Receptor
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
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-]
9ZD A:201;
 Valid;
 none;
 Kd = 0.175 uM
432.326 C14 H21 N6 O8 P C[C@H...
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 283 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 235 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 193 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
Ligand no: 1; Ligand: 9ZD; Similar ligands found: 321
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 A 0.670732 0.906667
6 AMP 0.670732 0.906667
7 ABM 0.666667 0.907895
8 45A 0.666667 0.907895
9 8LH 0.663043 0.922078
10 A12 0.651163 0.873418
11 AP2 0.651163 0.873418
12 8LQ 0.648936 0.922078
13 CA0 0.647727 0.909091
14 A2D 0.647059 0.883117
15 TXA 0.642857 0.922078
16 8QN 0.642105 0.946667
17 KG4 0.640449 0.909091
18 BA3 0.632184 0.883117
19 DAL AMP 0.631579 0.921053
20 M33 0.629214 0.921053
21 SRP 0.62766 0.897436
22 ADP 0.625 0.907895
23 AP5 0.625 0.883117
24 B4P 0.625 0.883117
25 8LE 0.623656 0.935065
26 SRA 0.623529 0.860759
27 PAJ 0.618557 0.9
28 AT4 0.617977 0.873418
29 AN2 0.617977 0.921053
30 PRX 0.615385 0.860759
31 APC 0.615385 0.873418
32 ANP 0.612903 0.909091
33 GAP 0.612903 0.884615
34 ADX 0.611111 0.8
35 RBY 0.608696 0.873418
36 ADV 0.608696 0.873418
37 AD9 0.608696 0.884615
38 ACP 0.604396 0.884615
39 HEJ 0.604396 0.907895
40 ATP 0.604396 0.907895
41 50T 0.604396 0.871795
42 4AD 0.602041 0.886076
43 AMO 0.602041 0.897436
44 ADP MG 0.6 0.881579
45 SON 0.6 0.922078
46 AQP 0.597826 0.907895
47 AR6 0.597826 0.907895
48 APR 0.597826 0.907895
49 5FA 0.597826 0.907895
50 AHX 0.59596 0.864198
51 PTJ 0.594059 0.935897
52 NB8 0.594059 0.8875
53 ME8 0.594059 0.878049
54 AGS 0.591398 0.8625
55 SAP 0.591398 0.8625
56 OAD 0.59 0.934211
57 LAD 0.584158 0.853659
58 MAP 0.581633 0.886076
59 DLL 0.58 0.921053
60 ACQ 0.578947 0.884615
61 TAT 0.578947 0.873418
62 T99 0.578947 0.873418
63 FA5 0.576923 0.897436
64 OOB 0.575758 0.921053
65 ATP MG 0.574468 0.881579
66 ADP PO3 0.574468 0.881579
67 APC MG 0.574468 0.858974
68 9X8 0.574257 0.886076
69 A5A 0.56701 0.823529
70 ATF 0.56701 0.873418
71 TSB 0.565657 0.813953
72 00A 0.564356 0.875
73 3OD 0.563107 0.934211
74 1ZZ 0.563107 0.855422
75 YAP 0.561905 0.886076
76 6YZ 0.561224 0.884615
77 5SV 0.56 0.819277
78 3UK 0.558824 0.909091
79 LMS 0.556818 0.8
80 XAH 0.556604 0.833333
81 VMS 0.555556 0.825581
82 HQG 0.555556 0.921053
83 54H 0.555556 0.825581
84 YLP 0.554545 0.835294
85 A1R 0.554455 0.829268
86 5AS 0.554348 0.775281
87 WAQ 0.553398 0.875
88 PR8 0.553398 0.843373
89 B5V 0.553398 0.897436
90 ADP ALF 0.55102 0.817073
91 ALF ADP 0.55102 0.817073
92 A22 0.55 0.896104
93 FYA 0.548077 0.848101
94 B5M 0.54717 0.910256
95 B5Y 0.54717 0.910256
96 ADP VO4 0.545455 0.871795
97 VO4 ADP 0.545455 0.871795
98 25A 0.544554 0.907895
99 OZV 0.544554 0.883117
