-->
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 (18)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 253 families.
1 5IPC Kd = 13 uM 6CE C20 H24 N7 O6 P S c1ccc2c(c1....
2 4EQG - A5A C13 H19 N7 O7 S C[C@@H](C(....
3 5I2E Kd = 0.23 uM 67D C23 H23 N7 O7 S c1ccc2c(c1....
4 3O1C - ADN C10 H13 N5 O4 c1nc(c2c(n....
5 5IPE - 6CG C10 H14 N5 O7 P S c1nc2c(n1[....
6 4RHN - RIB C5 H10 O5 C([C@@H]1[....
7 3O1X - ADN C10 H13 N5 O4 c1nc(c2c(n....
8 4ZKL - JB6 C24 H34 N10 O13 P2 S2 c1nc(c2c(n....
9 3QGZ - ADN C10 H13 N5 O4 c1nc(c2c(n....
10 5I2F - BS5 C20 H29 N9 O7 S2 c1nc(c2c(n....
11 1KPF - AMP C10 H14 N5 O7 P c1nc(c2c(n....
12 5WA9 Kd = 0.175 uM 9ZD C14 H21 N6 O8 P C[C@H](C(=....
13 4EQH - WSA C21 H24 N8 O7 S c1ccc2c(c1....
14 1RZY Ki = 1.25 uM 5AS C12 H18 N6 O6 S CCNS(=O)(=....
15 4EQE - KAA C16 H26 N8 O7 S c1nc(c2c(n....
16 5WA8 Kd = 0.587 uM 9ZA C14 H21 N6 O8 P C[C@@H](C(....
17 6B42 - D5M C10 H14 N5 O6 P c1nc(c2c(n....
18 3RHN - 5GP C10 H14 N5 O8 P c1nc2c(n1[....
70% Homology Family (20)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 209 families.
1 5IPC Kd = 13 uM 6CE C20 H24 N7 O6 P S c1ccc2c(c1....
2 4EQG - A5A C13 H19 N7 O7 S C[C@@H](C(....
3 5I2E Kd = 0.23 uM 67D C23 H23 N7 O7 S c1ccc2c(c1....
4 3O1C - ADN C10 H13 N5 O4 c1nc(c2c(n....
5 5IPE - 6CG C10 H14 N5 O7 P S c1nc2c(n1[....
6 4RHN - RIB C5 H10 O5 C([C@@H]1[....
7 3O1X - ADN C10 H13 N5 O4 c1nc(c2c(n....
8 4ZKL - JB6 C24 H34 N10 O13 P2 S2 c1nc(c2c(n....
9 3QGZ - ADN C10 H13 N5 O4 c1nc(c2c(n....
10 5I2F - BS5 C20 H29 N9 O7 S2 c1nc(c2c(n....
11 1KPF - AMP C10 H14 N5 O7 P c1nc(c2c(n....
12 5WA9 Kd = 0.175 uM 9ZD C14 H21 N6 O8 P C[C@H](C(=....
13 4EQH - WSA C21 H24 N8 O7 S c1ccc2c(c1....
14 1RZY Ki = 1.25 uM 5AS C12 H18 N6 O6 S CCNS(=O)(=....
15 4EQE - KAA C16 H26 N8 O7 S c1nc(c2c(n....
16 5WA8 Kd = 0.587 uM 9ZA C14 H21 N6 O8 P C[C@@H](C(....
17 6B42 - D5M C10 H14 N5 O6 P c1nc(c2c(n....
18 3RHN - 5GP C10 H14 N5 O8 P c1nc2c(n1[....
19 5RHN - 8BR C10 H13 Br N5 O7 P c1nc(c2c(n....
20 4INI - AMP C10 H14 N5 O7 P c1nc(c2c(n....
50% Homology Family (22)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 173 families.
1 5IPC Kd = 13 uM 6CE C20 H24 N7 O6 P S c1ccc2c(c1....
2 4EQG - A5A C13 H19 N7 O7 S C[C@@H](C(....
3 5I2E Kd = 0.23 uM 67D C23 H23 N7 O7 S c1ccc2c(c1....
4 3O1C - ADN C10 H13 N5 O4 c1nc(c2c(n....
