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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: 299
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 AP5 0.634146 0.893333
13 B4P 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 AR6 0.586207 0.893333
24 APR 0.586207 0.893333
25 ANP 0.58427 0.894737
26 AMP 0.580247 0.891892
27 A 0.580247 0.891892
28 AD9 0.579545 0.894737
29 SAP 0.579545 0.871795
30 AGS 0.579545 0.871795
31 A2R 0.576087 0.906667
32 DAT 0.574713 0.932432
33 A22 0.569892 0.906667
34 T99 0.566667 0.883117
35 TAT 0.566667 0.883117
36 A2P 0.564706 0.90411
37 A3P 0.564706 0.917808
38 CA0 0.563218 0.87013
39 ADX 0.563218 0.807229
40 25L 0.561224 0.906667
41 5AL 0.56044 0.857143
42 50T 0.556818 0.881579
43 ATF 0.554348 0.883117
44 APC 0.550562 0.907895
45 PRX 0.550562 0.87013
46 3AT 0.549451 0.945205
47 NA7 0.546392 0.933333
48 PPS 0.543478 0.829268
49 A1R 0.541667 0.909091
50 ADQ 0.541667 0.894737
51 ABM 0.541176 0.844156
52 2AM 0.536585 0.917808
53 DTP 0.532609 0.932432
54 SRP 0.531915 0.883117
55 8QN 0.53125 0.857143
56 25A 0.53125 0.893333
57 3AM 0.53012 0.90411
58 AP2 0.528736 0.907895
59 A12 0.528736 0.907895
60 A3R 0.525773 0.909091
61 3OD 0.52 0.87013
62 OVE 0.517647 0.881579
63 SRA 0.517647 0.846154
64 V3L 0.516129 0.893333
65 9X8 0.515152 0.848101
66 OAD 0.515152 0.87013
67 7D7 0.513158 0.746667
68 AU1 0.511111 0.894737
69 ADP PO3 0.51087 0.866667
70 AMO 0.510204 0.883117
71 PAJ 0.510204 0.839506
72 00A 0.50505 0.814815
73 AHX 0.50505 0.873418
74 BIS 0.504951 0.884615
75 OOB 0.5 0.857143
76 5SV 0.5 0.82716
77 DDS 0.5 0.905405
78 128 0.495413 0.738636
79 LAD 0.49505 0.8625
80 4AD 0.494949 0.871795
81 6AD 0.494737 0.839506
82 RBY 0.494624 0.883117
83 ADV 0.494624 0.883117
84 12D 0.490741 0.747126
85 NB8 0.490196 0.85
86 FYA 0.490196 0.881579
87 ME8 0.490196 0.819277
88 PTJ 0.490196 0.82716
89 DLL 0.49 0.857143
90 MAP 0.489796 0.871795
91 ALF ADP 0.489583 0.802469
92 ADP ALF 0.489583 0.802469
93 RAB 0.487179 0.797297
94 ADN 0.487179 0.797297
95 XYA 0.487179 0.797297
96 G5P 0.485981 0.85
97 3UK 0.485149 0.846154
98 ADP VO4 0.484536 0.857143
99 VO4 ADP 0.484536 0.857143
100 GAP 0.484211 0.846154
101 SON 0.483516 0.883117
102 DQV 0.481481 0.881579
103 9SN 0.480769 0.804878
104 B5V 0.480392 0.835443
105 PR8 0.480392 0.875
106 WAQ 0.480392 0.884615
107 G3A 0.476636 0.85
108 FA5 0.47619 0.858974
109 YAP 0.47619 0.848101
110 B5Y 0.47619 0.825
111 TXA 0.475728 0.858974
112 1ZZ 0.475728 0.819277
113 AFH 0.472222 0.8625
114 XAH 0.471698 0.841463
115 LMS 0.471264 0.764706
116 PO4 PO4 A A A A PO4 0.470588 0.853333
117 ADP BMA 0.470588 0.87013
118 A A A 0.470588 0.881579
119 9ZD 0.47 0.8375
120 9ZA 0.47 0.8375
121 TXP 0.469565 0.873418
122 A4P 0.469027 0.802326
123 TXD 0.468468 0.860759
124 UP5 0.468468 0.848101
125 GTA 0.46789 0.819277
126 4UV 0.46729 0.825
127 A A 0.466019 0.868421
128 NJP 0.465517 0.871795
129 ODP 0.465517 0.839506
130 ITT 0.462366 0.866667
131 ATP A A A 0.462264 0.855263
132 B5M 0.462264 0.825
133 0WD 0.461538 0.85
134 NPW 0.46087 0.864198
135 NDP 0.46087 0.85
136 D5M 0.460674 0.905405
137 DA 0.460674 0.905405
