Receptor
PDB id Resolution Class Description Source Keywords
5WA8 1.3 Å EC: 3.-.-.- HUMAN HISTIDINE TRIAD NUCLEOTIDE BINDING PROTEIN 1 (HHINT1) MUTANT NUCLEOSIDE L-ALA PHOSPHORAMIDATE SUBSTRATE COMPLEX HOMO SAPIENS HISTIDINE TRIAD HYDROLASE
Ref.: A CRYSTAL STRUCTURE BASED GUIDE TO THE DESIGN OF HU HISTIDINE TRIAD NUCLEOTIDE BINDING PROTEIN 1 (HHINT ACTIVATED PROTIDES. MOL. PHARM. V. 14 3987 2017
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CL B:201;
 Invalid;
 none;
 submit data
35.453 Cl [Cl-]
9ZA A:201;
 Valid;
 none;
 Kd = 0.587 uM
432.326 C14 H21 N6 O8 P C[C@@...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5WA9 1.15 Å EC: 3.-.-.- HUMAN HISTIDINE TRIAD NUCLEOTIDE BINDING PROTEIN 1 (HHINT1) MUTANT NUCLEOSIDE D-ALA PHOSPHORAMIDATE SUBSTRATE COMPLEX HOMO SAPIENS HISTIDINE TRIAD HYDROLASE
Ref.: A CRYSTAL STRUCTURE BASED GUIDE TO THE DESIGN OF HU HISTIDINE TRIAD NUCLEOTIDE BINDING PROTEIN 1 (HHINT ACTIVATED PROTIDES. MOL. PHARM. V. 14 3987 2017
Members (22)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 312 families.
1 6N3V Kd = 2.45 uM KB7 C13 H18 N6 O6 CCNC(=O)OC....
2 5IPC Kd = 13 uM 6CE C20 H24 N7 O6 P S c1ccc2c(c1....
3 4EQG - A5A C13 H19 N7 O7 S C[C@@H](C(....
4 6N3W Kd = 1.56 uM KBJ C19 H22 N6 O6 c1ccc(cc1)....
5 5I2E Kd = 0.23 uM 67D C23 H23 N7 O7 S c1ccc2c(c1....
6 3O1C - ADN C10 H13 N5 O4 c1nc(c2c(n....
7 6N3X Kd = 8.09 uM KBD C18 H20 N6 O6 c1ccc(cc1)....
8 5IPE - 6CG C10 H14 N5 O7 P S c1nc2c(n1[....
9 4RHN - RIB C5 H10 O5 C([C@@H]1[....
10 3O1X - ADN C10 H13 N5 O4 c1nc(c2c(n....
11 4ZKL - JB6 C24 H34 N10 O13 P2 S2 c1nc(c2c(n....
12 3QGZ - ADN C10 H13 N5 O4 c1nc(c2c(n....
13 5I2F - BS5 C20 H29 N9 O7 S2 c1nc(c2c(n....
14 1KPF - AMP C10 H14 N5 O7 P c1nc(c2c(n....
15 5WA9 Kd = 0.175 uM 9ZD C14 H21 N6 O8 P C[C@H](C(=....
16 4EQH - WSA C21 H24 N8 O7 S c1ccc2c(c1....
17 1RZY Ki = 1.25 uM 5AS C12 H18 N6 O6 S CCNS(=O)(=....
18 4EQE - KAA C16 H26 N8 O7 S c1nc(c2c(n....
19 6N3Y Kd = 3.65 uM HHJ C21 H23 N7 O6 c1ccc2c(c1....
20 5WA8 Kd = 0.587 uM 9ZA C14 H21 N6 O8 P C[C@@H](C(....
21 6B42 - D5M C10 H14 N5 O6 P c1nc(c2c(n....
22 3RHN - 5GP C10 H14 N5 O8 P c1nc2c(n1[....
70% Homology Family (24)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 261 families.