5 5IPE - 6CG C10 H14 N5 O7 P S c1nc2c(n1[....
6 4RHN - RIB C5 H10 O5 C([C@@H]1[....
7 3O1X - ADN C10 H13 N5 O4 c1nc(c2c(n....
8 4ZKL - JB6 C24 H34 N10 O13 P2 S2 c1nc(c2c(n....
9 3QGZ - ADN C10 H13 N5 O4 c1nc(c2c(n....
10 5I2F - BS5 C20 H29 N9 O7 S2 c1nc(c2c(n....
11 1KPF - AMP C10 H14 N5 O7 P c1nc(c2c(n....
12 5WA9 Kd = 0.175 uM 9ZD C14 H21 N6 O8 P C[C@H](C(=....
13 4EQH - WSA C21 H24 N8 O7 S c1ccc2c(c1....
14 1RZY Ki = 1.25 uM 5AS C12 H18 N6 O6 S CCNS(=O)(=....
15 4EQE - KAA C16 H26 N8 O7 S c1nc(c2c(n....
16 5WA8 Kd = 0.587 uM 9ZA C14 H21 N6 O8 P C[C@@H](C(....
17 6B42 - D5M C10 H14 N5 O6 P c1nc(c2c(n....
18 3RHN - 5GP C10 H14 N5 O8 P c1nc2c(n1[....
19 5RHN - 8BR C10 H13 Br N5 O7 P c1nc(c2c(n....
20 3N1T - 5GP C10 H14 N5 O8 P c1nc2c(n1[....
21 3N1S - 5GP C10 H14 N5 O8 P c1nc2c(n1[....
22 4INI - AMP C10 H14 N5 O7 P c1nc(c2c(n....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 9ZD; Similar ligands found: 301
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 AMP 0.670732 0.906667
6 A 0.670732 0.906667
7 ABM 0.666667 0.907895
8 AP2 0.651163 0.873418
9 A12 0.651163 0.873418
10 CA0 0.647727 0.909091
11 A2D 0.647059 0.883117
12 TXA 0.642857 0.922078
13 8QN 0.642105 0.946667
14 BA3 0.632184 0.883117
15 DAL AMP 0.631579 0.921053
16 M33 0.629214 0.921053
17 SRP 0.62766 0.897436
18 ADP 0.625 0.907895
19 AP5 0.625 0.883117
20 B4P 0.625 0.883117
21 SRA 0.623529 0.860759
22 PAJ 0.618557 0.9
23 AT4 0.617977 0.873418
24 AN2 0.617977 0.921053
25 APC 0.615385 0.873418
26 PRX 0.615385 0.860759
27 ANP 0.612903 0.909091
28 GAP 0.612903 0.884615
29 ADX 0.611111 0.8
30 AD9 0.608696 0.884615
31 RBY 0.608696 0.873418
32 ADV 0.608696 0.873418
33 ACP 0.604396 0.884615
34 HEJ 0.604396 0.907895
35 ATP 0.604396 0.907895
36 50T 0.604396 0.871795
37 4AD 0.602041 0.886076
38 AMO 0.602041 0.897436
39 SON 0.6 0.922078
40 5FA 0.597826 0.907895
41 APR 0.597826 0.907895
42 AQP 0.597826 0.907895
43 AR6 0.597826 0.907895
44 AHX 0.59596 0.864198
45 PTJ 0.594059 0.935897
46 ME8 0.594059 0.878049
47 NB8 0.594059 0.8875
48 SAP 0.591398 0.8625
49 AGS 0.591398 0.8625
50 OAD 0.59 0.934211
51 LAD 0.584158 0.853659
52 MAP 0.581633 0.886076
53 DLL 0.58 0.921053
54 T99 0.578947 0.873418
55 ACQ 0.578947 0.884615
56 TAT 0.578947 0.873418
57 FA5 0.576923 0.897436
58 OOB 0.575758 0.921053
59 ADP PO3 0.574468 0.881579
60 9X8 0.574257 0.886076
61 A5A 0.56701 0.823529
62 ATF 0.56701 0.873418
63 TSB 0.565657 0.813953
64 00A 0.564356 0.875
65 1ZZ 0.563107 0.855422
66 3OD 0.563107 0.934211
67 YAP 0.561905 0.886076
68 6YZ 0.561224 0.884615
