Receptor
PDB id Resolution Class Description Source Keywords
4IKS 1.7 Å EC: 3.4.11.18 CRYSTAL STRUCTURE OF TRUNCATED (DELTA 1-89) HUMAN METHIONINE AMINOPEPTIDASE TYPE 1 IN COMPLEX WITH N1-(5-CHLORO-6-METHYL( PYRIDIN-2-YL)PYRIMIDIN-4-YL)-N2-(6-(TRIFLUOROMETHYL)PYRIDIET HANE-1,2-DIAMINE HOMO SAPIENS PITA-BREAD FOLD AMINOPEPTIDASE RIBOSOME HYDROLASE
Ref.: IDENTIFICATION, BIOCHEMICAL AND STRUCTURAL EVALUATI SPECIES-SPECIFIC INHIBITORS AGAINST TYPE I METHIONI AMINOPEPTIDASES J.MED.CHEM. V. 56 5295 2013
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CO A:404;
A:403;
A:402;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
submit data
58.933 Co [Co+2...
K A:405;
Part of Protein;
none;
submit data
39.098 K [K+]
GOL A:406;
Invalid;
none;
submit data
92.094 C3 H8 O3 C(C(C...
TFD A:401;
Valid;
none;
ic50 = 7.23 uM
408.808 C18 H16 Cl F3 N6 Cc1c(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4IKR 1.78 Å EC: 3.4.11.18 CRYSTAL STRUCTURE OF TYPE 1 HUMAN METHIONINE AMINOPEPTIDASE WITH 2-(4-(5-CHLORO-6-METHYL-2-(PYRIDIN-2-YL)PYRIMIDIN-4-YLP IPERAZIN-1-YL)ETHANOL HOMO SAPIENS PITA-BREAD FOLD AMINOPEPTIDASE RIBOSOME HYDROLASE
Ref.: IDENTIFICATION, BIOCHEMICAL AND STRUCTURAL EVALUATI SPECIES-SPECIFIC INHIBITORS AGAINST TYPE I METHIONI AMINOPEPTIDASES J.MED.CHEM. V. 56 5295 2013
Members (20)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 8 families.
1 2NQ6 ic50 = 1.5 uM HM4 C14 H16 N4 O3 S CC(C)(C)OC....
2 4U69 Ki = 54.8 uM Q07 C6 H16 N O3 P CCC[C@H](C....
3 2G6P ic50 = 0.6 uM HM2 C18 H17 Cl N4 Cc1c(c(nc(....
4 4U73 Ki = 6.6 uM Q02 C7 H10 N O3 P c1ccc(cc1)....
5 4IKT ic50 = 0.67 uM TFV C18 H16 Cl F3 N6 Cc1c(c(nc(....
6 4U6Z Ki = 3.9 uM Q07 C6 H16 N O3 P CCC[C@H](C....
7 4U70 Ki = 9.5 uM Q04 C8 H18 N O3 P C1CCC(CC1)....
8 4FLI ic50 = 3.59 uM Y16 C14 H26 N2 O6 CC(C)(C)/C....
9 4U6C Ki = 9.9 uM Q06 C8 H18 N O3 P C1CCC(C1)C....
10 4IKR ic50 = 0.59 uM PVP C16 H20 Cl N5 O Cc1c(c(nc(....
11 4FLK ic50 = 5.58 uM Y10 C21 H31 N O5 CC(C)(C)/C....
12 4IKU ic50 = 1.79 uM SHX C19 H18 Cl N5 O Cc1c(c(nc(....
13 2NQ7 ic50 = 2.9 uM HM5 C14 H16 N4 O2 S CC(C)(C)C(....
14 4FLL ic50 = 5.14 uM YZ6 C25 H35 N O6 CC(C)(C)/C....
15 4U71 Ki = 6 uM Q03 C7 H16 N O3 P C1CCC(CC1)....