100 MYR AMP 0.542857 0.833333
101 ARG AMP 0.541284 0.823529
102 48N 0.540541 0.8875
103 52H 0.54 0.816092
104 YLC 0.539823 0.855422
105 YLB 0.539823 0.835294
106 LSS 0.539216 0.797753
107 A3R 0.539216 0.829268
108 ADQ 0.539216 0.884615
109 9SN 0.537736 0.864198
110 TYR AMP 0.537037 0.8625
111 4UV 0.537037 0.886076
112 TAD 0.536364 0.831325
113 G5A 0.536082 0.775281
114 53H 0.534653 0.816092
115 TYM 0.530973 0.897436
116 SSA 0.53 0.775281
117 SMM 0.53 0.744186
118 LEU LMS 0.528846 0.788889
119 AOC 0.527473 0.769231
120 7MD 0.527273 0.855422
121 4UU 0.527273 0.886076
122 GA7 0.527273 0.85
123 YLA 0.525862 0.813953
124 RAB 0.52439 0.766234
125 ADN 0.52439 0.766234
126 XYA 0.52439 0.766234
127 5CD 0.52381 0.753247
128 AMP DBH 0.522936 0.8375
129 DQV 0.522523 0.896104
130 4UW 0.522124 0.9
131 AYB 0.521368 0.825581
132 5CA 0.519608 0.775281
133 NVA LMS 0.519231 0.769231
134 BIS 0.518868 0.851852
135 JB6 0.518868 0.829268
136 OMR 0.517544 0.845238
137 F2R 0.516949 0.835294
138 3DH 0.516854 0.746835
139 ADP BMA 0.514286 0.860759
140 25L 0.514019 0.896104
141 7MC 0.513043 0.857143
142 AP0 0.513043 0.841463
143 5N5 0.511905 0.74359
144 MTA 0.511364 0.769231
145 A3P 0.510638 0.906667
146 NSS 0.509615 0.775281
147 DSZ 0.509615 0.795455
148 A A 0.509434 0.883117
149 NXX 0.508772 0.897436
150 NAI 0.508772 0.851852
151 TXD 0.508772 0.851852
152 DND 0.508772 0.897436
153 A4D 0.505882 0.74359
154 EP4 0.505747 0.772152
155 8X1 0.504854 0.75
156 ATP A A A 0.504587 0.87013
157 ATP A 0.504587 0.87013
158 AHZ 0.504425 0.833333
159 LAQ 0.504425 0.833333
160 AF3 ADP 3PG 0.504348 0.831325
161 TXE 0.504348 0.851852
162 IOT 0.504274 0.825581
163 COD 0.5 0.806818
164 M2T 0.5 0.753086
165 6RE 0.5 0.714286
166 DTA 0.5 0.7375
167 AFH 0.5 0.831325
168 CNA 0.495798 0.873418
169 6V0 0.495652 0.841463
170 NAX 0.495652 0.821429
171 GTA 0.495575 0.878049
172 P5A 0.495327 0.741935
173 GSU 0.495327 0.795455
174 KAA 0.495327 0.75
175 YLY 0.491935 0.825581
176 G3A 0.491071 0.864198
177 9K8 0.490741 0.731183
178 5X8 0.489796 0.759494
179 H1Q 0.489796 0.846154
180 J7C 0.489362 0.722892
181 7D5 0.488889 0.822785
182 LPA AMP 0.486957 0.811765
183 G5P 0.486726 0.864198
184 AR6 AR6 0.486726 0.883117
185 YSA 0.486486 0.775281
186 S7M 0.485437 0.709302
187 SAM 0.485149 0.729412
188 6MZ 0.484211 0.92
189 DZD 0.483607 0.831325
190 5AD 0.481928 0.72
191 EEM 0.480392 0.729412
192 PAP 0.48 0.894737
193 SA8 0.48 0.746988
194 80F 0.479675 0.813953
195 A3D 0.479675 0.909091
196 A2P 0.479167 0.893333
197 3AM 0.478261 0.868421
198 8PZ 0.477477 0.775281
199 NAD 0.47541 0.896104
200 T5A 0.475 0.813953
201 A3T 0.474747 0.792208
202 SFG 0.474747 0.746835
203 A3N 0.473684 0.716049
204 IMO 0.473684 0.868421
205 B1U 0.473214 0.734043
206 NAQ 0.472441 0.8875
207 BT5 0.471545 0.825581
208 6IA 0.470588 0.831325
209 V3L 0.470588 0.933333
210 A4P 0.470588 0.795455
211 UP5 0.470085 0.8625