1 6N3V Kd = 2.45 uM KB7 C13 H18 N6 O6 CCNC(=O)OC....
2 5IPC Kd = 13 uM 6CE C20 H24 N7 O6 P S c1ccc2c(c1....
3 4EQG - A5A C13 H19 N7 O7 S C[C@@H](C(....
4 6N3W Kd = 1.56 uM KBJ C19 H22 N6 O6 c1ccc(cc1)....
5 5I2E Kd = 0.23 uM 67D C23 H23 N7 O7 S c1ccc2c(c1....
6 3O1C - ADN C10 H13 N5 O4 c1nc(c2c(n....
7 6N3X Kd = 8.09 uM KBD C18 H20 N6 O6 c1ccc(cc1)....
8 5IPE - 6CG C10 H14 N5 O7 P S c1nc2c(n1[....
9 4RHN - RIB C5 H10 O5 C([C@@H]1[....
10 3O1X - ADN C10 H13 N5 O4 c1nc(c2c(n....
11 4ZKL - JB6 C24 H34 N10 O13 P2 S2 c1nc(c2c(n....
12 3QGZ - ADN C10 H13 N5 O4 c1nc(c2c(n....
13 5I2F - BS5 C20 H29 N9 O7 S2 c1nc(c2c(n....
14 1KPF - AMP C10 H14 N5 O7 P c1nc(c2c(n....
15 5WA9 Kd = 0.175 uM 9ZD C14 H21 N6 O8 P C[C@H](C(=....
16 4EQH - WSA C21 H24 N8 O7 S c1ccc2c(c1....
17 1RZY Ki = 1.25 uM 5AS C12 H18 N6 O6 S CCNS(=O)(=....
18 4EQE - KAA C16 H26 N8 O7 S c1nc(c2c(n....
19 6N3Y Kd = 3.65 uM HHJ C21 H23 N7 O6 c1ccc2c(c1....
20 5WA8 Kd = 0.587 uM 9ZA C14 H21 N6 O8 P C[C@@H](C(....
21 6B42 - D5M C10 H14 N5 O6 P c1nc(c2c(n....
22 3RHN - 5GP C10 H14 N5 O8 P c1nc2c(n1[....
23 5RHN - 8BR C10 H13 Br N5 O7 P c1nc(c2c(n....
24 4INI - AMP C10 H14 N5 O7 P c1nc(c2c(n....
50% Homology Family (26)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 214 families.
1 6N3V Kd = 2.45 uM KB7 C13 H18 N6 O6 CCNC(=O)OC....
2 5IPC Kd = 13 uM 6CE C20 H24 N7 O6 P S c1ccc2c(c1....
3 4EQG - A5A C13 H19 N7 O7 S C[C@@H](C(....
4 6N3W Kd = 1.56 uM KBJ C19 H22 N6 O6 c1ccc(cc1)....
5 5I2E Kd = 0.23 uM 67D C23 H23 N7 O7 S c1ccc2c(c1....
6 3O1C - ADN C10 H13 N5 O4 c1nc(c2c(n....
7 6N3X Kd = 8.09 uM KBD C18 H20 N6 O6 c1ccc(cc1)....
8 5IPE - 6CG C10 H14 N5 O7 P S c1nc2c(n1[....
9 4RHN - RIB C5 H10 O5 C([C@@H]1[....
10 3O1X - ADN C10 H13 N5 O4 c1nc(c2c(n....
11 4ZKL - JB6 C24 H34 N10 O13 P2 S2 c1nc(c2c(n....
12 3QGZ - ADN C10 H13 N5 O4 c1nc(c2c(n....
13 5I2F - BS5 C20 H29 N9 O7 S2 c1nc(c2c(n....
14 1KPF - AMP C10 H14 N5 O7 P c1nc(c2c(n....
15 5WA9 Kd = 0.175 uM 9ZD C14 H21 N6 O8 P C[C@H](C(=....