16 4HXX - 1AY C28 H29 Cl2 N5 Cc1c(c(nc(....
17 4IKS ic50 = 7.23 uM TFD C18 H16 Cl F3 N6 Cc1c(c(nc(....
18 4U6E Ki = 111.6 uM Q02 C7 H10 N O3 P c1ccc(cc1)....
19 4U1B Ki = 4.9 uM Q08 C8 H20 N O3 P CCCC(CCC)[....
20 4FLJ ic50 = 7.45 uM Y08 C22 H38 N2 O6 CC(C)(C)/C....
70% Homology Family (21)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 2NQ6 ic50 = 1.5 uM HM4 C14 H16 N4 O3 S CC(C)(C)OC....
2 4U69 Ki = 54.8 uM Q07 C6 H16 N O3 P CCC[C@H](C....
3 2G6P ic50 = 0.6 uM HM2 C18 H17 Cl N4 Cc1c(c(nc(....
4 4U73 Ki = 6.6 uM Q02 C7 H10 N O3 P c1ccc(cc1)....
5 4IKT ic50 = 0.67 uM TFV C18 H16 Cl F3 N6 Cc1c(c(nc(....
6 4U6Z Ki = 3.9 uM Q07 C6 H16 N O3 P CCC[C@H](C....
7 4U70 Ki = 9.5 uM Q04 C8 H18 N O3 P C1CCC(CC1)....
8 4FLI ic50 = 3.59 uM Y16 C14 H26 N2 O6 CC(C)(C)/C....
9 4U6C Ki = 9.9 uM Q06 C8 H18 N O3 P C1CCC(C1)C....
10 4IKR ic50 = 0.59 uM PVP C16 H20 Cl N5 O Cc1c(c(nc(....
11 4FLK ic50 = 5.58 uM Y10 C21 H31 N O5 CC(C)(C)/C....
12 4IKU ic50 = 1.79 uM SHX C19 H18 Cl N5 O Cc1c(c(nc(....
13 2NQ7 ic50 = 2.9 uM HM5 C14 H16 N4 O2 S CC(C)(C)C(....
14 4FLL ic50 = 5.14 uM YZ6 C25 H35 N O6 CC(C)(C)/C....
15 4U71 Ki = 6 uM Q03 C7 H16 N O3 P C1CCC(CC1)....
16 4HXX - 1AY C28 H29 Cl2 N5 Cc1c(c(nc(....
17 4IKS ic50 = 7.23 uM TFD C18 H16 Cl F3 N6 Cc1c(c(nc(....
18 4U6E Ki = 111.6 uM Q02 C7 H10 N O3 P c1ccc(cc1)....
19 4U1B Ki = 4.9 uM Q08 C8 H20 N O3 P CCCC(CCC)[....
20 4FLJ ic50 = 7.45 uM Y08 C22 H38 N2 O6 CC(C)(C)/C....
21 4IU6 - FZ1 C24 H23 N5 O COc1ccc(cc....
50% Homology Family (69)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 2NQ6 ic50 = 1.5 uM HM4 C14 H16 N4 O3 S CC(C)(C)OC....
2 4U69 Ki = 54.8 uM Q07 C6 H16 N O3 P CCC[C@H](C....
3 2G6P ic50 = 0.6 uM HM2 C18 H17 Cl N4 Cc1c(c(nc(....
4 4U73 Ki = 6.6 uM Q02 C7 H10 N O3 P c1ccc(cc1)....
5 4IKT ic50 = 0.67 uM TFV C18 H16 Cl F3 N6 Cc1c(c(nc(....
6 4U6Z Ki = 3.9 uM Q07 C6 H16 N O3 P CCC[C@H](C....
7 4U70 Ki = 9.5 uM Q04 C8 H18 N O3 P C1CCC(CC1)....
8 4FLI ic50 = 3.59 uM Y16 C14 H26 N2 O6 CC(C)(C)/C....
