0.914634
10 GP3 0.597826 0.9
11 GDP 0.591398 0.923077
12 G3D 0.561224 0.935065
13 GSP 0.561224 0.878049
14 DTP 0.557895 0.909091
15 GAV 0.55 0.888889
16 G4P 0.55 0.935065
17 DC DG 0.53913 0.891566
18 GNH 0.536082 0.911392
19 G1R 0.535354 0.911392
20 G2R 0.533981 0.961538
21 GNP 0.53 0.9
22 5GP 0.521277 0.910256
23 G 0.521277 0.910256
24 GCP 0.52 0.924051
25 GPX 0.514563 0.922078
26 GPD 0.513514 0.902439
27 G5P 0.509091 0.9
28 GTG 0.504587 0.86747
29 G3A 0.5 0.9
30 G2P 0.5 0.936709
31 GDC 0.495413 0.888889
32 GKE 0.495413 0.888889
33 GDD 0.495413 0.888889
34 GMV 0.49505 0.9
35 DI 0.494737 0.960526
36 6CK 0.486486 0.86747
37 DAT 0.484536 0.909091
38 Y9Z 0.481818 0.880952
39 GP2 0.48 0.936709
40 JB2 0.477876 0.888889
41 GDR 0.477477 0.888889
42 GFB 0.477477 0.888889
43 GPG 0.472222 0.888889
44 GDP MG 0.470588 0.853659
45 DU DU DU DU BRU DG DU 0.469697 0.840909
46 3GP 0.46875 0.897436
47 2GP 0.46875 0.935065
48 GDP BEF 0.466019 0.833333
49 ALF 5GP 0.466019 0.823529
50 GKD 0.464912 0.888889
51 GCP G 0.462264 0.864198
52 BGO 0.462185 0.878049
53 8DG 0.461538 0.857143
54 GDX 0.46087 0.9
55 P2G 0.459184 0.860759
56 MGP 0.456311 0.888889
57 JB3 0.453782 0.878049
58 GDP ALF 0.453704 0.823529
59 BEF GDP 0.45283 0.823529
60 GTP MG 0.45283 0.853659
61 6G0 0.451923 0.888889
62 CAG 0.451613 0.818182
63 GMP 0.450549 0.810127
64 P1G 0.45 0.873418
65 NGD 0.45 0.888889
66 YGP 0.446429 0.835294
67 3PD UM3 0.446281 0.86747
68 G1G 0.444444 0.857143
69 DG DC 0.44186 0.925926
70 GDP AF3 0.440367 0.823529
71 N5P 0.439252 0.75
72 DUT 0.438776 0.7875
73 DG DA DC DG 0.43662 0.880952
74 01G 0.433628 0.903614
75 DA DC DG DA 0.433566 0.880952
76 TPG 0.430769 0.782609
77 DCP 0.43 0.848101
78 G G 0.428571 0.864198
79 CF2 0.428571 0.802326
80 GGM 0.427419 0.857143
81 2MD 0.427419 0.827586
82 U2G 0.42623 0.86747
83 CG2 0.419355 0.86747
84 MGD 0.417323 0.827586
85 DG DT DC 0.416667 0.850575
86 TTP 0.415842 0.759036
87 MD1 0.415385 0.848837
88 PGD 0.415385 0.857143
89 G G U 0.415254 0.8875
90 DA DU DG DA 0.414634 0.835294
91 FEG 0.414634 0.858824
92 ZGP 0.41129 0.848837
93 DDS 0.409524 0.858974
94 3AT 0.409524 0.871795
95 DBG 0.409091 0.878049
96 3ZE 0.407767 0.886076
97 6U4 0.407407 0.853659
98 GDP 7MG 0.40678 0.843373
99 GPC 0.40625 0.816092
100 SGP 0.401961 0.807229
101 7D4 0.401961 0.814815
102 AGO 0.401575 0.86747
103 DC DG DA DC 0.401408 0.902439
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3RSR; Ligand: N5P; Similar sites found: 36
This union binding pocket(no: 1) in the query (biounit: 3rsr.bio1) has 48 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1O9U ADZ 0.03019 0.42946 1.71429
2 3P3N AKG 0.00449 0.45259 1.7192
3 2F2U M77 0.01928 0.40428 1.74129
4 1C1L GAL BGC 0.03996 0.41162 2.18978
5 1SQ5 PAU 0.02453 0.40782 2.27273
6 2Z9V PXM 0.006949 0.43258 2.29592
7 2E1A MSE 0.008146 0.42469 2.66667
8 2O2C G6Q 0.009186 0.40624 2.77325
9 3CXQ GLP 0.01264 0.42572 3.26087
10 3F81 STT 0.02446 0.43441 3.27869
11 4COQ SAN 0.03605 0.40894 3.64372
12 3ZPG 5GP 0.04556 0.41972 3.66492
13 1Z44 FMN 0.006744 0.41534 4.14201
14 1WDA BAG 0.01064 0.41961 4.1791
15 3BY8 MLT 0.009661 0.44251 4.22535
16 1YOA FMN 0.01841 0.45677 4.40252
17 2Q37 3AL 0.00621 0.44009 4.41989
18 1RZM E4P 0.003893 0.46214 4.43787
19 1RZM PEP 0.02324 0.40888 4.43787
20 3DGB MUC 0.009478 0.41329 4.45026
21 4E28 9MZ 0.02696 0.41508 5.23077
22 4E28 0MZ 0.04417 0.40023 5.23077
23 2QLX RM4 0.009524 0.44282 5.55556
24 3A1I UNU 0.02105 0.40264 5.75816
25 3S9K CIT 0.03052 0.45203 5.9322
26 1V6A TRE 0.02638 0.41078 6.62651
27 3LXI CAM 0.03935 0.41244 6.65083
28 2V5E SCR 0.0063 0.47454 6.93069
29 1G8S MET 0.002123 0.46819 7.82609
30 1TUV VK3 0.01132 0.45244 7.89474
31 1SS4 GSH 0.0009084 0.53291 9.80392
32 1SS4 CIT 0.004571 0.48019 9.80392
33 2A2X NA9 0.002673 0.41933 11.7647
34 4F4S EFO 0.02417 0.4081 14.4737
35 4F8L GAL 0.003255 0.50085 16.5517
36 3SHR CMP 0.006297 0.42496 17.3913
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