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 11 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 (8)
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....
7 2WGH - DTP C10 H16 N5 O12 P3 c1nc(c2c(n....
8 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 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....
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: 324
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 HEJ 0.650602 0.918919
8 ATP 0.650602 0.918919
9 AQP 0.642857 0.918919
10 5FA 0.642857 0.918919
11 A2D 0.6375 0.893333
12 B4P 0.634146 0.893333
13 AP5 0.634146 0.893333
14 AN2 0.626506 0.906667
15 BA3 0.621951 0.893333
16 6YZ 0.617977 0.92
17 AT4 0.607143 0.883117
18 7D5 0.602564 0.88
19 ACQ 0.602273 0.92
20 M33 0.6 0.881579
21 ACP 0.593023 0.92
22 AV2 0.588889 0.868421
23 APR 0.586207 0.893333
24 AR6 0.586207 0.893333
25 ANP 0.58427 0.894737
26 AMP 0.580247 0.891892
27 A 0.580247 0.891892
28 AGS 0.579545 0.871795
29 SAP 0.579545 0.871795
30 AD9 0.579545 0.894737
31 A2R 0.576087 0.906667
32 DAT 0.574713 0.932432
33 KG4 0.574713 0.87013
34 A22 0.569892 0.906667
35 T99 0.566667 0.883117
36 TAT 0.566667 0.883117
37 A3P 0.564706 0.917808
38 A2P 0.564706 0.90411
39 ADX 0.563218 0.807229
40 CA0 0.563218 0.87013
41 25L 0.561224 0.906667
42 5AL 0.56044 0.857143
43 HQG 0.55914 0.906667
44 50T 0.556818 0.881579
45 ATF 0.554348 0.883117
46 APC 0.550562 0.907895
47 PRX 0.550562 0.87013
48 3AT 0.549451 0.945205
49 NA7 0.546392 0.933333
50 PPS 0.543478 0.829268
51 8LE 0.543478 0.825
52 A1R 0.541667 0.909091
53 ADQ 0.541667 0.894737
54 ABM 0.541176 0.844156
55 45A 0.541176 0.844156
56 2AM 0.536585 0.917808
57 ADP MG 0.534091 0.866667
58 DTP 0.532609 0.932432
59 8LH 0.531915 0.858974
60 SRP 0.531915 0.883117
61 25A 0.53125 0.893333
62 8QN 0.53125 0.857143
63 3AM 0.53012 0.90411
64 A12 0.528736 0.907895
65 AP2 0.528736 0.907895
66 A3R 0.525773 0.909091
67 3OD 0.52 0.87013
68 OVE 0.517647 0.881579
69 SRA 0.517647 0.846154
70 V3L 0.516129 0.893333
71 OZV 0.515464 0.893333
72 9X8 0.515152 0.848101
73 OAD 0.515152 0.87013
74 7D7 0.513158 0.746667
75 AU1 0.511111 0.894737
76 ADP PO3 0.51087 0.866667
77 APC MG 0.51087 0.844156
78 ATP MG 0.51087 0.866667
79 PAJ 0.510204 0.839506
80 AMO 0.510204 0.883117
81 8LQ 0.505155 0.858974
82 00A 0.50505 0.814815
83 AHX 0.50505 0.873418
84 BIS 0.504951 0.884615
85 5SV 0.5 0.82716
86 DDS 0.5 0.905405
87 OOB 0.5 0.857143
88 128 0.495413 0.738636
89 LAD 0.49505 0.8625
90 4AD 0.494949 0.871795
91 6AD 0.494737 0.839506
92 RBY 0.494624 0.883117
93 ADV 0.494624 0.883117
94 12D 0.490741 0.747126
95 NB8 0.490196 0.85
96 ME8 0.490196 0.819277
97 PTJ 0.490196 0.82716
98 FYA 0.490196 0.881579
99 DLL 0.49 0.857143
100 MAP 0.489796 0.871795
101 ALF ADP 0.489583 0.802469