138 GGZ 0.46 0.783133
139 DAL AMP 0.46 0.833333
140 48N 0.459459 0.85
141 4UU 0.458716 0.825
142 HFD 0.458333 0.871795
143 NZQ 0.456897 0.8625
144 5N5 0.45679 0.773333
145 NAI 0.455357 0.8375
146 NAX 0.455357 0.851852
147 DND 0.455357 0.858974
148 NXX 0.455357 0.858974
149 6V0 0.455357 0.82716
150 F2R 0.452991 0.865854
151 J7V 0.451613 0.772727
152 OMR 0.451327 0.831325
153 TYM 0.451327 0.858974
154 TXE 0.451327 0.860759
155 A4D 0.451219 0.773333
156 5CD 0.451219 0.736842
157 LAQ 0.45045 0.819277
158 6RE 0.449438 0.7625
159 XNP 0.449153 0.851852
160 ADJ 0.448276 0.831325
161 139 0.448276 0.851852
162 T5A 0.448276 0.821429
163 AP0 0.447368 0.82716
164 4TC 0.447368 0.85
165 YLP 0.446429 0.843373
166 DCA 0.446281 0.847059
167 ETB 0.446281 0.835294
168 GA7 0.445455 0.883117
169 HDV 0.444444 0.87013
170 A3G 0.444444 0.779221
171 AOC 0.444444 0.753247
172 4UW 0.442478 0.795181
173 2VA 0.442105 0.75641
174 A3T 0.442105 0.776316
175 80F 0.441667 0.8
176 5AS 0.44086 0.761364
177 J7C 0.43956 0.772152
178 0T1 0.439024 0.847059
179 COA 0.439024 0.847059
180 NAD 0.436975 0.857143
181 COD 0.436975 0.835294
182 SCO 0.436508 0.847059
183 A3S 0.43617 0.789474
184 7DD 0.43617 0.905405
185 EP4 0.435294 0.691358
186 YLC 0.434783 0.841463
187 UPA 0.434783 0.860759
188 YLB 0.434783 0.843373
189 JB6 0.433962 0.884615
190 101 0.433333 0.905405
191 AR6 AR6 0.432432 0.844156
192 CNA 0.432203 0.858974
193 NAP 0.432 0.87013
194 APU 0.431034 0.871795
195 PUA 0.430894 0.8625
196 DTA 0.430233 0.721519
197 M2T 0.430233 0.674699
198 A5A 0.43 0.747126
199 MYR AMP 0.429907 0.797619
200 TM1 0.429907 0.735632
201 A3D 0.429752 0.846154
202 SO8 0.428571 0.746835
203 AMX 0.428571 0.857143
204 CAO 0.428571 0.818182
205 30N 0.428571 0.774194
206 TAP 0.428571 0.8375
207 COS 0.428571 0.827586
208 NAE 0.427419 0.825
209 5X8 0.427083 0.721519
210 QQX 0.426966 0.78481
211 3KK 0.426357 0.827586
212 FYN 0.426357 0.847059
213 MTA 0.425287 0.708861
214 7L1 0.425197 0.818182
215 NA0 0.425197 0.858974
216 CMX 0.425197 0.847059
217 5AD 0.425 0.68
218 SAM 0.424242 0.674419
219 YLA 0.423729 0.843373
220 CA6 0.423077 0.75
221 COK 0.423077 0.827586
222 ACK 0.422222 0.837838
223 QQY 0.422222 0.794872
224 ZAS 0.422222 0.703704
225 FAM 0.421875 0.827586
226 FCX 0.421875 0.818182
227 ACO 0.421875 0.818182
228 Y3J 0.421687 0.662338
229 AYB 0.420168 0.833333
230 NMX 0.419847 0.782609
231 7MD 0.419643 0.8875
232 HAX 0.418605 0.827586
233 NVA 2AD 0.418367 0.7625
234 TSB 0.417476 0.758621
235 1DG 0.417323 0.85
236 DG1 0.417323 0.85
237 3AD 0.416667 0.808219
238 3DH 0.41573 0.708861
239 IOT 0.415254 0.855422
240 TYR AMP 0.414414 0.825
241 AMP DBH 0.414414 0.822785
242 G5A 0.414141 0.761364
243 VRT 0.414141 0.772152
244 EAD 0.414062 0.807229
245 IVC 0.413534 0.837209
246 BTX 0.413223 0.843373
247 NEC 0.413043 0.705128
248 NAQ 0.412698 0.804878
249 AHZ 0.412281 0.776471
250 MCD 0.412214 0.827586
251 OXK 0.412214 0.827586
252 SOP 0.412214 0.827586
253 SSA 0.411765 0.781609
254 SMM 0.411765 0.670455
255 BT5 0.409836 0.833333
256 ZID 0.409449 0.846154
257 CO6 0.409091 0.827586
258 CMC 0.409091 0.827586
