Structure of PDB 8rkr Chain A Binding Site BS01

Receptor Information
>8rkr Chain A (length=532) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VANEPVLAFTQGSPERDALQKALKDLKGRMEAIPCVVGDEEVWTSDVQYQ
VSPFNHGHKVAKFCYADKSLLNKAIEAALAARKEWDLKPIADRAQIFLKA
ADMLSGPRRAEILAKTMVGQGKTVIQAEIDAAAELIDFFRFNAKYAVELE
GQQPISVPPSTNSTVYRGLEGFVAAISPFNFTAIGGNLAGAPALMGNVVL
WKPSDTAMLASYAVYRILREAGLPPNIIQFVPADGPLFGDTVTSSEHLCG
INFTGSVPTFKHLWKQVAQNLDRFHTFPRLAGECGGKNFHFVHRSADVES
VVSGTLRSAFEYGGQKCSACSRLYVPHSLWPQIKGRLLEEHSRIKVGDPA
EDFGTFFSAVIDAKSFARIKKWLEHARSSPSLTILAGGKCDDSVGYFVEP
CIVESKDPQEPIMKEEIFGPVLSVYVYPDDKYKETLQLVDSTTSYGLTGA
VFSQDKDVVQEATKVLRNAAGNFYINDKSTGSIVGQQPFGGARASGTNDK
PGGPHYILRWTSPQVIKETHKPLGDWSYAYMQ
Ligand information
Ligand IDA1H1O
InChIInChI=1S/C42H31O5P/c43-41-37-33-15-35(31-13-27-23-9-21(25(27)11-29(31)33)17-5-1-3-7-19(17)23)39(37)42(47-48(44,45)46)40-36-16-34(38(40)41)30-12-26-22-10-24(28(26)14-32(30)36)20-8-4-2-6-18(20)22/h1-8,11-14,21-24,33-36,43H,9-10,15-16H2,(H2,44,45,46)/t21-,22+,23+,24-,33-,34+,35+,36-
InChIKeyHFERXAIYEUEWDE-FCODNRGNSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7c1ccc2c(c1)C3CC2c4c3cc5c(c4)C6CC5c7c6c(c8c(c7O)C9CC8c1c9cc2c(c1)C1CC2c2c1cccc2)OP(=O)(O)O
CACTVS 3.385Oc1c2[CH]3C[CH](c4cc5[CH]6C[CH](c7ccccc67)c5cc34)c2c(O[P](O)(O)=O)c8[CH]9C[CH](c%10cc%11[CH]%12C[CH](c%13ccccc%12%13)c%11cc9%10)c18
OpenEye OEToolkits 2.0.7c1ccc2c(c1)[C@H]3C[C@@H]2c4c3cc5c(c4)[C@@H]6C[C@H]5c7c6c(c8c(c7O)[C@H]9C[C@@H]8c1c9cc2c(c1)[C@@H]1C[C@H]2c2c1cccc2)OP(=O)(O)O
CACTVS 3.385Oc1c2[C@H]3C[C@H](c4cc5[C@@H]6C[C@@H](c7ccccc67)c5cc34)c2c(O[P](O)(O)=O)c8[C@H]9C[C@H](c%10cc%11[C@@H]%12C[C@@H](c%13ccccc%12%13)c%11cc9%10)c18
FormulaC42 H31 O5 P
Name(1R,5S,9S,16R,20R,24S,28S,35R)-22-(Dihydroxyphosphoryloxy)tridecacyclo[22.14.1.15,20.19,16.128,35.02,23.04,21.06,19.08,17.010,15.025,38.027,36.029,34]dotetraconta-2(23),3,6,8(17),10,12,14,18,21,25,27(36),29,31,33,37-pentadecaen-3-ol
ChEMBL
DrugBank
ZINC
PDB chain8rkr Chain A Residue 601 [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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PDB8rkr How Do Molecular Tweezers Bind to Proteins? Lessons from X-ray Crystallography.
Resolution1.2 Å
Binding residue
(original residue number in PDB)		R399 K402 W403 E405 H406
Binding residue
(residue number reindexed from 1)		R368 K371 W372 E374 H375
Annotation score1
Enzymatic activity
Enzyme Commision number 1.2.1.88: L-glutamate gamma-semialdehyde dehydrogenase.
Gene Ontology
Molecular Function
GO:0003842 1-pyrroline-5-carboxylate dehydrogenase activity
GO:0004029 aldehyde dehydrogenase (NAD+) activity
GO:0005515 protein binding
GO:0009055 electron transfer activity
GO:0016491 oxidoreductase activity
GO:0016620 oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor
GO:0042802 identical protein binding
Biological Process
GO:0006560 proline metabolic process
GO:0006562 proline catabolic process
GO:0010133 proline catabolic process to glutamate
GO:0019470 4-hydroxyproline catabolic process
Cellular Component
GO:0005739 mitochondrion
GO:0005759 mitochondrial matrix
GO:0005829 cytosol

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:8rkr, PDBe:8rkr, PDBj:8rkr
PDBsum8rkr
PubMed38675584
UniProtP30038|AL4A1_HUMAN Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial (Gene Name=ALDH4A1)

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