102 ADP ALF 0.489583 0.802469
103 XYA 0.487179 0.797297
104 RAB 0.487179 0.797297
105 ADN 0.487179 0.797297
106 G5P 0.485981 0.85
107 3UK 0.485149 0.846154
108 ADP VO4 0.484536 0.857143
109 VO4 ADP 0.484536 0.857143
110 GAP 0.484211 0.846154
111 SON 0.483516 0.883117
112 DQV 0.481481 0.881579
113 9SN 0.480769 0.804878
114 B5V 0.480392 0.835443
115 WAQ 0.480392 0.884615
116 PR8 0.480392 0.875
117 G3A 0.476636 0.85
118 FA5 0.47619 0.858974
119 YAP 0.47619 0.848101
120 B5Y 0.47619 0.825
121 1ZZ 0.475728 0.819277
122 TXA 0.475728 0.858974
123 AFH 0.472222 0.8625
124 XAH 0.471698 0.841463
125 LMS 0.471264 0.764706
126 ADP BMA 0.470588 0.87013
127 A A A 0.470588 0.881579
128 PO4 PO4 A A A A PO4 0.470588 0.853333
129 9ZD 0.47 0.8375
130 9ZA 0.47 0.8375
131 TXP 0.469565 0.873418
132 A4P 0.469027 0.802326
133 UP5 0.468468 0.848101
134 TXD 0.468468 0.860759
135 GTA 0.46789 0.819277
136 4UV 0.46729 0.825
137 A A 0.466019 0.868421
138 NJP 0.465517 0.871795
139 ODP 0.465517 0.839506
140 ITT 0.462366 0.866667
141 B5M 0.462264 0.825
142 ATP A 0.462264 0.855263
143 ATP A A A 0.462264 0.855263
144 0WD 0.461538 0.85
145 NDP 0.46087 0.85
146 NPW 0.46087 0.864198
147 DA 0.460674 0.905405
148 D5M 0.460674 0.905405
149 DAL AMP 0.46 0.833333
150 GGZ 0.46 0.783133
151 48N 0.459459 0.85
152 4UU 0.458716 0.825
153 HFD 0.458333 0.871795
154 JSQ 0.458333 0.871795
155 LQJ 0.457944 0.893333
156 NZQ 0.456897 0.8625
157 5N5 0.45679 0.773333
158 6V0 0.455357 0.82716
159 NAX 0.455357 0.851852
160 NXX 0.455357 0.858974
161 DND 0.455357 0.858974
162 NAI 0.455357 0.8375
163 F2R 0.452991 0.865854
164 J4G 0.451923 0.896104
165 J7V 0.451613 0.772727
166 OMR 0.451327 0.831325
167 TYM 0.451327 0.858974
168 TXE 0.451327 0.860759
169 A4D 0.451219 0.773333
170 5CD 0.451219 0.736842
171 LAQ 0.45045 0.819277
172 NO7 0.45 0.883117
173 6RE 0.449438 0.7625
174 XNP 0.449153 0.851852
175 139 0.448276 0.851852
176 ADJ 0.448276 0.831325
177 T5A 0.448276 0.821429
178 AP0 0.447368 0.82716
179 4TC 0.447368 0.85
180 YLP 0.446429 0.843373
181 ETB 0.446281 0.835294
182 DCA 0.446281 0.847059
183 GA7 0.445455 0.883117
184 HDV 0.444444 0.87013
185 A3G 0.444444 0.779221
186 AOC 0.444444 0.753247
187 4UW 0.442478 0.795181
188 A3T 0.442105 0.776316
189 2VA 0.442105 0.75641
190 80F 0.441667 0.8
191 5AS 0.44086 0.761364
192 J7C 0.43956 0.772152
193 0T1 0.439024 0.847059
194 COA 0.439024 0.847059
195 COD 0.436975 0.835294
196 NAD 0.436975 0.857143
197 SCO 0.436508 0.847059
198 7DD 0.43617 0.905405
199 A3S 0.43617 0.789474
200 EP4 0.435294 0.691358
201 UPA 0.434783 0.860759
202 YLC 0.434783 0.841463
203 YLB 0.434783 0.843373
204 JB6 0.433962 0.884615
205 101 0.433333 0.905405
206 AR6 AR6 0.432432 0.844156
207 CNA 0.432203 0.858974
208 NAP 0.432 0.87013
209 APU 0.431034 0.871795
