Structure of PDB 8td2 Chain B Binding Site BS01

Receptor Information
>8td2 Chain B (length=281) 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
LESGGFRSLLINAVEASCIRTRELQSMADQE
Ligand information
Ligand IDNAI
InChIInChI=1S/C21H29N7O14P2/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(32)14(30)11(41-21)6-39-44(36,37)42-43(34,35)38-5-10-13(29)15(31)20(40-10)27-3-1-2-9(4-27)18(23)33/h1,3-4,7-8,10-11,13-16,20-21,29-32H,2,5-6H2,(H2,23,33)(H,34,35)(H,36,37)(H2,22,24,25)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
InChIKeyBOPGDPNILDQYTO-NNYOXOHSSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)N5C=CCC(=C5)C(=O)N)O)O)O)O)N
CACTVS 3.341NC(=O)C1=CN(C=CC1)[C@@H]2O[C@H](CO[P@@](O)(=O)O[P@](O)(=O)OC[C@H]3O[C@H]([C@H](O)[C@@H]3O)n4cnc5c(N)ncnc45)[C@@H](O)[C@H]2O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)N5C=CCC(=C5)C(=O)N)O)O)O)O)N
CACTVS 3.341NC(=O)C1=CN(C=CC1)[CH]2O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O)[CH]3O)n4cnc5c(N)ncnc45)[CH](O)[CH]2O
FormulaC21 H29 N7 O14 P2
Name1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE;
NADH
ChEMBLCHEMBL1234616
DrugBankDB00157
ZINCZINC000008215403
PDB chain8td2 Chain B Residue 401 [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]
PDB8td2 Screening a knowledge-based library of low molecular weight compounds against the proline biosynthetic enzyme 1-pyrroline-5-carboxylate 1 (PYCR1)
Resolution1.65 Å
Binding residue
(original residue number in PDB)		A8 G9 Q10 L11 P35 L39 N56 A69 V70 K71 P72 I74 I78 C95 A96 A97 M121 T122 T124
Binding residue
(residue number reindexed from 1)		A14 G15 Q16 L17 P41 L45 N62 A75 V76 K77 P78 I80 I84 C101 A102 A103 M127 T128 T130
Annotation score4
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:8td2, PDBe:8td2, PDBj:8td2
PDBsum8td2
PubMed39133178
UniProtP32322|P5CR1_HUMAN Pyrroline-5-carboxylate reductase 1, mitochondrial (Gene Name=PYCR1)

[Back to BioLiP]