Structure of PDB 6ra1 Chain A Binding Site BS02

Receptor Information
>6ra1 Chain A (length=164) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GNPLVYLDVDANGKPLGRVVLELKADVVPKTAENFRALCTGEKGFGYKGS
TFHRVIPSFMCQAGDFTNHNGTGGKSIYGSRFPDENFTLKHVGPGVLSMA
NAGPNTNGSQFFICTIKTDWLDGKHVVFGHVIEGMDVVKKIESFGSKSGR
TSKKIVITDCGQLS
Ligand information
Ligand IDJVQ
InChIInChI=1S/C13H16N2O3/c1-2-15-7-9-5-11-12(18-8-17-11)6-10(9)14-4-3-13(15)16/h5-6,14H,2-4,7-8H2,1H3
InChIKeyLCKKANZPYFOBHG-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7CCN1Cc2cc3c(cc2NCCC1=O)OCO3
CACTVS 3.385CCN1Cc2cc3OCOc3cc2NCCC1=O
FormulaC13 H16 N2 O3
Name14-ethyl-4,6-dioxa-10,14-diazatricyclo[7.6.0.0^{3,7}]pentadeca-1(9),2,7-trien-13-one
ChEMBLCHEMBL3438117
DrugBank
ZINCZINC000299851959
PDB chain6ra1 Chain A Residue 302 [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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PDB6ra1 Discovery of novel Cyclophilin D inhibitors starting from three dimensional fragments with millimolar potencies.
Resolution2.0 Å
Binding residue
(original residue number in PDB)		T115 G116 G117 S123 R124 A143 N144 T149 Q153
Binding residue
(residue number reindexed from 1)		T72 G73 G74 S80 R81 A100 N101 T106 Q110
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=2.00,Kd>10mM
Enzymatic activity
Catalytic site (original residue number in PDB) R97 F102 Q105 N144 F155 L164 H168
Catalytic site (residue number reindexed from 1) R54 F59 Q62 N101 F112 L121 H125
Enzyme Commision number 5.2.1.8: peptidylprolyl isomerase.
Gene Ontology
Molecular Function
GO:0003755 peptidyl-prolyl cis-trans isomerase activity
Biological Process
GO:0000413 protein peptidyl-prolyl isomerization
GO:0006457 protein folding

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Molecular Function
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Biological Process
External links
PDB RCSB:6ra1, PDBe:6ra1, PDBj:6ra1
PDBsum6ra1
PubMed31635932
UniProtP30405|PPIF_HUMAN Peptidyl-prolyl cis-trans isomerase F, mitochondrial (Gene Name=PPIF)

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