210 PUA 0.430894 0.8625
211 M2T 0.430233 0.674699
212 DTA 0.430233 0.721519
213 A5A 0.43 0.747126
214 TM1 0.429907 0.735632
215 MYR AMP 0.429907 0.797619
216 A3D 0.429752 0.846154
217 SO8 0.428571 0.746835
218 30N 0.428571 0.774194
219 COS 0.428571 0.827586
220 TAP 0.428571 0.8375
221 AMX 0.428571 0.857143
222 CAO 0.428571 0.818182
223 NAE 0.427419 0.825
224 H1Q 0.427083 0.831169
225 5X8 0.427083 0.721519
226 QQX 0.426966 0.78481
227 3KK 0.426357 0.827586
228 FYN 0.426357 0.847059
229 MTA 0.425287 0.708861
230 CMX 0.425197 0.847059
231 7L1 0.425197 0.818182
232 NA0 0.425197 0.858974
233 5AD 0.425 0.68
234 SAM 0.424242 0.674419
235 YLA 0.423729 0.843373
236 CA6 0.423077 0.75
237 COK 0.423077 0.827586
238 ZAS 0.422222 0.703704
239 QQY 0.422222 0.794872
240 ACK 0.422222 0.837838
241 FCX 0.421875 0.818182
242 ACO 0.421875 0.818182
243 FAM 0.421875 0.827586
244 Y3J 0.421687 0.662338
245 AYB 0.420168 0.833333
246 NMX 0.419847 0.782609
247 7MD 0.419643 0.8875
248 HAX 0.418605 0.827586
249 NVA 2AD 0.418367 0.7625
250 TSB 0.417476 0.758621
251 DG1 0.417323 0.85
252 1DG 0.417323 0.85
253 3AD 0.416667 0.808219
254 9BG 0.416667 0.873418
255 3DH 0.41573 0.708861
256 IOT 0.415254 0.855422
257 AMP DBH 0.414414 0.822785
258 TYR AMP 0.414414 0.825
259 VRT 0.414141 0.772152
260 G5A 0.414141 0.761364
261 EAD 0.414062 0.807229
262 IVC 0.413534 0.837209
263 KGJ 0.413534 0.774194
264 BTX 0.413223 0.843373
265 NEC 0.413043 0.705128
266 N5O 0.413043 0.766234
267 NAQ 0.412698 0.804878
268 AHZ 0.412281 0.776471
269 SOP 0.412214 0.827586
270 YZS 0.412214 0.75
271 MCD 0.412214 0.827586
272 OXK 0.412214 0.827586
273 KGP 0.412214 0.75
274 SSA 0.411765 0.781609
275 SMM 0.411765 0.670455
276 BT5 0.409836 0.833333
277 ZID 0.409449 0.846154
278 CMC 0.409091 0.827586
279 CO6 0.409091 0.827586
280 1VU 0.409091 0.818182
281 LPA AMP 0.408696 0.797619
282 AS 0.408602 0.858974
283 ZZB 0.408333 0.755814
284 VMS 0.407767 0.730337
285 54H 0.407767 0.730337
286 MC4 0.407407 0.782609
287 ANZ 0.40708 0.759036
288 ARG AMP 0.40708 0.831325
289 A U 0.40678 0.825
290 SCD 0.406015 0.847059
291 2MC 0.406015 0.791209
292 CAJ 0.406015 0.827586
293 2KQ 0.404412 0.808989
294 KGA 0.404412 0.765957
295 KFV 0.404412 0.757895
296 S4M 0.404255 0.689655
297 GJV 0.404255 0.753086
298 ZDA 0.40404 0.842105
299 5CA 0.403846 0.781609
300 53H 0.403846 0.722222
301 TAD 0.403509 0.839506
302 A1S 0.402985 0.827586
303 1HE 0.402985 0.808989
304 BCO 0.402985 0.827586
305 3HC 0.402985 0.837209
306 MLC 0.402985 0.827586
307 1CZ 0.402878 0.818182
308 CC5 0.402439 0.77027
309 AF3 ADP 3PG 0.401709 0.795181
310 G A A A 0.401639 0.82716
311 NDE 0.401515 0.858974
312 P1H 0.401515 0.809524
313 FAQ 0.40146 0.827586
314 SO5 0.4 0.742268
315 MAO 0.4 0.741176
316 YE1 0.4 0.837209
