Structure of PDB 6bh8 Chain B Binding Site BS02

Receptor Information
>6bh8 Chain B (length=410) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EKRIFGAVLLFSWTVYLWETFLAQRQRRIYKTTTHVPPELGQIMDSETFE
KSRLYQLDKSTFSFWSGLYSETEGTLILLFGGIPYLWRLSGRFCGYAGFG
PEYEITQSLVFLLLATLFSALAGLPWSLYNTFVIEEKHGFNQQTLGFFMK
DAIKKFVVTQCILLPVSSLLLYIIKIGGDYFFIYAWLFTLVVSLVLVTIY
ADYIAPLFDKFTPLPEGKLKEEIEVMAKSIDFPLTKVYVVEGSKRSSHSN
AYFKRIVLFDTLGCKNEEVLAVLGHELGHWKLGHTVKNIIISQMNSFLCF
FLFAVLIGRKELFAAFGFYDSQPTLIGLLIIFQFIFSPYNEVLSFCLTVL
SRRFEFQADAFAKKLGKAKDLYSALIKLNKDNLGFPVSDWLFSMWHYSHP
PLLERLQALK
Ligand information
Ligand IDRDF
InChIInChI=1S/C23H34N3O10P/c1-11(2)8-16(26-37(33,34)36-23-20(29)19(28)18(27)12(3)35-23)21(30)25-17(22(31)32)9-13-10-24-15-7-5-4-6-14(13)15/h4-7,10-12,16-20,23-24,27-29H,8-9H2,1-3H3,(H,25,30)(H,31,32)(H2,26,33,34)/t12-,16-,17-,18-,19+,20+,23-/m0/s1
InChIKeyZPHBZEQOLSRPAK-XLCYBJAPSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC1C(C(C(C(O1)OP(=O)(NC(CC(C)C)C(=O)NC(Cc2c[nH]c3c2cccc3)C(=O)O)O)O)O)O
ACDLabs 10.04O=P(OC1OC(C(O)C(O)C1O)C)(O)NC(C(=O)NC(C(=O)O)Cc3c2ccccc2nc3)CC(C)C
OpenEye OEToolkits 1.5.0C[C@H]1[C@@H]([C@H]([C@H]([C@@H](O1)O[P@](=O)(N[C@@H](CC(C)C)C(=O)N[C@@H](Cc2c[nH]c3c2cccc3)C(=O)O)O)O)O)O
CACTVS 3.341CC(C)C[C@H](N[P@@](O)(=O)O[C@@H]1O[C@@H](C)[C@H](O)[C@@H](O)[C@H]1O)C(=O)N[C@@H](Cc2c[nH]c3ccccc23)C(O)=O
CACTVS 3.341CC(C)C[CH](N[P](O)(=O)O[CH]1O[CH](C)[CH](O)[CH](O)[CH]1O)C(=O)N[CH](Cc2c[nH]c3ccccc23)C(O)=O
FormulaC23 H34 N3 O10 P
NameN-ALPHA-L-RHAMNOPYRANOSYLOXY(HYDROXYPHOSPHINYL)-L-LEUCYL-L-TRYPTOPHAN;
PHOSPHORAMIDON
ChEMBLCHEMBL479579
DrugBankDB02557
ZINCZINC000004475339
PDB chain6bh8 Chain B Residue 502 [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]
PDB6bh8 Phosphoramidon inhibits the integral membrane protein zinc metalloprotease ZMPSTE24.
Resolution3.85 Å
Binding residue
(original residue number in PDB)		S264 N265 V332 H335 E336 H339 E415 N442 H459 R465
Binding residue
(residue number reindexed from 1)		S249 N250 V272 H275 E276 H279 E355 N382 H399 R405
Annotation score1
Enzymatic activity
Enzyme Commision number 3.4.24.84: Ste24 endopeptidase.
Gene Ontology
Molecular Function
GO:0003690 double-stranded DNA binding
GO:0004175 endopeptidase activity
GO:0004222 metalloendopeptidase activity
GO:0005515 protein binding
GO:0008233 peptidase activity
GO:0008235 metalloexopeptidase activity
GO:0008237 metallopeptidase activity
GO:0046872 metal ion binding
Biological Process
GO:0001889 liver development
GO:0001942 hair follicle development
GO:0003007 heart morphogenesis
GO:0003229 ventricular cardiac muscle tissue development
GO:0003231 cardiac ventricle development
GO:0003417 growth plate cartilage development
GO:0006281 DNA repair
GO:0006325 chromatin organization
GO:0006355 regulation of DNA-templated transcription
GO:0006508 proteolysis
GO:0006925 inflammatory cell apoptotic process
GO:0006974 DNA damage response
GO:0006997 nucleus organization
GO:0006998 nuclear envelope organization
GO:0007346 regulation of mitotic cell cycle
GO:0007628 adult walking behavior
GO:0008016 regulation of heart contraction
GO:0008340 determination of adult lifespan
GO:0008360 regulation of cell shape
GO:0008544 epidermis development
GO:0010506 regulation of autophagy
GO:0010628 positive regulation of gene expression
GO:0010629 negative regulation of gene expression
GO:0010906 regulation of glucose metabolic process
GO:0016485 protein processing
GO:0019216 regulation of lipid metabolic process
GO:0030282 bone mineralization
GO:0030327 prenylated protein catabolic process
GO:0030500 regulation of bone mineralization
GO:0032006 regulation of TOR signaling
GO:0032350 regulation of hormone metabolic process
GO:0035264 multicellular organism growth
GO:0040014 regulation of multicellular organism growth
GO:0040029 epigenetic regulation of gene expression
GO:0043007 maintenance of rDNA
GO:0043516 regulation of DNA damage response, signal transduction by p53 class mediator
GO:0044029 positive regulation of gene expression via chromosomal CpG island demethylation
GO:0044255 cellular lipid metabolic process
GO:0048145 regulation of fibroblast proliferation
GO:0048538 thymus development
GO:0050688 regulation of defense response to virus
GO:0050905 neuromuscular process
GO:0051276 chromosome organization
GO:0051604 protein maturation
GO:0055013 cardiac muscle cell development
GO:0060307 regulation of ventricular cardiac muscle cell membrane repolarization
GO:0060993 kidney morphogenesis
GO:0061337 cardiac conduction
GO:0061762 CAMKK-AMPK signaling cascade
GO:0070302 regulation of stress-activated protein kinase signaling cascade
GO:0071480 cellular response to gamma radiation
GO:0071586 CAAX-box protein processing
GO:0072423 response to DNA damage checkpoint signaling
GO:1903463 regulation of mitotic cell cycle DNA replication
GO:1903522 regulation of blood circulation
GO:1903799 negative regulation of miRNA processing
GO:1990036 calcium ion import into sarcoplasmic reticulum
GO:2000730 regulation of termination of RNA polymerase I transcription
GO:2000772 regulation of cellular senescence
Cellular Component
GO:0005634 nucleus
GO:0005635 nuclear envelope
GO:0005637 nuclear inner membrane
GO:0005768 endosome
GO:0005783 endoplasmic reticulum
GO:0005789 endoplasmic reticulum membrane
GO:0016020 membrane
GO:0031901 early endosome membrane
GO:0031902 late endosome membrane
GO:0032991 protein-containing complex
GO:0070062 extracellular exosome

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6bh8, PDBe:6bh8, PDBj:6bh8
PDBsum6bh8
PubMed30082509
UniProtO75844|FACE1_HUMAN CAAX prenyl protease 1 homolog (Gene Name=ZMPSTE24)

[Back to BioLiP]