16 4EQH - WSA C21 H24 N8 O7 S c1ccc2c(c1....
17 1RZY Ki = 1.25 uM 5AS C12 H18 N6 O6 S CCNS(=O)(=....
18 4EQE - KAA C16 H26 N8 O7 S c1nc(c2c(n....
19 6N3Y Kd = 3.65 uM HHJ C21 H23 N7 O6 c1ccc2c(c1....
20 5WA8 Kd = 0.587 uM 9ZA C14 H21 N6 O8 P C[C@@H](C(....
21 6B42 - D5M C10 H14 N5 O6 P c1nc(c2c(n....
22 3RHN - 5GP C10 H14 N5 O8 P c1nc2c(n1[....
23 5RHN - 8BR C10 H13 Br N5 O7 P c1nc(c2c(n....
24 3N1T - 5GP C10 H14 N5 O8 P c1nc2c(n1[....
25 3N1S - 5GP C10 H14 N5 O8 P c1nc2c(n1[....
26 4INI - AMP C10 H14 N5 O7 P c1nc(c2c(n....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: 9ZA; Similar ligands found: 345
No: Ligand ECFP6 Tc MDL keys Tc
1 9ZD 1 1
2 9ZA 1 1
3 AU1 0.686047 0.909091
4 5AL 0.677778 0.946667
5 V2G 0.677778 0.911392
6 AMP 0.670732 0.906667
7 A 0.670732 0.906667
8 45A 0.666667 0.907895
9 ABM 0.666667 0.907895
10 8LH 0.663043 0.922078
11 A12 0.651163 0.873418
12 AP2 0.651163 0.873418
13 QA7 0.648936 0.935065
14 8LQ 0.648936 0.922078
15 CA0 0.647727 0.909091
16 A2D 0.647059 0.883117
17 AMP MG 0.642857 0.868421
18 TXA 0.642857 0.922078
19 8QN 0.642105 0.946667
20 KG4 0.640449 0.909091
21 BA3 0.632184 0.883117
22 DAL AMP 0.631579 0.921053
23 M33 0.629214 0.921053
24 SRP 0.62766 0.897436
25 ADP 0.625 0.907895
26 AP5 0.625 0.883117
27 B4P 0.625 0.883117
28 8LE 0.623656 0.935065
29 SRA 0.623529 0.860759
30 PAJ 0.618557 0.9
31 AN2 0.617977 0.921053
32 AT4 0.617977 0.873418
33 APC 0.615385 0.873418
34 PRX 0.615385 0.860759
35 ANP 0.612903 0.909091
36 GAP 0.612903 0.884615
37 ADX 0.611111 0.8
38 ADV 0.608696 0.873418
39 AD9 0.608696 0.884615
40 RBY 0.608696 0.873418
41 ACP 0.604396 0.884615
42 50T 0.604396 0.871795
43 HEJ 0.604396 0.907895
44 ATP 0.604396 0.907895
45 AMO 0.602041 0.897436
46 4AD 0.602041 0.886076
47 SON 0.6 0.922078
48 ADP BEF 0.6 0.881579
49 ADP MG 0.6 0.881579
50 AQP 0.597826 0.907895
51 5FA 0.597826 0.907895
52 APR 0.597826 0.907895
53 AR6 0.597826 0.907895
54 AHX 0.59596 0.864198
55 NB8 0.594059 0.8875
56 ME8 0.594059 0.878049
57 PTJ 0.594059 0.935897
58 AGS 0.591398 0.8625
59 OAD 0.59 0.934211
60 LAD 0.584158 0.853659
61 MAP 0.581633 0.886076
62 DLL 0.58 0.921053
63 TAT 0.578947 0.873418
64 T99 0.578947 0.873418
65 ACQ 0.578947 0.884615
66 FA5 0.576923 0.897436
67 OOB 0.575758 0.921053
68 ADP PO3 0.574468 0.881579
69 APC MG 0.574468 0.858974
70 ATP MG 0.574468 0.881579
71 9X8 0.574257 0.886076
72 BEF ADP 0.568421 0.858974
73 A5A 0.56701 0.823529
