Structure of PDB 6ydx Chain A Binding Site BS01

Receptor Information
>6ydx Chain A (length=856) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NGKLFPWAQIRLPTAVVPLRYELSLHPNLTSMTFRGSVTISVQALQVTWN
IILHSTGHNISRVTFMSAVSSQEKQAEILEYAYHGQIAIVAPEALLAGHN
YTLKIEYSANISSSYYGFYGFSYTDESNEKKYFAATQFEPLAARSAFPCF
DEPAFKATFIIKIIRDEQYTALSNMPKKSSGLVQDEFSESVKMSTYLVAF
IVGEMKNLSQDVNGTLVSIYAVPEKIGQVHYALETTVKLLEFFQNYFEIQ
YPLKKLDLVAIPDFEAGAMENWGLLTFREETLLYDSNTSSMADRKLVTKI
IAHELAHQWFGNLVTMKWWNDLWLNEGFATFMEYFSLEKIFKELSSYEDF
LDARFKTMKKDSLNSSHPISSSVQSSEQIEEMFDSLSYFKGSSLLLMLKT
YLSEDVFQHAVVLYLHNHSYASIQSDDLWDSFNEVTNQTLDVKRMMKTWT
LQKGFPLVTVQKKGKELFIQQERFFLYLWHIPLSYVTEGRNYSKYQSVSL
LDKKSGVINLTEEVLWVKVNINMNGYYIVHYADDDWEALIHQLKINPYVL
SDKDRANLINNIFELAGLGKVPLKRAFDLINYLGNENHTAPITEALFQTD
LIYNLLEKLGYMDLASRLVTRVFKLLQNQIQQQTWTDEGTPSMRELRSAL
LEFACTHNLGNCSTTAMKLFDDWMASNGTQSLPTDVMTTVFKVGAKTDKG
WSFLLGKYISIGSEAEKNKILEALASSEDVRKLYWLMKSSLNGDNFRTQK
LSFIIRTVGRHFPGHLLAWDFVKENWNKLVQKFPLGSYTIQNIVAGSTYL
FSTKTHLSEVQAFFENQSEATFRLRCVQEALEVIQLNIQWMEKNLKSLTW
WLRTET
Ligand information
Ligand IDONN
InChIInChI=1S/C26H32N4O6S2/c27-21-9-10-37-38-15-22(26(36)28-14-18-4-2-1-3-17(18)12-24(33)34)30-23(32)13-19(29-25(21)35)11-16-5-7-20(31)8-6-16/h1-8,19,21-22,31H,9-15,27H2,(H,28,36)(H,29,35)(H,30,32)(H,33,34)/t19-,21-,22-/m0/s1
InChIKeyVZYRMNZEFCZSER-BVSLBCMMSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7c1ccc(c(c1)CC(=O)O)CNC(=O)[C@@H]2CSSCC[C@@H](C(=O)N[C@H](CC(=O)N2)Cc3ccc(cc3)O)N
CACTVS 3.385N[CH]1CCSSC[CH](NC(=O)C[CH](Cc2ccc(O)cc2)NC1=O)C(=O)NCc3ccccc3CC(O)=O
CACTVS 3.385N[C@H]1CCSSC[C@H](NC(=O)C[C@H](Cc2ccc(O)cc2)NC1=O)C(=O)NCc3ccccc3CC(O)=O
OpenEye OEToolkits 2.0.7c1ccc(c(c1)CC(=O)O)CNC(=O)C2CSSCCC(C(=O)NC(CC(=O)N2)Cc3ccc(cc3)O)N
FormulaC26 H32 N4 O6 S2
Name2-[2-[[[(4~{R},8~{S},11~{S})-11-azanyl-8-[(4-hydroxyphenyl)methyl]-6,10-bis(oxidanylidene)-1,2-dithia-5,9-diazacyclotridec-4-yl]carbonylamino]methyl]phenyl]ethanoic acid
ChEMBLCHEMBL1277623
DrugBank
ZINCZINC000064447539
PDB chain6ydx Chain A Residue 1101 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB6ydx Structural Basis of Inhibition of Insulin-Regulated Aminopeptidase by a Macrocyclic Peptidic Inhibitor.
Resolution3.2 Å
Binding residue
(original residue number in PDB)		G428 A429 E431 I461 H464 E465 E487 E494 D545 Y549 Y961
Binding residue
(residue number reindexed from 1)		G267 A268 E270 I300 H303 E304 E326 E333 D384 Y388 Y788
Annotation score1
Binding affinityBindingDB: Ki=3.3nM
Enzymatic activity
Catalytic site (original residue number in PDB) E431 H464 E465 H468 E487 E541 Y549
Catalytic site (residue number reindexed from 1) E270 H303 E304 H307 E326 E380 Y388
Enzyme Commision number 3.4.11.3: cystinyl aminopeptidase.
Gene Ontology
Molecular Function
GO:0008237 metallopeptidase activity
GO:0008270 zinc ion binding
Biological Process
GO:0006508 proteolysis

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:6ydx, PDBe:6ydx, PDBj:6ydx
PDBsum6ydx
PubMed32676150
UniProtQ9UIQ6|LCAP_HUMAN Leucyl-cystinyl aminopeptidase (Gene Name=LNPEP)

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