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 (2D)
Ligand no: 1; Ligand: 2A5; Similar ligands found: 330
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 HEJ 0.650602 0.918919
9 5FA 0.642857 0.918919
10 AQP 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 CUU 0.593023 0.945205
23 AV2 0.588889 0.868421
24 APR 0.586207 0.893333
25 AR6 0.586207 0.893333
26 ANP 0.58427 0.894737
27 A 0.580247 0.891892
28 AMP 0.580247 0.891892
29 AD9 0.579545 0.894737
30 AGS 0.579545 0.871795
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 AMP MG 0.554217 0.853333
47 PRX 0.550562 0.87013
48 APC 0.550562 0.907895
49 3AT 0.549451 0.945205
50 NA7 0.546392 0.933333
51 PPS 0.543478 0.829268
52 8LE 0.543478 0.825
53 ADQ 0.541667 0.894737
54 A1R 0.541667 0.909091
55 45A 0.541176 0.844156
56 ABM 0.541176 0.844156
57 2AM 0.536585 0.917808
58 ADP MG 0.534091 0.866667
59 ADP BEF 0.534091 0.866667
60 DTP 0.532609 0.932432
61 SRP 0.531915 0.883117
62 8LH 0.531915 0.858974
63 25A 0.53125 0.893333
64 8QN 0.53125 0.857143
65 3AM 0.53012 0.90411
66 A12 0.528736 0.907895
67 AP2 0.528736 0.907895
68 A3R 0.525773 0.909091
69 JNT 0.520408 0.945946
70 3OD 0.52 0.87013
71 SRA 0.517647 0.846154
72 OVE 0.517647 0.881579
73 V3L 0.516129 0.893333
74 OZV 0.515464 0.893333
75 OAD 0.515152 0.87013
76 9X8 0.515152 0.848101
77 7D7 0.513158 0.746667
78 AU1 0.511111 0.894737
79 ATP MG 0.51087 0.866667
80 APC MG 0.51087 0.844156
81 ADP PO3 0.51087 0.866667
82 AMO 0.510204 0.883117
83 PAJ 0.510204 0.839506
84 BEF ADP 0.505376 0.844156
85 QA7 0.505155 0.825
86 8LQ 0.505155 0.858974
87 00A 0.50505 0.814815
88 AHX 0.50505 0.873418
89 BIS 0.504951 0.884615
90 OOB 0.5 0.857143
91 5SV 0.5 0.82716
92 DDS 0.5 0.905405
93 128 0.495413 0.738636
94 LAD 0.49505 0.8625
95 4AD 0.494949 0.871795
96 6AD 0.494737 0.839506
97 ADV 0.494624 0.883117
98 RBY 0.494624 0.883117
99 12D 0.490741 0.747126
100 KMQ 0.490385 0.858974
101 NB8 0.490196 0.85
102 PTJ 0.490196 0.82716
103 ME8 0.490196 0.819277
104 FYA 0.490196 0.881579
105 DLL 0.49 0.857143
106 MAP 0.489796 0.871795
107 ALF ADP 0.489583 0.802469
108 VO4 ADP 0.489583 0.87013
109 ANP MG 0.489583 0.857143
110 XYA 0.487179 0.797297
111 RAB 0.487179 0.797297
112 ADN 0.487179 0.797297
113 G5P 0.485981 0.85
114 3UK 0.485149 0.846154
115 GAP 0.484211 0.846154
116 SON 0.483516 0.883117
117 DQV 0.481481 0.881579
118 9SN 0.480769 0.804878
119 PR8 0.480392 0.875
120 WAQ 0.480392 0.884615
121 B5V 0.480392 0.835443
122 V2G 0.479167 0.897436
123 G3A 0.476636 0.85
124 B5Y 0.47619 0.825
125 FA5 0.47619 0.858974
126 TXA 0.475728 0.858974
127 1ZZ 0.475728 0.819277
128 AFH 0.472222 0.8625
