Structure of PDB 8td5 Chain D Binding Site BS03

Receptor Information
>8td5 Chain D (length=279) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NLYFQSMSVGFIGAGQLAFALAKGFTAAGVLAAHKIMASSPDMDLATVSA
LRKMGVKLTPHNKETVQHSDVLFLAVKPHIIPFILDEIGADIEDRHIVVS
CAAGVTISSIEKKLSAFRPAPRVIRCMTNTPVVVREGATVYATGTHAQVE
DGRLMEQLLSSVGFCTEVEEDLIDAVTGLSGSGPAYAFTALDALADGGVK
MGLPRRLAVRLGAQALLGAAKMLLHSEQHPGQLKDNVSSPGGATIHALHV
LESGGFRSLLINAVEASCIRTRELQSMAD
Ligand information
Ligand IDUJP
InChIInChI=1S/C5H8O2S/c6-5(7)4-2-1-3-8-4/h4H,1-3H2,(H,6,7)/t4-/m1/s1
InChIKeyMZOYMQRKTJRHGJ-SCSAIBSYSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01C(O)(C1CCCS1)=O
OpenEye OEToolkits 2.0.7C1C[C@@H](SC1)C(=O)O
CACTVS 3.385OC(=O)[CH]1CCCS1
OpenEye OEToolkits 2.0.7C1CC(SC1)C(=O)O
CACTVS 3.385OC(=O)[C@H]1CCCS1
FormulaC5 H8 O2 S
Name(2R)-thiolane-2-carboxylic acid
ChEMBL
DrugBank
ZINCZINC000000900769
PDB chain8td5 Chain D Residue 402 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB8td5 Screening a knowledge-based library of low molecular weight compounds against the proline biosynthetic enzyme 1-pyrroline-5-carboxylate 1 (PYCR1)
Resolution1.81 Å
Binding residue
(original residue number in PDB)		S233 A237 T238
Binding residue
(residue number reindexed from 1)		S239 A243 T244
Annotation score1
Gene Ontology
Molecular Function
GO:0004735 pyrroline-5-carboxylate reductase activity
GO:0005515 protein binding
GO:0016491 oxidoreductase activity
GO:0042802 identical protein binding
Biological Process
GO:0006561 proline biosynthetic process
GO:0034599 cellular response to oxidative stress
GO:0051881 regulation of mitochondrial membrane potential
GO:0055129 L-proline biosynthetic process
GO:1903377 negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway
Cellular Component
GO:0005739 mitochondrion
GO:0005759 mitochondrial matrix

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8td5, PDBe:8td5, PDBj:8td5
PDBsum8td5
PubMed39133178
UniProtP32322|P5CR1_HUMAN Pyrroline-5-carboxylate reductase 1, mitochondrial (Gene Name=PYCR1)

[Back to BioLiP]