69 5SV 0.56 0.819277
70 3UK 0.558824 0.909091
71 LMS 0.556818 0.8
72 XAH 0.556604 0.833333
73 VMS 0.555556 0.825581
74 54H 0.555556 0.825581
75 YLP 0.554545 0.835294
76 A1R 0.554455 0.829268
77 5AS 0.554348 0.775281
78 WAQ 0.553398 0.875
79 PR8 0.553398 0.843373
80 B5V 0.553398 0.897436
81 ALF ADP 0.55102 0.817073
82 ADP ALF 0.55102 0.817073
83 A22 0.55 0.896104
84 FYA 0.548077 0.848101
85 B5Y 0.54717 0.910256
86 B5M 0.54717 0.910256
87 ADP VO4 0.545455 0.871795
88 VO4 ADP 0.545455 0.871795
89 25A 0.544554 0.907895
90 MYR AMP 0.542857 0.833333
91 ARG AMP 0.541284 0.823529
92 48N 0.540541 0.8875
93 52H 0.54 0.816092
94 YLC 0.539823 0.855422
95 YLB 0.539823 0.835294
96 LSS 0.539216 0.797753
97 A3R 0.539216 0.829268
98 ADQ 0.539216 0.884615
99 9SN 0.537736 0.864198
100 TYR AMP 0.537037 0.8625
101 4UV 0.537037 0.886076
102 TAD 0.536364 0.831325
103 G5A 0.536082 0.775281
104 53H 0.534653 0.816092
105 TYM 0.530973 0.897436
106 SMM 0.53 0.744186
107 SSA 0.53 0.775281
108 LEU LMS 0.528846 0.788889
109 AOC 0.527473 0.769231
110 GA7 0.527273 0.85
111 4UU 0.527273 0.886076
112 7MD 0.527273 0.855422
113 YLA 0.525862 0.813953
114 RAB 0.52439 0.766234
115 ADN 0.52439 0.766234
116 XYA 0.52439 0.766234
117 5CD 0.52381 0.753247
118 AMP DBH 0.522936 0.8375
119 DQV 0.522523 0.896104
120 4UW 0.522124 0.9
121 AYB 0.521368 0.825581
122 5CA 0.519608 0.775281
123 NVA LMS 0.519231 0.769231
124 JB6 0.518868 0.829268
125 BIS 0.518868 0.851852
126 OMR 0.517544 0.845238
127 F2R 0.516949 0.835294
128 3DH 0.516854 0.746835
129 ADP BMA 0.514286 0.860759
130 25L 0.514019 0.896104
131 7MC 0.513043 0.857143
132 AP0 0.513043 0.841463
133 5N5 0.511905 0.74359
134 MTA 0.511364 0.769231
135 A3P 0.510638 0.906667
136 DSZ 0.509615 0.795455
137 NSS 0.509615 0.775281
138 A A 0.509434 0.883117
139 NXX 0.508772 0.897436
140 NAI 0.508772 0.851852
141 DND 0.508772 0.897436
142 TXD 0.508772 0.851852
143 A4D 0.505882 0.74359
144 EP4 0.505747 0.772152
145 8X1 0.504854 0.75
146 ATP A A A 0.504587 0.87013
147 LAQ 0.504425 0.833333
148 AHZ 0.504425 0.833333
149 TXE 0.504348 0.851852
150 AF3 ADP 3PG 0.504348 0.831325
151 IOT 0.504274 0.825581
152 COD 0.5 0.806818
153 DTA 0.5 0.7375
154 AFH 0.5 0.831325
155 M2T 0.5 0.753086
156 6RE 0.5 0.714286
157 CNA 0.495798 0.873418
158 6V0 0.495652 0.841463
159 NAX 0.495652 0.821429
160 GTA 0.495575 0.878049
161 KAA 0.495327 0.75
162 P5A 0.495327 0.741935
163 GSU 0.495327 0.795455
164 YLY 0.491935 0.825581
165 G3A 0.491071 0.864198
166 9K8 0.490741 0.731183
167 5X8 0.489796 0.759494
168 J7C 0.489362 0.722892
169 7D5 0.488889 0.822785