129 XAH 0.471698 0.841463
130 LMS 0.471264 0.764706
131 PO4 PO4 A A A A PO4 0.470588 0.853333
132 ADP BMA 0.470588 0.87013
133 9ZA 0.47 0.8375
134 9ZD 0.47 0.8375
135 TXP 0.469565 0.873418
136 A4P 0.469027 0.802326
137 TXD 0.468468 0.860759
138 UP5 0.468468 0.848101
139 GTA 0.46789 0.819277
140 4UV 0.46729 0.825
141 NJP 0.465517 0.871795
142 ODP 0.465517 0.839506
143 ITT 0.462366 0.866667
144 ATP A 0.462264 0.855263
145 B5M 0.462264 0.825
146 ATP A A A 0.462264 0.855263
147 0WD 0.461538 0.85
148 NPW 0.46087 0.864198
149 NDP 0.46087 0.85
150 D5M 0.460674 0.905405
151 DA 0.460674 0.905405
152 L3W 0.460177 0.858974
153 DAL AMP 0.46 0.833333
154 GGZ 0.46 0.783133
155 48N 0.459459 0.85
156 4UU 0.458716 0.825
157 HFD 0.458333 0.871795
158 JSQ 0.458333 0.871795
159 LQJ 0.457944 0.893333
160 NZQ 0.456897 0.8625
161 5N5 0.45679 0.773333
162 DND 0.455357 0.858974
163 NAI 0.455357 0.8375
164 6V0 0.455357 0.82716
165 NAX 0.455357 0.851852
166 F2R 0.452991 0.865854
167 J4G 0.451923 0.896104
168 J7V 0.451613 0.772727
169 TYM 0.451327 0.858974
170 OMR 0.451327 0.831325
171 TXE 0.451327 0.860759
172 5CD 0.451219 0.736842
173 A4D 0.451219 0.773333
174 LAQ 0.45045 0.819277
175 NO7 0.45 0.883117
176 6RE 0.449438 0.7625
177 XNP 0.449153 0.851852
178 DZ4 0.44898 0.907895
179 139 0.448276 0.851852
180 T5A 0.448276 0.821429
181 ADJ 0.448276 0.831325
182 AP0 0.447368 0.82716
183 4TC 0.447368 0.85
184 YLP 0.446429 0.843373
185 ETB 0.446281 0.835294
186 DCA 0.446281 0.847059
187 GA7 0.445455 0.883117
188 HDV 0.444444 0.87013
189 A3G 0.444444 0.779221
190 AOC 0.444444 0.753247
191 4UW 0.442478 0.795181
192 2VA 0.442105 0.75641
193 A3T 0.442105 0.776316
194 80F 0.441667 0.8
195 5AS 0.44086 0.761364
196 J7C 0.43956 0.772152
197 COA 0.439024 0.847059
198 0T1 0.439024 0.847059
199 COD 0.436975 0.835294
200 NAD 0.436975 0.857143
201 SCO 0.436508 0.847059
202 7DD 0.43617 0.905405
203 A3S 0.43617 0.789474
204 EP4 0.435294 0.691358
205 UPA 0.434783 0.860759
206 YLC 0.434783 0.841463
207 YLB 0.434783 0.843373
208 JB6 0.433962 0.884615
209 NWW 0.433735 0.693333
210 101 0.433333 0.905405
211 AR6 AR6 0.432432 0.844156
212 CNA 0.432203 0.858974
213 NAP 0.432 0.87013
214 38V 0.432 0.841463
215 APU 0.431034 0.871795
216 PUA 0.430894 0.8625
217 DTA 0.430233 0.721519
218 M2T 0.430233 0.674699
219 A5A 0.43 0.747126
220 TM1 0.429907 0.735632
221 MYR AMP 0.429907 0.797619
222 A3D 0.429752 0.846154
223 SO8 0.428571 0.746835
224 AMX 0.428571 0.857143
225 CAO 0.428571 0.818182
226 TAP 0.428571 0.8375
227 COS 0.428571 0.827586
228 30N 0.428571 0.774194
229 NAE 0.427419 0.825
230 5X8 0.427083 0.721519
231 H1Q 0.427083 0.831169