317 LCV 0.4 0.742268
318 CO7 0.4 0.827586
319 CAA 0.4 0.837209
320 COO 0.4 0.827586
321 8OD 0.4 0.87013
322 MCA 0.4 0.818182
323 3D1 0.4 0.824324
324 3L1 0.4 0.824324
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 DG 0.775 0.986842
4 DGP 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 HF7 0.556701 0.897436
16 GAV 0.55 0.888889
17 G4P 0.55 0.935065
18 DC DG 0.53913 0.891566
19 GNH 0.536082 0.911392
20 G1R 0.535354 0.911392
21 G2R 0.533981 0.961538
22 9GM 0.53 0.9
23 GNP 0.53 0.9
24 G 0.521277 0.910256
25 5GP 0.521277 0.910256
26 GCP 0.52 0.924051
27 GPX 0.514563 0.922078
28 GPD 0.513514 0.902439
29 G5P 0.509091 0.9
30 GTG 0.504587 0.86747
31 G2P 0.5 0.936709
32 G3A 0.5 0.9
33 GKE 0.495413 0.888889
34 GDD 0.495413 0.888889
35 GDC 0.495413 0.888889
36 GMV 0.49505 0.9
37 DI 0.494737 0.960526
38 6CK 0.486486 0.86747
39 DAT 0.484536 0.909091
40 Y9Z 0.481818 0.880952
41 GP2 0.48 0.936709
42 JB2 0.477876 0.888889
43 GDR 0.477477 0.888889
44 GFB 0.477477 0.888889
45 GPG 0.472222 0.888889
46 3GP 0.46875 0.897436
47 2GP 0.46875 0.935065
48 ALF 5GP 0.466019 0.823529
49 GKD 0.464912 0.888889
50 BGO 0.462185 0.878049
51 8DG 0.461538 0.857143
52 GDX 0.46087 0.9
53 P2G 0.459184 0.860759
54 MGP 0.456311 0.888889
55 JB3 0.453782 0.878049
56 ALF GDP 0.453704 0.823529
57 GDP ALF 0.453704 0.823529
58 6G0 0.451923 0.888889
59 CAG 0.451613 0.818182
60 GMP 0.450549 0.810127
61 NGD 0.45 0.888889
62 P1G 0.45 0.873418
63 YGP 0.446429 0.835294
64 3PD UM3 0.446281 0.86747
65 G1G 0.444444 0.857143
66 DG DC 0.44186 0.925926
67 GCP G 0.441441 0.873418
68 GDP AF3 0.440367 0.823529
69 F6G 0.44 0.8375
70 N5P 0.439252 0.75
71 DUT 0.438776 0.7875
72 DG DA DC DG 0.43662 0.880952
73 01G 0.433628 0.903614
74 C1Z 0.432432 0.935065
75 TPG 0.430769 0.782609
76 DCP 0.43 0.848101
77 CF2 0.428571 0.802326
78 GGM 0.427419 0.857143
79 2MD 0.427419 0.827586
80 U2G 0.42623 0.86747
81 CG2 0.419355 0.86747
82 KB7 0.419048 0.785714
83 MGD 0.417323 0.827586
84 TTP 0.415842 0.759036
85 MD1 0.415385 0.848837
86 PGD 0.415385 0.857143
87 FEG 0.414634 0.858824
88 DA DU DG DA 0.414634 0.835294
89 G G 0.413793 0.876543
90 ZGP 0.41129 0.848837
91 DDS 0.409524 0.858974
92 3AT 0.409524 0.871795
93 DBG 0.409091 0.878049
94 3ZE 0.407767 0.886076
95 6U4 0.407407 0.853659
96 GDP 7MG 0.40678 0.843373
97 GPC 0.40625 0.816092
98 523 0.403846 0.788235
99 DA DC DG DA 0.402685 0.914634
100 7D4 0.401961 0.814815
101 SGP 0.401961 0.807229
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 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: 3rsr.bio1) has 48 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 3RSR; Ligand: N5P; 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: 3rsr.bio1) has 48 residues
No: Leader PDB Ligand Sequence Similarity
APoc FAQ
Feedback