170 LPA AMP 0.486957 0.811765
171 G5P 0.486726 0.864198
172 AR6 AR6 0.486726 0.883117
173 YSA 0.486486 0.775281
174 S7M 0.485437 0.709302
175 SAM 0.485149 0.729412
176 DZD 0.483607 0.831325
177 5AD 0.481928 0.72
178 EEM 0.480392 0.729412
179 SA8 0.48 0.746988
180 PAP 0.48 0.894737
181 80F 0.479675 0.813953
182 A3D 0.479675 0.909091
183 A2P 0.479167 0.893333
184 3AM 0.478261 0.868421
185 8PZ 0.477477 0.775281
186 NAD 0.47541 0.896104
187 T5A 0.475 0.813953
188 A3T 0.474747 0.792208
189 SFG 0.474747 0.746835
190 A3N 0.473684 0.716049
191 IMO 0.473684 0.868421
192 NAQ 0.472441 0.8875
193 BT5 0.471545 0.825581
194 6IA 0.470588 0.831325
195 V3L 0.470588 0.933333
196 A4P 0.470588 0.795455
197 UP5 0.470085 0.8625
198 2A5 0.47 0.8375
199 N0B 0.46875 0.813953
200 GJV 0.46875 0.705882
201 S4M 0.46875 0.666667
202 2AM 0.467391 0.857143
203 PPS 0.466019 0.8
204 NAJ PZO 0.464 0.841463
205 MAO 0.463918 0.776471
206 SXZ 0.463636 0.75
207 AMP NAD 0.463415 0.896104
208 A3G 0.463158 0.75
209 NEC 0.463158 0.721519
210 ADJ 0.46281 0.802326
211 UPA 0.462185 0.851852
212 4TC 0.462185 0.841463
213 2SA 0.461538 0.897436
214 SAI 0.460784 0.731707
215 SAH 0.460784 0.740741
216 ZAS 0.457447 0.740741
217 M24 0.456693 0.865854
218 A3S 0.454545 0.759494
219 WSA 0.453782 0.784091
220 0UM 0.453704 0.717647
221 7D3 0.453608 0.825
222 NAE 0.453125 0.886076
223 OVE 0.452632 0.825
224 6AD 0.451923 0.876543
225 FB0 0.451852 0.8
226 BTX 0.451613 0.813953
227 4TA 0.451613 0.802326
228 ATR 0.45098 0.881579
229 139 0.45082 0.821429
230 EAD 0.450382 0.843373
231 MHZ 0.45 0.715909
232 7D4 0.45 0.825
233 NAJ PYZ 0.449612 0.802326
234 DSH 0.447917 0.682353
235 2VA 0.445545 0.794872
236 A A A 0.445455 0.848101
237 GEK 0.444444 0.73494
238 4YB 0.444444 0.777778
239 G A A A 0.44 0.841463
240 A7D 0.44 0.728395
241 7C5 0.439655 0.8125
242 A2R 0.439252 0.921053
243 8Q2 0.438017 0.75
244 P1H 0.437037 0.823529
245 A5D 0.436893 0.7375
246 62X 0.436364 0.724138
247 ITT 0.435644 0.857143
248 ZID 0.435115 0.884615
249 71V 0.434343 0.829268
250 HFD 0.432692 0.8625
251 SO8 0.432692 0.78481
252 6C6 0.432692 0.82716
253 K15 0.432432 0.701149
254 6FA 0.431655 0.835294
255 649 0.429752 0.741935
256 A G 0.428571 0.851852
257 3NZ 0.428571 0.777778
258 Y3J 0.426966 0.679487
259 NDE 0.426471 0.897436
260 AMZ 0.425532 0.857143
261 C2R 0.425532 0.87013
262 U A G G 0.425197 0.851852
263 FNK 0.423611 0.8
264 ARU 0.423423 0.831325
265 NVA 2AD 0.423077 0.73494
266 PGS 0.421569 0.807229
267 KB1 0.421053 0.697674
268 Z5A 0.421053 0.795455
269 NA7 0.419643 0.873418