74 ATF 0.56701 0.873418
75 ANP MG 0.56701 0.896104
76 TSB 0.565657 0.813953
77 00A 0.564356 0.875
78 3OD 0.563107 0.934211
79 1ZZ 0.563107 0.855422
80 6YZ 0.561224 0.884615
81 5SV 0.56 0.819277
82 3UK 0.558824 0.909091
83 LMS 0.556818 0.8
84 XAH 0.556604 0.833333
85 HQG 0.555556 0.921053
86 VMS 0.555556 0.825581
87 54H 0.555556 0.825581
88 YLP 0.554545 0.835294
89 A1R 0.554455 0.829268
90 5AS 0.554348 0.775281
91 B5V 0.553398 0.897436
92 WAQ 0.553398 0.875
93 PR8 0.553398 0.843373
94 VO4 ADP 0.55102 0.884615
95 ALF ADP 0.55102 0.817073
96 A22 0.55 0.896104
97 JNT 0.54902 0.860759
98 FYA 0.548077 0.848101
99 B5Y 0.54717 0.910256
100 B5M 0.54717 0.910256
101 25A 0.544554 0.907895
102 OZV 0.544554 0.883117
103 MYR AMP 0.542857 0.833333
104 ARG AMP 0.541284 0.823529
105 48N 0.540541 0.8875
106 52H 0.54 0.816092
107 YLB 0.539823 0.835294
108 YLC 0.539823 0.855422
109 ADQ 0.539216 0.884615
110 A3R 0.539216 0.829268
111 LSS 0.539216 0.797753
112 9SN 0.537736 0.864198
113 4UV 0.537037 0.886076
114 TAD 0.536364 0.831325
115 G5A 0.536082 0.775281
116 53H 0.534653 0.816092
117 KMQ 0.53271 0.897436
118 TYM 0.530973 0.897436
119 SSA 0.53 0.775281
120 SMM 0.53 0.744186
121 LEU LMS 0.528846 0.786517
122 AOC 0.527473 0.769231
123 GA7 0.527273 0.85
124 7MD 0.527273 0.855422
125 4UU 0.527273 0.886076
126 YLA 0.525862 0.813953
127 ADN 0.52439 0.766234
128 RAB 0.52439 0.766234
129 XYA 0.52439 0.766234
130 5CD 0.52381 0.753247
131 AMP DBH 0.522936 0.8375
132 DQV 0.522523 0.896104
133 4UW 0.522124 0.9
134 AYB 0.521368 0.825581
135 5CA 0.519608 0.775281
136 NVA LMS 0.519231 0.769231
137 JB6 0.518868 0.829268
138 BIS 0.518868 0.851852
139 OMR 0.517544 0.845238
140 F2R 0.516949 0.835294
141 3DH 0.516854 0.746835
142 ADP BMA 0.514286 0.860759
143 25L 0.514019 0.896104
144 7MC 0.513043 0.857143
145 AP0 0.513043 0.841463
146 5N5 0.511905 0.74359
147 MTA 0.511364 0.769231
148 A3P 0.510638 0.906667
149 NSS 0.509615 0.775281
150 DSZ 0.509615 0.795455
151 TXD 0.508772 0.851852
152 NAI 0.508772 0.851852
153 DND 0.508772 0.897436
154 A4D 0.505882 0.74359
155 EP4 0.505747 0.772152
156 8X1 0.504854 0.75
157 ATP A 0.504587 0.87013
158 ATP A A A 0.504587 0.87013
159 AHZ 0.504425 0.833333
160 LAQ 0.504425 0.833333
161 TXE 0.504348 0.851852
162 AF3 ADP 3PG 0.504348 0.831325
163 ALF ADP 3PG 0.504348 0.831325
164 IOT 0.504274 0.825581
165 DTA 0.5 0.7375
166 M2T 0.5 0.753086
167 6RE 0.5 0.714286
168 L3W 0.5 0.873418
