Structure of PDB 7pb0 Chain A Binding Site BS01

Receptor Information
>7pb0 Chain A (length=321) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GELSLWERFCANIIKAGPMPKHIAFIMDGNRRYAKKCQVERQEGHSQGFN
KLAETLRWCLNLGILEVTVYAFSIENFKRSKSEVDGLMDLARQKFSRLME
EKEKLQKHGVCIRVLGDLHLLPLDLQELIAQAVQATKNYNKCFLNVCFAY
TSRHEISNAVREMAWGVEQGLLDPSDISESLLDKCLYTNRSPHPDILIRT
SGEVRLSDFLLWQTSHSCLVFQPVLWPEYTFWNLFEAILQFQMNHSVLQK
ARDMYAEERKRQQLERDQATVTEQLLREGLQASGDAQLRRTRLHKLSARR
EERVQGFLQALELKRADWLAR
Ligand information
Ligand IDISY
InChIInChI=1S/C5H12O6P2S/c1-5(2)3-4-14-13(9,10)11-12(6,7)8/h1,3-4H2,2H3,(H,9,10)(H2,6,7,8)
InChIKeyYLTQZUVQWVAPNP-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0CC(=C)CCSP(=O)(O)OP(=O)(O)O
OpenEye OEToolkits 1.7.0CC(=C)CCS[P@@](=O)(O)OP(=O)(O)O
ACDLabs 12.01O=P(O)(OP(=O)(O)SCCC(=C)\C)O
CACTVS 3.370CC(=C)CCS[P](O)(=O)O[P](O)(O)=O
FormulaC5 H12 O6 P2 S
Name3-methylbut-3-enylsulfanyl(phosphonooxy)phosphinic acid;
Isopentyl S-Thiolodiphosphate
ChEMBLCHEMBL448120
DrugBank
ZINC
PDB chain7pb0 Chain A 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]
PDB7pb0 Structural basis for long-chain isoprenoid synthesis by cis -prenyltransferases.
Resolution2.301 Å
Binding residue
(original residue number in PDB)		I32 D34 Y76 A77 F78 N82 R205 R211 S213
Binding residue
(residue number reindexed from 1)		I26 D28 Y70 A71 F72 N76 R199 R205 S207
Annotation score2
Enzymatic activity
Enzyme Commision number 2.5.1.87: ditrans,polycis-polyprenyl diphosphate synthase [(2E,6E)-farnesyl diphosphate specific].
Gene Ontology
Molecular Function
GO:0002094 polyprenyltransferase activity
GO:0005515 protein binding
GO:0016740 transferase activity
GO:0016765 transferase activity, transferring alkyl or aryl (other than methyl) groups
GO:0045547 dehydrodolichyl diphosphate synthase activity
GO:0046872 metal ion binding
Biological Process
GO:0006486 protein glycosylation
GO:0006489 dolichyl diphosphate biosynthetic process
GO:0006629 lipid metabolic process
GO:0016094 polyprenol biosynthetic process
Cellular Component
GO:0005783 endoplasmic reticulum
GO:0005789 endoplasmic reticulum membrane
GO:0016020 membrane
GO:1904423 dehydrodolichyl diphosphate synthase complex

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:7pb0, PDBe:7pb0, PDBj:7pb0
PDBsum7pb0
PubMed35584224
UniProtQ86SQ9|DHDDS_HUMAN Dehydrodolichyl diphosphate synthase complex subunit DHDDS (Gene Name=DHDDS)

[Back to BioLiP]