270 VRT 0.419048 0.743902
271 U A 0.418605 0.875
272 6K6 0.418182 0.87013
273 AVV 0.418182 0.819277
274 0WD 0.417323 0.864198
275 FAS 0.415493 0.845238
276 FAD 0.415493 0.845238
277 ETB 0.415385 0.848837
278 DCA 0.415385 0.818182
279 3AT 0.415094 0.883117
280 AAT 0.411215 0.666667
281 NDC 0.410072 0.841463
282 D3Y 0.409091 0.740741
283 7D7 0.409091 0.696203
284 COA 0.409091 0.818182
285 0T1 0.409091 0.818182
286 KH3 0.408333 0.693182
287 AV2 0.407407 0.835443
288 PO4 PO4 A A A A PO4 0.40708 0.844156
289 A6D 0.40708 0.701149
290 ACO 0.404412 0.791209
291 FDA 0.404255 0.827586
292 D5M 0.40404 0.822785
293 DA 0.40404 0.822785
294 NIA 0.402062 0.795181
295 FAY 0.401361 0.833333
296 AAM 0.4 0.906667
297 CAO 0.4 0.791209
298 30N 0.4 0.75
299 COS 0.4 0.8
300 AMX 0.4 0.827586
301 2MC 0.4 0.765957
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: 72
This union binding pocket(no: 1) in the query (biounit: 5wa9.bio1) has 45 residues
No: Leader PDB Ligand Sequence Similarity
1 4JGP PYR None
2 1S68 AMP None
3 3LQV ADE None
4 1DCP HBI None
5 5XG5 A2G None
6 4LWU 20U None
7 2ZQO NGA None
8 1OFZ FUC None
9 2AGC DAO None
10 2HO2 PRO PRO PRO PRO PRO PRO PRO PRO PRO LEU None
11 4CSD MFU 2.32558
12 5MUA GAL 2.32558
13 4CS9 AMP 3.10078
14 3OCP CMP 3.10078
15 5IM3 DTP 3.10078
16 1WRA PC 3.10078
17 6F7X MFU 3.33333
18 2BMB PMM 3.87597
19 5AVF TAU 4.65116
20 4LH7 1X8 4.65116
21 3PTG 932 4.65116
22 5CDH TLA 4.65116
23 1NBU PH2 5.04202
24 2QL9 CIT 5.15464
25 2XOC ADP 5.42636
26 1SQL GUN 5.42636
27 6F9G PUT 5.42636
28 1U6R IOM 5.42636
29 3DLS ADP 5.42636
30 5BV3 M7G 6.20155
31 4FGC PQ0 6.20155
32 5TKL G3H 6.20155
33 5F90 GLA GAL 6.20155
34 3KLL MAL 6.20155
35 5ME4 HP4 6.20155
36 3VSV XYS 6.20155
37 5F90 GLA GAL BGC 5VQ 6.20155
38 2PNC CLU 6.20155
39 1VRP IOM 6.20155
40 3ZW2 NAG GAL FUC 6.89655
41 3ZW0 FUC 6.89655
42 3ZW2 GLA NAG GAL FUC 6.89655
43 4IPN 1FT 6.97674
44 1SZ0 M6P 6.97674
45 4NFE BEN 7.75194
46 4AVB CMP 7.75194
47 1LCK GLU GLY GLN PTR GLN PRO GLN PRO ALA 7.75194
48 6EOM ALA LYS 7.75194
49 3ANY 2A3 9.30233
50 5OKT 9XK 9.30233
51 3BP1 GUN 10.0775
52 4BTV RB3 10.0775
53 5COU ATP 10.0775
54 2AF6 FAD 10.8527
55 6GR0 F8W 10.8527
56 1OIJ AKG 11.6279
57 1YQC GLV 12.4031
58 5KK4 44E 12.5
59 4CQK PIO 12.766
60 4YMJ 4EJ 13.1783
61 3FSY SCA 14.4578
62 6E8I PTR 15.5039
63 4PZ6 GMP 15.5039
64 1M0W ANP 15.5039
65 5HVJ ANP 17.0543
66 3X01 AMP 26.3566
67 2Q4H AMP 27.1318
68 5FIT AP2 27.907
69 3TY5 ADP 32.5581
70 3TY5 ATP 32.5581
71 4XBA GMP 33.3333
72 4XBA 5GP 33.3333
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