169 COD 0.5 0.806818
170 AFH 0.5 0.831325
171 CNA 0.495798 0.873418
172 NAX 0.495652 0.821429
173 6V0 0.495652 0.841463
174 GTA 0.495575 0.878049
175 KAA 0.495327 0.75
176 GSU 0.495327 0.795455
177 P5A 0.495327 0.741935
178 YLY 0.491935 0.825581
179 G3A 0.491071 0.864198
180 9K8 0.490741 0.731183
181 O02 0.49 0.864198
182 H1Q 0.489796 0.846154
183 5X8 0.489796 0.759494
184 J7C 0.489362 0.722892
185 7D5 0.488889 0.822785
186 NAD TDB 0.487179 0.883117
187 NAD IBO 0.487179 0.883117
188 LPA AMP 0.486957 0.811765
189 AR6 AR6 0.486726 0.883117
190 G5P 0.486726 0.864198
191 YSA 0.486486 0.775281
192 S7M 0.485437 0.709302
193 SAM 0.485149 0.729412
194 6MZ 0.484211 0.92
195 DZD 0.483607 0.831325
196 5AD 0.481928 0.72
197 EEM 0.480392 0.729412
198 PAP 0.48 0.894737
199 SA8 0.48 0.746988
200 A3D 0.479675 0.909091
201 80F 0.479675 0.813953
202 A2P 0.479167 0.893333
203 3AM 0.478261 0.868421
204 8PZ 0.477477 0.775281
205 NAD 0.47541 0.896104
206 T5A 0.475 0.813953
207 A3T 0.474747 0.792208
208 SFG 0.474747 0.746835
209 A3N 0.473684 0.716049
210 IMO 0.473684 0.868421
211 B1U 0.473214 0.734043
212 NAQ 0.472441 0.8875
213 BT5 0.471545 0.825581
214 NWW 0.471264 0.710526
215 6IA 0.470588 0.831325
216 V3L 0.470588 0.933333
217 A4P 0.470588 0.795455
218 UP5 0.470085 0.8625
219 2A5 0.47 0.8375
220 S4M 0.46875 0.666667
221 N0B 0.46875 0.813953
222 GJV 0.46875 0.705882
223 J4G 0.46789 0.910256
224 2AM 0.467391 0.857143
225 PPS 0.466019 0.8
226 NAJ PZO 0.464 0.841463
227 MAO 0.463918 0.776471
228 SXZ 0.463636 0.75
229 AMP NAD 0.463415 0.896104
230 NEC 0.463158 0.721519
231 A3G 0.463158 0.75
232 ADJ 0.46281 0.802326
233 UPA 0.462185 0.851852
234 4TC 0.462185 0.841463
235 2SA 0.461538 0.897436
236 SAI 0.460784 0.731707
237 SAH 0.460784 0.740741
238 ZAS 0.457447 0.740741
239 M24 0.456693 0.865854
240 A3S 0.454545 0.759494
241 WSA 0.453782 0.784091
242 0UM 0.453704 0.717647
243 7D3 0.453608 0.825
244 D4F 0.453125 0.833333
245 NAE 0.453125 0.886076
246 OVE 0.452632 0.825
247 6AD 0.451923 0.876543
248 FB0 0.451852 0.8
249 4TA 0.451613 0.802326
250 NWQ 0.451613 0.736842
251 BTX 0.451613 0.813953
252 ATR 0.45098 0.881579
253 139 0.45082 0.821429
254 EAD 0.450382 0.843373
255 7D4 0.45 0.825
256 MHZ 0.45 0.715909
257 NAJ PYZ 0.449612 0.802326
258 DSH 0.447917 0.682353
259 2VA 0.445545 0.794872
260 QXG 0.445455 0.752809
261 QXP 0.444444 0.761364
262 GEK 0.444444 0.73494
263 4YB 0.444444 0.777778
264 A7D 0.44 0.728395
