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Structure of PDB 6r8o Chain A Binding Site BS01

Receptor Information
>6r8o 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 IDJV2
InChIInChI=1S/C26H32N4O4S/c1-35-24-7-3-2-5-17(24)21-6-4-10-30(21)25(32)14-28-26(33)27-13-16-8-9-19-18(11-16)23-12-20(29-19)22(31)15-34-23/h2-3,5,7-9,11,20-23,29,31H,4,6,10,12-15H2,1H3,(H2,27,28,33)/t20-,21-,22-,23-/m1/s1
InChIKeyBICVGZIZTMOLHN-SSGKUCQKSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CSc1ccccc1[C@H]2CCCN2C(=O)CNC(=O)NCc3ccc4N[C@@H]5C[C@@H](OC[C@H]5O)c4c3
OpenEye OEToolkits 2.0.7CSc1ccccc1C2CCCN2C(=O)CNC(=O)NCc3ccc4c(c3)C5CC(N4)C(CO5)O
CACTVS 3.385CSc1ccccc1[CH]2CCCN2C(=O)CNC(=O)NCc3ccc4N[CH]5C[CH](OC[CH]5O)c4c3
OpenEye OEToolkits 2.0.7CSc1ccccc1[C@H]2CCCN2C(=O)CNC(=O)NCc3ccc4c(c3)[C@H]5C[C@@H](N4)[C@@H](CO5)O
FormulaC26 H32 N4 O4 S
Name1-(((2R,3S,6R)-3-hydroxy-2,3,4,6-tetrahydro-1H-2,6-methanobenzo[c][1,5]oxazocin-8-yl)methyl)-3-(2-((R)-2-(2-(methylthio)phenyl)pyrrolidin-1-yl)-2-oxoethyl)urea
ChEMBLCHEMBL4470490
DrugBank
ZINC
PDB chain6r8o Chain A Residue 304 [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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PDB6r8o Discovery of novel Cyclophilin D inhibitors starting from three dimensional fragments with millimolar potencies.
Resolution1.36 Å
Binding residue
(original residue number in PDB)		R97 F102 M103 Q105 S123 A143 N144 T149 Q153 F155
Binding residue
(residue number reindexed from 1)		R54 F59 M60 Q62 S80 A100 N101 T106 Q110 F112
Annotation score1
Binding affinityMOAD: Kd=0.67uM
PDBbind-CN: -logKd/Ki=8.22,Kd=0.006uM
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

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:6r8o, PDBe:6r8o, PDBj:6r8o
PDBsum6r8o
PubMed31635932
UniProtP30405|PPIF_HUMAN Peptidyl-prolyl cis-trans isomerase F, mitochondrial (Gene Name=PPIF)

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