232 QQX 0.426966 0.78481
233 3KK 0.426357 0.827586
234 FYN 0.426357 0.847059
235 ALF ADP 3PG 0.426087 0.795181
236 KL2 0.425287 0.815789
237 MTA 0.425287 0.708861
238 CMX 0.425197 0.847059
239 NA0 0.425197 0.858974
240 7L1 0.425197 0.818182
241 5AD 0.425 0.68
242 SAM 0.424242 0.674419
243 YLA 0.423729 0.843373
244 COK 0.423077 0.827586
245 CA6 0.423077 0.75
246 ACK 0.422222 0.837838
247 ZAS 0.422222 0.703704
248 QQY 0.422222 0.794872
249 FCX 0.421875 0.818182
250 ACO 0.421875 0.818182
251 FAM 0.421875 0.827586
252 Y3J 0.421687 0.662338
253 AYB 0.420168 0.833333
254 NMX 0.419847 0.782609
255 7MD 0.419643 0.8875
256 HAX 0.418605 0.827586
257 NVA 2AD 0.418367 0.7625
258 TSB 0.417476 0.758621
259 1DG 0.417323 0.85
260 DG1 0.417323 0.85
261 9BG 0.416667 0.873418
262 3AD 0.416667 0.808219
263 3DH 0.41573 0.708861
264 IOT 0.415254 0.855422
265 AMP DBH 0.414414 0.822785
266 VRT 0.414141 0.772152
267 G5A 0.414141 0.761364
268 EAD 0.414062 0.807229
269 IVC 0.413534 0.837209
270 KGJ 0.413534 0.774194
271 BTX 0.413223 0.843373
272 NEC 0.413043 0.705128
273 N5O 0.413043 0.766234
274 NAQ 0.412698 0.804878
275 AHZ 0.412281 0.776471
276 YZS 0.412214 0.75
277 OXK 0.412214 0.827586
278 KGP 0.412214 0.75
279 SOP 0.412214 0.827586
280 MCD 0.412214 0.827586
281 SMM 0.411765 0.670455
282 SSA 0.411765 0.781609
283 BT5 0.409836 0.833333
284 ZID 0.409449 0.846154
285 CMC 0.409091 0.827586
286 CO6 0.409091 0.827586
287 1VU 0.409091 0.818182
288 LPA AMP 0.408696 0.797619
289 AS 0.408602 0.858974
290 ZZB 0.408333 0.755814
291 VMS 0.407767 0.730337
292 54H 0.407767 0.730337
293 MC4 0.407407 0.782609
294 ARG AMP 0.40708 0.831325
295 ANZ 0.40708 0.759036
296 2MC 0.406015 0.791209
297 CAJ 0.406015 0.827586
298 SCD 0.406015 0.847059
299 KGA 0.404412 0.765957
300 2KQ 0.404412 0.808989
301 KFV 0.404412 0.757895
302 GJV 0.404255 0.753086
303 S4M 0.404255 0.689655
304 ZDA 0.40404 0.842105
305 53H 0.403846 0.722222
306 5CA 0.403846 0.781609
307 TAD 0.403509 0.839506
308 3HC 0.402985 0.837209
309 BCO 0.402985 0.827586
310 1HE 0.402985 0.808989
311 A1S 0.402985 0.827586
312 MLC 0.402985 0.827586
313 1CZ 0.402878 0.818182
314 CC5 0.402439 0.77027
315 AF3 ADP 3PG 0.401709 0.795181
316 P1H 0.401515 0.809524
317 NDE 0.401515 0.858974
318 FAQ 0.40146 0.827586
319 NWQ 0.4 0.675325
320 8OD 0.4 0.87013
321 MCA 0.4 0.818182
322 3D1 0.4 0.824324
323 LCV 0.4 0.742268
324 CAA 0.4 0.837209
325 YE1 0.4 0.837209
326 MAO 0.4 0.741176
327 SO5 0.4 0.742268
328 3L1 0.4 0.824324
329 COO 0.4 0.827586
330 CO7 0.4 0.827586
Ligand no: 2; Ligand: DGT; Similar ligands found: 97
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 0O2 0.622449 0.935065
