Structure of PDB 6ydx Chain B Binding Site BS01

Receptor Information
>6ydx Chain B (length=853) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KLFPWAQIRLPTAVVPLRYELSLHPNLTSMTFRGSVTISVQALQVTWNII
LHSTGHNISRVTFMSAVSSQEKQAEILEYAYHGQIAIVAPEALLAGHNYT
LKIEYSANISSSYYGFYGFSYTDESNEKKYFAATQFEPLAARSAFPCFDE
PAFKATFIIKIIRDEQYTALSNMPKKSSVVLDDGLVQDEFSESVKMSTYL
VAFIVGEMKNLSQDVNGTLVSIYAVPEKIGQVHYALETTVKLLEFFQNYF
EIQYPLKKLDLVAIPDFEAGAMENWGLLTFREETLLYDSNTSSMADRKLV
TKIIAHELAHQWFGNLVTMKWWNDLWLNEGFATFMEYFSLEKIFKELSSY
EDFLDARFKTMKKDSLNSSHPISSSVQSSEQIEEMFDSLSYFKGSSLLLM
LKTYLSEDVFQHAVVLYLHNHSYASIQSDDLWDSFNEVTNQDVKRMMKTW
TLQKGFPLVTVQKKGKELFIQQERFFLYLWHIPLSYVTEGRNYSKYQSVS
LLDKKSGVINLTEEVLWVKVNINMNGYYIVHYADDDWEALIHQLKINPYV
LSDKDRANLINNIFELAGLGKVPLKRAFDLINYLGNENHTAPITEALFQT
DLIYNLLEKLGYMDLASRLVTRVFKLLQNQIQQQTWTDEGTPSMRELRSA
LLEFACTHNLGNCSTTAMKLFDDWMASNGTQSLPTDVMTTVFKVGAKTDK
GWSFLLGKYISIGSEAEKNKILEALASSEDVRKLYWLMKSSLNGDNFRTQ
KLSFIIRTVGRHFPGHLLAWDFVKENWNKLVQKFPLGSYTIQNIVAGSTY
LFSTKTHLSEVQAFFENQSEATFRLRCVQEALEVIQLNIQWMEKNLKSLT
WWL
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 B 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 M430 R439 K460 I461 H464 E487 S925 R929 Y961
Binding residue
(residue number reindexed from 1)		G270 A271 M272 R281 K302 I303 H306 E329 S753 R757 Y789
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) E273 H306 E307 H310 E329 E383 Y391
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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