259 1VU 0.409091 0.818182
260 LPA AMP 0.408696 0.797619
261 AS 0.408602 0.858974
262 ZZB 0.408333 0.755814
263 54H 0.407767 0.730337
264 VMS 0.407767 0.730337
265 MC4 0.407407 0.782609
266 ARG AMP 0.40708 0.831325
267 ANZ 0.40708 0.759036
268 A U 0.40678 0.825
269 CAJ 0.406015 0.827586
270 2MC 0.406015 0.791209
271 SCD 0.406015 0.847059
272 2KQ 0.404412 0.808989
273 S4M 0.404255 0.689655
274 GJV 0.404255 0.753086
275 ZDA 0.40404 0.842105
276 53H 0.403846 0.722222
277 5CA 0.403846 0.781609
278 TAD 0.403509 0.839506
279 MLC 0.402985 0.827586
280 1HE 0.402985 0.808989
281 BCO 0.402985 0.827586
282 A1S 0.402985 0.827586
283 3HC 0.402985 0.837209
284 1CZ 0.402878 0.818182
285 CC5 0.402439 0.77027
286 AF3 ADP 3PG 0.401709 0.795181
287 G A A A 0.401639 0.82716
288 NDE 0.401515 0.858974
289 P1H 0.401515 0.809524
290 FAQ 0.40146 0.827586
291 YE1 0.4 0.837209
292 MAO 0.4 0.741176
293 COO 0.4 0.827586
294 MCA 0.4 0.818182
295 CO7 0.4 0.827586
296 3D1 0.4 0.824324
297 8OD 0.4 0.87013
298 3L1 0.4 0.824324
299 CAA 0.4 0.837209
Ligand no: 2; Ligand: DGT; Similar ligands found: 100
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 GSP 0.561224 0.878049
13 G3D 0.561224 0.935065
14 DTP 0.557895 0.909091
15 HF7 0.556701 0.897436
16 G4P 0.55 0.935065
17 GAV 0.55 0.888889
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 5GP 0.521277 0.910256
25 G 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 G3A 0.5 0.9
32 G2P 0.5 0.936709
33 GDC 0.495413 0.888889
34 GDD 0.495413 0.888889
35 GKE 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 GFB 0.477477 0.888889
44 GDR 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 GDP ALF 0.453704 0.823529
57 ALF GDP 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 N5P 0.439252 0.75
70 DUT 0.438776 0.7875
71 DG DA DC DG 0.43662 0.880952
72 01G 0.433628 0.903614
73 C1Z 0.432432 0.935065
74 TPG 0.430769 0.782609
75 DCP 0.43 0.848101
76 CF2 0.428571 0.802326
77 2MD 0.427419 0.827586
78 GGM 0.427419 0.857143
79 U2G 0.42623 0.86747
80 CG2 0.419355 0.86747
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 DA DU DG DA 0.414634 0.835294
86 FEG 0.414634 0.858824
87 G G 0.413793 0.876543
88 ZGP 0.41129 0.848837
89 DDS 0.409524 0.858974
90 3AT 0.409524 0.871795
91 DBG 0.409091 0.878049
92 3ZE 0.407767 0.886076
93 6U4 0.407407 0.853659
94 GDP 7MG 0.40678 0.843373
95 GPC 0.40625 0.816092
96 DA DC DG DA 0.402685 0.914634
97 SGP 0.401961 0.807229
98 7D4 0.401961 0.814815
99 AGO 0.401575 0.86747
100 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: 18
This union binding pocket(no: 1) in the query (biounit: 3rsr.bio1) has 48 residues
No: Leader PDB Ligand Sequence Similarity
1 5JBE MAL 1.46396
2 5OCQ CIT 1.75439
3 1IZC PYR 1.76991
4 3HQP OXL 1.80361
5 3UNG ADP 1.8759
6 6D2O 4MZ 2.39234
7 2HHP FLC 2.45283
8 4RL4 PPV 3.77358
9 3KLL MAL 3.94144
10 5FS0 5JC 4.2654
11 5KBE IPH 4.36681
12 5TQZ GLC 4.66667
13 3LXI CAM 6.65083
14 2CHT TSA 7.87402
15 6F5W KG1 8.94309
16 4JX1 CAM 15.0442
17 4JX1 CAH 15.0442
18 1RV0 NDG 16.25
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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