8 CGP 0.6 0.914634
9 GP3 0.597826 0.9
10 GDP 0.591398 0.923077
11 GSP 0.561224 0.878049
12 G3D 0.561224 0.935065
13 DTP 0.557895 0.909091
14 HF7 0.556701 0.897436
15 GAV 0.55 0.888889
16 G4P 0.55 0.935065
17 GNH 0.536082 0.911392
18 G1R 0.535354 0.911392
19 G2R 0.533981 0.961538
20 9GM 0.53 0.9
21 GNP 0.53 0.9
22 G 0.521277 0.910256
23 5GP 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 G2P 0.5 0.936709
30 G3A 0.5 0.9
31 GKE 0.495413 0.888889
32 GDD 0.495413 0.888889
33 GDC 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 GFB 0.477477 0.888889
42 GDR 0.477477 0.888889
43 QBQ 0.475248 0.910256
44 GPG 0.472222 0.888889
45 2GP 0.46875 0.935065
46 3GP 0.46875 0.897436
47 ALF 5GP 0.466019 0.823529
48 GKD 0.464912 0.888889
49 BGO 0.462185 0.878049
50 8DG 0.461538 0.857143
51 GDP BEF 0.461538 0.864198
52 GDX 0.46087 0.9
53 P2G 0.459184 0.860759
54 GTP MG 0.457143 0.886076
55 MGP 0.456311 0.888889
56 JB3 0.453782 0.878049
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 P1G 0.45 0.873418
62 NGD 0.45 0.888889
63 YGP 0.446429 0.835294
64 3PD UM3 0.446281 0.86747
65 G1G 0.444444 0.857143
66 GDP AF3 0.440367 0.823529
67 F6G 0.44 0.8375
68 N5P 0.439252 0.75
69 DUT 0.438776 0.7875
70 01G 0.433628 0.903614
71 C1Z 0.432432 0.935065
72 TPG 0.430769 0.782609
73 DCP 0.43 0.848101
74 CF2 0.428571 0.802326
75 GGM 0.427419 0.857143
76 2MD 0.427419 0.827586
77 U2G 0.42623 0.86747
78 CZF 0.423077 0.860759
79 CG2 0.419355 0.86747
80 KB7 0.419048 0.785714
81 MGD 0.417323 0.827586
82 TTP 0.415842 0.759036
83 MD1 0.415385 0.848837
84 PGD 0.415385 0.857143
85 FEG 0.414634 0.858824
86 ZGP 0.41129 0.848837
87 3AT 0.409524 0.871795
88 DDS 0.409524 0.858974
89 DBG 0.409091 0.878049
90 3ZE 0.407767 0.886076
91 6U4 0.407407 0.853659
92 GDP 7MG 0.40678 0.843373
93 GPC 0.40625 0.816092
94 523 0.403846 0.788235
95 SGP 0.401961 0.807229
96 7D4 0.401961 0.814815
97 AGO 0.401575 0.86747
Similar Ligands (3D)
Ligand no: 1; Ligand: 2A5; Similar ligands found: 3
No: Ligand Similarity coefficient
1 GDP 0.8973
2 CDP 0.8762
3 M7G 0.8698
Ligand no: 2; Ligand: DGT; Similar ligands found: 24
No: Ligand Similarity coefficient
1 HDV 0.9878
2 DZ4 0.9790
3 JSQ 0.9693
4 HFD 0.9578
5 HEJ 0.9531
6 ANP 0.9413
7 AGS 0.9355
8 ATP 0.9177
9 ACP 0.9114
10 ADP BEF 0.9102
11 ADP ALF 0.9081
12 MGT 0.9047
13 HF4 0.9026
14 APC 0.9014
15 ALF ADP 0.8890
16 2KH 0.8809
17 UTP 0.8773
18 8GD 0.8707
19 ADP 0.8685
20 SAM 0.8665
21 8QN 0.8658
22 CTP 0.8611
23 BEF ADP 0.8591
24 IDP 0.8537
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
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