Receptor
PDB id Resolution Class Description Source Keywords
5VAD 2.36 Å EC: 6.1.1.17_6.1.1.15 CRYSTAL STRUCTURE OF HUMAN PROLYL-TRNA SYNTHETASE (PRS) IN C WITH INHIBITOR HOMO SAPIENS AMINOACYL-TRNA SYNTHETASE ATP DEPENDENT INHIBITOR LIGASE-INHIBITOR COMPLEX
Ref.: DISCOVERY OF A NOVEL PROLYL-TRNA SYNTHETASE INHIBIT ELUCIDATION OF ITS BINDING MODE TO THE ATP SITE IN WITH L-PROLINE. BIOCHEM. BIOPHYS. RES. V. 488 393 2017 COMMUN.
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
PRO A:1602;
B:1602;
Valid;
Valid;
none;
none;
submit data
115.13 C5 H9 N O2 C1C[C...
ZN B:1603;
A:1603;
Part of Protein;
Part of Protein;
none;
none;
submit data
65.409 Zn [Zn+2...
91Y A:1601;
B:1601;
Valid;
Valid;
none;
none;
Kd = 0.76 nM
364.441 C21 H24 N4 O2 c1ccc...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5VAD 2.36 Å EC: 6.1.1.17_6.1.1.15 CRYSTAL STRUCTURE OF HUMAN PROLYL-TRNA SYNTHETASE (PRS) IN C WITH INHIBITOR HOMO SAPIENS AMINOACYL-TRNA SYNTHETASE ATP DEPENDENT INHIBITOR LIGASE-INHIBITOR COMPLEX
Ref.: DISCOVERY OF A NOVEL PROLYL-TRNA SYNTHETASE INHIBIT ELUCIDATION OF ITS BINDING MODE TO THE ATP SITE IN WITH L-PROLINE. BIOCHEM. BIOPHYS. RES. V. 488 393 2017 COMMUN.
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 5VAD Kd = 0.76 nM 91Y C21 H24 N4 O2 c1ccc2c(c1....
2 4HVC - HFG C16 H17 Br Cl N3 O3 c1c2c(cc(c....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 5VAD Kd = 0.76 nM 91Y C21 H24 N4 O2 c1ccc2c(c1....
2 4HVC - HFG C16 H17 Br Cl N3 O3 c1c2c(cc(c....
50% Homology Family (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 4YDQ ic50 = 9 nM HFG C16 H17 Br Cl N3 O3 c1c2c(cc(c....
2 4Q15 ic50 = 275 nM HFG C16 H17 Br Cl N3 O3 c1c2c(cc(c....
3 5IFU ic50 = 34 uM GBM C23 H28 Cl N3 O5 S COc1ccc(cc....
4 4WI1 ic50 = 74 uM 3O6 C18 H13 F5 N4 O Cn1c(c(c(n....
5 5VAD Kd = 0.76 nM 91Y C21 H24 N4 O2 c1ccc2c(c1....
6 4HVC - HFG C16 H17 Br Cl N3 O3 c1c2c(cc(c....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: PRO; Similar ligands found: 3
No: Ligand ECFP6 Tc MDL keys Tc
1 PRO 1 1
2 YCP 0.769231 0.875
3 LPD 0.571429 0.722222
Ligand no: 2; Ligand: 91Y; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 91Y 1 1
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5VAD; Ligand: PRO; Similar sites found: 42
This union binding pocket(no: 1) in the query (biounit: 5vad.bio1) has 18 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3QVP FAD 0.0318 0.40746 1.74419
2 3HXU A5A 0.001877 0.44312 1.81406
3 2G30 ALA ALA PHE 0.003264 0.42679 1.93798
4 2ZTG A5A 0.001594 0.41778 2.02977
5 2CJ9 SSA 0.005112 0.41733 2.13178
6 3L5R 47X 0.04646 0.4188 2.45902
7 1YFS ALA 0.00003684 0.41716 2.7957
8 5U3B 7TD 0.01195 0.41415 3.01003
9 2Y6Q I7T 0.01389 0.42823 3.01508
10 1TT8 PHB 0.008797 0.4164 3.04878
11 1QY1 PRZ 0.0108 0.40592 3.44828
12 4P8K 38C 0.03183 0.41746 3.54167
13 3ACL 3F1 0.007731 0.40507 3.71622
14 4WCX MET 0.01459 0.40905 4.16667
15 3E9I XAH 0.002519 0.44668 4.25963
16 3MTX PGT 0.02292 0.40288 4.63576
17 4X6F 3XU 0.01318 0.42221 4.7619
18 2YKL NLD 0.001227 0.43234 5.09259
19 3DLG GWE 0.02742 0.42149 5.45455