212 2A5 0.47 0.8375
213 GJV 0.46875 0.705882
214 S4M 0.46875 0.666667
215 N0B 0.46875 0.813953
216 J4G 0.46789 0.910256
217 2AM 0.467391 0.857143
218 PPS 0.466019 0.8
219 NAJ PZO 0.464 0.841463
220 MAO 0.463918 0.776471
221 SXZ 0.463636 0.75
222 AMP NAD 0.463415 0.896104
223 A3G 0.463158 0.75
224 NEC 0.463158 0.721519
225 ADJ 0.46281 0.802326
226 UPA 0.462185 0.851852
227 4TC 0.462185 0.841463
228 2SA 0.461538 0.897436
229 SAH 0.460784 0.740741
230 SAI 0.460784 0.731707
231 ZAS 0.457447 0.740741
232 M24 0.456693 0.865854
233 A3S 0.454545 0.759494
234 WSA 0.453782 0.784091
235 0UM 0.453704 0.717647
236 7D3 0.453608 0.825
237 NAE 0.453125 0.886076
238 OVE 0.452632 0.825
239 6AD 0.451923 0.876543
240 FB0 0.451852 0.8
241 BTX 0.451613 0.813953
242 4TA 0.451613 0.802326
243 ATR 0.45098 0.881579
244 139 0.45082 0.821429
245 EAD 0.450382 0.843373
246 7D4 0.45 0.825
247 MHZ 0.45 0.715909
248 NAJ PYZ 0.449612 0.802326
249 DSH 0.447917 0.682353
250 2VA 0.445545 0.794872
251 A A A 0.445455 0.848101
252 GEK 0.444444 0.73494
253 4YB 0.444444 0.777778
254 G A A A 0.44 0.841463
255 A7D 0.44 0.728395
256 7C5 0.439655 0.8125
257 A2R 0.439252 0.921053
258 8Q2 0.438017 0.75
259 P1H 0.437037 0.823529
260 KOY 0.436975 0.797468
261 A5D 0.436893 0.7375
262 62X 0.436364 0.724138
263 ITT 0.435644 0.857143
264 ZID 0.435115 0.884615
265 71V 0.434343 0.829268
266 N5O 0.43299 0.716049
267 6C6 0.432692 0.82716
268 JSQ 0.432692 0.8625
269 HFD 0.432692 0.8625
270 SO8 0.432692 0.78481
271 K15 0.432432 0.701149
272 6FA 0.431655 0.835294
273 649 0.429752 0.741935
274 A G 0.428571 0.851852
275 3NZ 0.428571 0.777778
276 Y3J 0.426966 0.679487
277 NDE 0.426471 0.897436
278 AMZ 0.425532 0.857143
279 C2R 0.425532 0.87013
280 U A G G 0.425197 0.851852
281 N5A 0.424242 0.691358
282 FNK 0.423611 0.8
283 ARU 0.423423 0.831325
284 NVA 2AD 0.423077 0.73494
285 PGS 0.421569 0.807229
286 Z5A 0.421053 0.795455
287 KB1 0.421053 0.697674
288 NA7 0.419643 0.873418
289 VRT 0.419048 0.743902
290 U A 0.418605 0.875
291 AVV 0.418182 0.819277
292 6K6 0.418182 0.87013
293 0WD 0.417323 0.864198
294 FAD 0.415493 0.845238
295 FAS 0.415493 0.845238
296 DCA 0.415385 0.818182
297 ETB 0.415385 0.848837
298 3AT 0.415094 0.883117
299 NO7 0.412844 0.85
300 AAT 0.411215 0.666667
301 NDC 0.410072 0.841463
302 D3Y 0.409091 0.740741
303 0T1 0.409091 0.818182
304 7D7 0.409091 0.696203
305 COA 0.409091 0.818182
306 KH3 0.408333 0.693182
307 AV2 0.407407 0.835443
308 A6D 0.40708 0.701149
309 PO4 PO4 A A A A PO4 0.40708 0.844156
310 ACO 0.404412 0.791209
311 FDA 0.404255 0.827586
312 D5M 0.40404 0.822785
313 DA 0.40404 0.822785
314 NIA 0.402062 0.795181
315 FAY 0.401361 0.833333
316 AMX 0.4 0.827586
317 COS 0.4 0.8
318 2MC 0.4 0.765957
319 AAM 0.4 0.906667
320 30N 0.4 0.75
321 CAO 0.4 0.791209
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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