9 4U6C Ki = 9.9 uM Q06 C8 H18 N O3 P C1CCC(C1)C....
10 4IKR ic50 = 0.59 uM PVP C16 H20 Cl N5 O Cc1c(c(nc(....
11 4FLK ic50 = 5.58 uM Y10 C21 H31 N O5 CC(C)(C)/C....
12 4IKU ic50 = 1.79 uM SHX C19 H18 Cl N5 O Cc1c(c(nc(....
13 2NQ7 ic50 = 2.9 uM HM5 C14 H16 N4 O2 S CC(C)(C)C(....
14 4FLL ic50 = 5.14 uM YZ6 C25 H35 N O6 CC(C)(C)/C....
15 4U71 Ki = 6 uM Q03 C7 H16 N O3 P C1CCC(CC1)....
16 4HXX - 1AY C28 H29 Cl2 N5 Cc1c(c(nc(....
17 4IKS ic50 = 7.23 uM TFD C18 H16 Cl F3 N6 Cc1c(c(nc(....
18 4U6E Ki = 111.6 uM Q02 C7 H10 N O3 P c1ccc(cc1)....
19 4U1B Ki = 4.9 uM Q08 C8 H20 N O3 P CCCC(CCC)[....
20 4FLJ ic50 = 7.45 uM Y08 C22 H38 N2 O6 CC(C)(C)/C....
21 2GG0 ic50 = 1.7 uM U11 C16 H20 F3 N3 O5 C[C@@H](C(....
22 1YVM Ki = 0.4 uM TMG C10 H7 N3 S c1ccc2c(c1....
23 2GU6 - NLP C5 H14 N O3 P CCCC[C@H](....
24 2Q95 ic50 = 1.6 uM A05 C11 H6 Cl N O5 c1cc(c(cc1....
25 2GG8 ic50 = 25 uM U15 C20 H31 N3 O5 Cc1ccc(cc1....
26 2GTX - NLP C5 H14 N O3 P CCCC[C@H](....
27 2EVC ic50 = 0.29 uM FC3 C12 H7 F3 O3 c1ccc(c(c1....
28 4A6W ic50 = 1.9 uM 5C1 C10 H7 Cl N2 O3 c1ccc(c(c1....
29 2GG3 ic50 = 0.58 uM U13 C9 H7 F N6 [H]/N=C/1C....
30 3D27 ic50 = 55.7 uM W29 C12 H12 O2 S CCc1ccsc1c....
31 2GG7 ic50 = 1.75 uM U14 C10 H8 N6 O2 [H]/N=C1/C....
32 2GU5 - NLP C5 H14 N O3 P CCCC[C@H](....
33 1XNZ ic50 = 0.24 uM FCD C11 H7 Cl O3 c1ccc(c(c1....
34 4A6V ic50 = 1.9 uM IKY C11 H7 F3 N2 O3 c1ccc(c(c1....
35 1C21 - MET C5 H11 N O2 S CSCC[C@@H]....
36 2Q92 ic50 = 1.1 uM B23 C11 H7 N O5 c1ccc(c(c1....
37 1C27 - NLP C5 H14 N O3 P CCCC[C@H](....
38 1C24 - MPJ C4 H12 N O2 P S CSCC[C@H](....
39 2EVO ic50 = 0.067 uM CT0 C10 H13 N3 O2 S c1csc(n1)N....
40 2P99 ic50 = 1.16 uM YE6 C11 H9 Cl N2 O2 c1ccc(c(c1....
41 2GG9 ic50 = 3.5 uM U16 C22 H35 N3 O5 CC(C)C[C@H....
42 2Q94 ic50 = 0.37 uM A04 C12 H7 F3 O4 c1ccc(c(c1....
43 2P98 Ki = 0.64 uM YE7 C12 H10 N4 O c1ccc2c(c1....
44 2GGB ic50 = 12 uM U17 C17 H33 N3 O6 CCCC[C@H](....
