Receptor
PDB id Resolution Class Description Source Keywords
6N3X 1.1 Å EC: 3.-.-.- HUMAN HISTIDINE TRIAD NUCLEOTIDE BINDING PROTEIN 1 (HINT1) W 5'-O-[1-BENZYL]CARBAMOYL GUANOSINE HOMO SAPIENS HINT HISTIDINE TRIAD HIT HYDROLASE
Ref.: INHIBITION OF HINT1 MODULATES SPINAL NOCICEPTION AN EVOKED BEHAVIOR IN MICE. ACS CHEM NEUROSCI V. 10 4385 2019
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
KBD A:201;
 Valid;
 Atoms found MORE than expected: % Diff = 1.2;
 Kd = 8.09 uM
416.388 C18 H20 N6 O6 c1ccc...
EDO A:202;
A:203;
 Invalid;
Invalid;
 none;
none;
 submit data
62.068 C2 H6 O2 C(CO)...
CL B:201;
 Invalid;
 none;
 submit data
35.453 Cl [Cl-]
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: KBD; Similar ligands found: 82
No: Ligand ECFP6 Tc MDL keys Tc
1 KBD 1 1
2 KBJ 0.789474 0.961039
3 KB7 0.772727 0.947368
4 5GP 0.612903 0.8375
5 G 0.612903 0.8375
6 GP3 0.587629 0.851852
7 GP2 0.581633 0.797619
8 GDP 0.581633 0.82716
9 GMV 0.58 0.807229
10 GMP 0.579545 0.88
11 GNH 0.575758 0.817073
12 G1R 0.574257 0.839506
13 GCP 0.574257 0.807229
14 9GM 0.568627 0.807229
15 GNP 0.568627 0.807229
16 GTP 0.564356 0.82716
17 Y9Z 0.559633 0.793103
18 G2P 0.553398 0.797619
19 GSP 0.553398 0.788235
20 ALF 5GP 0.54902 0.77907
21 GDP BEF 0.543689 0.817073
22 GAV 0.542857 0.797619
23 G2R 0.542056 0.819277
24 GTP MG 0.538462 0.8375
25 GDP AF3 0.53271 0.77907
26 3GP 0.525773 0.825
27 GPG 0.522936 0.864198
28 GDP ALF 0.518519 0.77907
29 GFB 0.513274 0.841463
30 GDR 0.513274 0.841463
31 GTG 0.513274 0.821429
32 JB3 0.512605 0.831325
33 YGP 0.508929 0.790698
34 GDX 0.508621 0.851852
35 NGD 0.508333 0.841463
36 DBG 0.507812 0.831325
37 GDC 0.504425 0.864198
38 GDD 0.504425 0.864198
39 GKE 0.504425 0.864198
40 JB2 0.5 0.841463
41 GPD 0.495726 0.811765
42 6CK 0.495652 0.821429
43 G3A 0.495652 0.851852
44 GDP 7MG 0.491379 0.841463
45 G5P 0.491379 0.851852
46 GKD 0.487179 0.864198
47 FEG 0.483607 0.813953
48 G3D 0.481481 0.814815
49 ZGP 0.479675 0.784091
50 CAG 0.472441 0.775281
51 2GP 0.465347 0.814815
52 MGD 0.460938 0.764045
53 2MD 0.460317 0.764045
54 U2G 0.459677 0.821429
55 G4P 0.459459 0.814815
56 0O2 0.45614 0.814815
57 CG2 0.452381 0.821429
58 BGO 0.448 0.831325
59 PGD 0.44697 0.790698
60 MD1 0.44697 0.764045
61 TPG 0.440298 0.741935
62 FE9 0.439394 0.686869
63 GGM 0.4375 0.811765
64 G1R G1R 0.42963 0.853659
65 I2C FE2 CMO CMO 0.428571 0.731183
66 AKW 0.425197 0.781609
67 5GP 5GP 0.422018 0.8125
68 HHJ 0.420635 0.961039
69 P1G 0.420561 0.780488
70 G4M 0.41958 0.837209
71 PGD O 0.416058 0.731183
72 P2G 0.415094 0.790123
73 35G 0.412844 0.8125
74 C2E 0.412844 0.825
75 PCG 0.412844 0.8125
76 GH3 0.412281 0.804878
77 MGQ 0.408696 0.864198
78 DG 0.40566 0.795181
79 DGP 0.40566 0.795181
80 GPX 0.405172 0.780488
81 G C 0.40458 0.831325
82 SGP 0.401869 0.72093
Similar Ligands (3D)
Ligand no: 1; Ligand: KBD; Similar ligands found: 0
No: Ligand Similarity coefficient
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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