265 7C5 0.439655 0.8125
266 A2R 0.439252 0.921053
267 8Q2 0.438017 0.75
268 P1H 0.437037 0.823529
269 KOY 0.436975 0.797468
270 A5D 0.436893 0.7375
271 62X 0.436364 0.724138
272 ITT 0.435644 0.857143
273 ZID 0.435115 0.884615
274 71V 0.434343 0.829268
275 N5O 0.43299 0.716049
276 SO8 0.432692 0.78481
277 6C6 0.432692 0.82716
278 HFD 0.432692 0.8625
279 JSQ 0.432692 0.8625
280 K15 0.432432 0.701149
281 6FA 0.431655 0.835294
282 V47 0.429907 0.779221
283 649 0.429752 0.741935
284 3NZ 0.428571 0.777778
285 R2V 0.428571 0.761364
286 K2K 0.428571 0.674419
287 Y3J 0.426966 0.679487
288 NDE 0.426471 0.897436
289 AMZ 0.425532 0.857143
290 C2R 0.425532 0.87013
291 38V 0.424242 0.833333
292 N5A 0.424242 0.691358
293 FNK 0.423611 0.8
294 ARU 0.423423 0.831325
295 K2H 0.423423 0.731707
296 NVA 2AD 0.423077 0.73494
297 KY2 0.422018 0.689655
298 PGS 0.421569 0.807229
299 Z5A 0.421053 0.795455
300 KB1 0.421053 0.697674
301 NA7 0.419643 0.873418
302 VRT 0.419048 0.743902
303 AVV 0.418182 0.819277
304 6K6 0.418182 0.87013
305 CUU 0.417476 0.883117
306 0WD 0.417323 0.864198
307 FAD 0.415493 0.845238
308 FAS 0.415493 0.845238
309 DCA 0.415385 0.818182
310 ETB 0.415385 0.848837
311 3AT 0.415094 0.883117
312 KYB 0.414414 0.689655
313 K3K 0.413793 0.731707
314 NO7 0.412844 0.85
315 O05 0.412281 0.775281
316 DZ4 0.411215 0.82716
317 AAT 0.411215 0.666667
318 KYE 0.410256 0.712644
319 NDC 0.410072 0.841463
320 0T1 0.409091 0.818182
321 COA 0.409091 0.818182
322 7D7 0.409091 0.696203
323 D3Y 0.409091 0.740741
324 KH3 0.408333 0.693182
325 KXW 0.408333 0.705882
326 AV2 0.407407 0.835443
327 A6D 0.40708 0.701149
328 PO4 PO4 A A A A PO4 0.40708 0.844156
329 K3E 0.40678 0.722892
330 ACO 0.404412 0.791209
331 FDA 0.404255 0.827586
332 NAD CJ3 0.40411 0.786517
333 DA 0.40404 0.822785
334 D5M 0.40404 0.822785
335 NIA 0.402062 0.795181
336 NX8 0.401869 0.674419
337 FAY 0.401361 0.833333
338 COS 0.4 0.8
339 30N 0.4 0.75
340 AAM 0.4 0.906667
341 K2R 0.4 0.871795
342 NAD BBN 0.4 0.813953
343 AMX 0.4 0.827586
344 2MC 0.4 0.765957
345 CAO 0.4 0.791209
Similar Ligands (3D)
Ligand no: 1; Ligand: 9ZA; Similar ligands found: 1
No: Ligand Similarity coefficient
1 KB7 0.8545
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5WA9; Ligand: 9ZD; 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: 5wa9.bio1) has 45 residues
No: Leader PDB Ligand Sequence Similarity
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