20 5DKK FMN 0.005723 0.41507 5.51724
21 4HIA FMN 0.009077 0.42599 5.68182
22 1VYF OLA 0.01003 0.41068 5.92593
23 4I54 1C1 0.01337 0.41307 5.94901
24 4NS0 PIO 0.0001897 0.51452 6.01504
25 1KGI T4A 0.008542 0.41396 6.29921
26 3A5Y KAA 0.001282 0.45441 6.66667
27 4MNS 2AX 0.0287 0.41214 6.91824
28 3A5Z KAA 0.001749 0.44968 7.0122
29 2JDR GLY ARG PRO ARG THR THR SER PHE ALA GLU 0.03254 0.41369 7.01754
30 2JDR L20 0.03254 0.41369 7.01754
31 5T2Z 017 0.01819 0.40534 7.07071
32 5DQ8 FLF 0.003209 0.43396 7.08333
33 3FSM 2NC 0.02357 0.40559 7.38916
34 1X7D ORN 0.02137 0.41077 7.42857
35 2VDF OCT 0.000361 0.48927 8.3004
36 1QKQ MAN 0.002736 0.42532 10.5634
37 2J3M PRI 0.000005202 0.56485 11.4341
38 2J3M ATP 0.000006613 0.55761 11.4341
39 4V24 GYR 0.01765 0.40057 11.8598
40 2YIP YIO 0.01773 0.405 15.2174
41 4HWT 1B2 0.0006278 0.45917 20.0969
42 3IAL PR8 0.0000003159 0.61925 48.8417
Pocket No.: 2; Query (leader) PDB : 5VAD; Ligand: PRO; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 5vad.bio1) has 18 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 5VAD; Ligand: 91Y; Similar sites found: 41
This union binding pocket(no: 3) in the query (biounit: 5vad.bio1) has 33 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2XGT NSS 0.00005261 0.48126 1.37931
2 3HXU A5A 0.000004486 0.46666 1.81406
3 2G30 ALA ALA PHE 0.007514 0.42679 1.93798
4 2ZTG A5A 0.000001345 0.59256 2.02977
5 2CJ9 SSA 0.0000002058 0.49283 2.13178
6 3NEM ATP 0.0001511 0.52062 2.28311
7 3NEM AMO 0.00008203 0.47751 2.28311
8 3TEG DAH 0.004763 0.41792 2.40964
9 12AS AMP 0.0002061 0.43002 2.72727
10 1G51 AMO 0.0001391 0.43751 3.10345
11 1DZT ATY 0.02561 0.41515 3.27869
12 2V0U FMN 0.01288 0.40498 4.10959
13 3E9I XAH 0.00004491 0.46194 4.25963
14 1DZK PRZ 0.01554 0.40765 4.4586
15 5EFW FMN 0.01592 0.40077 5
16 4NS0 PIO 0.0004625 0.51829 6.01504
17 4H2X G5A 0.00000701 0.5531 6.35838
18 4H2V AMP 0.000018 0.44477 6.35838
19 3MF2 AMP 0.00002976 0.44228 6.35838
20 4H2W AMP 0.00001661 0.42098 6.35838
21 4H2W 5GP 0.00009485 0.40268 6.35838
22 4IAW LIZ 0.02133 0.41161 6.38298
23 3A5Y KAA 0.0002234 0.42578 6.66667
24 2Z6C FMN 0.01029 0.40942 6.97674
25 3A5Z KAA 0.0003617 0.42026 7.0122
26 2VDF OCT 0.0009289 0.48927 8.3004
27 2CJA ATP 0.000001237 0.45047 9.30233
28 1QKQ MAN 0.006356 0.42532 10.5634
29 2J3M PRI 0.000000004155 0.57117 11.4341
30 2J3M ATP 0.000000003074 0.56911 11.4341
31 5E89 TD2 0.01498 0.40841 12.2302
32 1WLE SRP 0.00001172 0.44674 12.7907
33 2YIP YIO 0.03176 0.40967 15.2174
34 3REU ATP 0.00002536 0.42391 15.3061
35 2I4O ATP 0.000002477 0.42616 15.9389
36 1SES AHX 0.000001668 0.59546 20.19
37 1SES AMP 0.00002322 0.56943 20.19
38 1I7M CG 0.03029 0.40756 23.8806
39 1WUW TSU 0.008396 0.45121 24.4444
40 4HWS 1B3 0.0000004949 0.50901 37.9562
41 3IAL PR8 0.00000000006709 0.61874 48.8417
Pocket No.: 4; Query (leader) PDB : 5VAD; Ligand: 91Y; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 5vad.bio1) has 33 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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