45 2EVM ic50 = 0.693 uM FC2 C11 H6 Cl2 O3 c1cc(c(cc1....
46 1C22 - MF3 C5 H8 F3 N O2 S C(CSC(F)(F....
47 1C23 - MPH C4 H12 N O3 P S CSCC[C@H](....
48 2Q96 ic50 = 1.2 uM A18 C12 H9 Cl O3 c1ccc(c(c1....
49 2BB7 ic50 = 2.14 uM QMS C10 H10 N2 O2 S CS(=O)(=O)....
50 2GG2 ic50 = 0.25 uM U12 C10 H7 F3 N6 c1cc(cc(c1....
51 2GGC - MET C5 H11 N O2 S CSCC[C@@H]....
52 2GU4 - NLP C5 H14 N O3 P CCCC[C@H](....
53 2Q93 ic50 = 0.56 uM B21 C12 H10 O4 COc1ccccc1....
54 2GG5 ic50 = 0.25 uM U19 C10 H7 F3 N6 [H]/N=C1/C....
55 3MAT - AHH ALA LEU VAL 0A9 n/a n/a
56 2P9A ic50 = 6.56 uM YE6 C11 H9 Cl N2 O2 c1ccc(c(c1....
57 4IU6 - FZ1 C24 H23 N5 O COc1ccc(cc....
58 1QXZ ic50 ~ 19 uM M3C C8 H14 N2 O2 S2 CSCC[C@@H]....
59 1QXY ic50 ~ 16 uM M2C C10 H16 N2 O2 S CSCC[C@@H]....
60 1QXW ic50 ~ 7 uM M1C C10 H22 N2 O2 CCCC[C@@H]....
61 3IU9 ic50 = 0.24 uM T07 C9 H8 Cl2 N4 S c1cc(c(cc1....
62 3IU7 ic50 = 16 uM FCD C11 H7 Cl O3 c1ccc(c(c1....
63 3PKE - Y10 C21 H31 N O5 CC(C)(C)/C....
64 3PKB ic50 = 0.62 uM Y16 C14 H26 N2 O6 CC(C)(C)/C....
65 3PKA ic50 = 0.54 uM Y02 C23 H37 N O6 Cc1cc(c(c(....
66 3PKC ic50 = 0.96 uM Y08 C22 H38 N2 O6 CC(C)(C)/C....
67 3IU8 ic50 = 0.58 uM T03 C9 H8 F N3 S c1cc(ccc1C....
68 3PKD ic50 = 0.76 uM Y10 C21 H31 N O5 CC(C)(C)/C....
69 1YJ3 - MET C5 H11 N O2 S CSCC[C@@H]....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: TFD; Similar ligands found: 3
No: Ligand ECFP6 Tc MDL keys Tc
1 TFD 1 1
2 TFV 0.675 0.956522
3 HM2 0.56962 0.866667
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4IKR; Ligand: PVP; Similar sites found: 14
This union binding pocket(no: 1) in the query (biounit: 4ikr.bio1) has 31 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4DHL 0K7 0.03599 0.40712 1.51976
2 4E3T HLN 0.0201 0.40447 1.82371
3 4WVW SLT 0.004606 0.45997 2.08333
4 2WBV SIA 0.02715 0.40115 2.1164
5 5JR6 01B PRO PRO ALA NH2 0.000007933 0.42759 3.03951
6 5E58 CPZ 0.04549 0.40055 3.34347
7 2Q09 DI6 0.0357 0.40266 6.07903
8 2QES ADE 0.02007 0.42063 6.13027
9 3SUT OAN 0.034 0.40007 6.38298
10 3KU0 ADE 0.02669 0.40102 7.96813
11 3B00 16A 0.01363 0.42032 8.08823
12 4ZWP M44 0.00001194 0.5912 8.20669
13 5M4Q PRO 0.000007132 0.59419 17.9331
14 4S00 AKR 0.0005141 0.50588 20.6687
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