Structure of PDB 6bh8 Chain A Binding Site BS02

Receptor Information

>6bh8 Chain A (length=371) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

EKRIFGAVLLFSWTVYLWETFLAQRQRRIYKTTTHVPPELGQIMDYLWRL
SGRFCGYAGFGPEYEITQSLVFLLLATLFSALAGLPWSLYNTFVIEEKHG
FNQQTLGFFMKDAIKKFVVTQCILLPVSSLLLYIIKIGGDYFFIYAWLFT
LVVSLVLVTIYADYIAPLFDKFTPLPEGKLKEEIEVMAKSIDFPLTKVYV
VEGSKRSSHSNAYFKRIVLFDTLGCKNEEVLAVLGHELGHWKLGHTVKNI
IISQMNSFLCFFLFAVLIGRKELFAAFGFYDSQPTLIGLLIIFQFIFSPY
NEVLSFCLTVLSRRFEFQADAFAKKLGKAKDLYSALIKLNKDNLGFPVSD
WLFSMWHYSHPPLLERLQALK

Ligand information

Ligand ID

RDF

InChI

InChI=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

InChIKey

ZPHBZEQOLSRPAK-XLCYBJAPSA-N

SMILES

Software	SMILES
OpenEye OEToolkits 1.5.0	CC1C(C(C(C(O1)OP(=O)(NC(CC(C)C)C(=O)NC(Cc2c[nH]c3c2cccc3)C(=O)O)O)O)O)O
ACDLabs 10.04	O=P(OC1OC(C(O)C(O)C1O)C)(O)NC(C(=O)NC(C(=O)O)Cc3c2ccccc2nc3)CC(C)C
OpenEye OEToolkits 1.5.0	C[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 3.341	CC(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 3.341	CC(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

Formula

C23 H34 N3 O10 P

Name

N-ALPHA-L-RHAMNOPYRANOSYLOXY(HYDROXYPHOSPHINYL)-L-LEUCYL-L-TRYPTOPHAN;
PHOSPHORAMIDON

PDB chain

6bh8 Chain A Residue 502 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure

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Structure summary

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PDB	6bh8 Phosphoramidon inhibits the integral membrane protein zinc metalloprotease ZMPSTE24.
Resolution	3.85 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)	S210 N211 V233 H236 E237 H240 E316 N343 H360 R366
Annotation score	1
Binding affinity	PDBbind-CN: -logKd/Ki=5.12,IC50=7.6uM

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

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Biological Process

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Cellular Component

External links

PDB	RCSB:6bh8, PDBe:6bh8, PDBj:6bh8
PDBsum	6bh8
PubMed	30082509
UniProt	O75844\|FACE1_HUMAN CAAX prenyl protease 1 homolog (Gene Name=ZMPSTE24)

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