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Receptor Information

>5yr4 Chain A (length=304) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

YRYTGKLRPHYPLMPTRPVPSYIQRPDYADHPLGMSESEQALKGTSQIKL
LSSEDIEGMRLVCRLAREVLDVAAGMIKPGVTTEEIDHAVHLACIARNCY
PSPLNYYNFPKSCCTSVNEVICHGIPDRRPLQEGDIVNVDITLYRNGYHG
DLNETFFVGEVDDGARKLVQTTYECLMQAIDAVKPGVRYRELGNIIQKHA
QANGFSVVRSYCGHGIHKLMHTAPNVPHYAKNKAVGVMKSGHVFTIEPMI
CEGGWQDETWPDGWTAVTRDGKRSAQFEHTLLVTDTGCEILTRRLDSARP
HFMS

Ligand ID

TN4

InChI

InChI=1S/C19H30ClNO6/c1-11(2)6-7-13-19(4,27-13)16-15(25-5)12(8-9-18(16,3)24)26-17(23)21-14(22)10-20/h6,12-13,15-16,24H,7-10H2,1-5H3,(H,21,22,23)/t12-,13-,15-,16+,18-,19+/m1/s1

InChIKey

OUUSPVSSNHLIGE-AGYLCKTBSA-N

SMILES

Software	SMILES
ACDLabs 12.01	ClCC(=O)NC(=O)OC2CCC(O)(C(C1(OC1C/C=C(/C)C)C)C2OC)C
OpenEye OEToolkits 1.7.2	CC(=CCC1C(O1)(C)C2C(C(CCC2(C)O)OC(=O)NC(=O)CCl)OC)C
CACTVS 3.370	CO[CH]1[CH](CC[C](C)(O)[CH]1[C]2(C)O[CH]2CC=C(C)C)OC(=O)NC(=O)CCl
OpenEye OEToolkits 1.7.2	CC(=CC[C@@H]1C(O1)(C)[C@H]2[C@@H]([C@@H](CC[C@@]2(C)O)OC(=O)NC(=O)CCl)OC)C
CACTVS 3.370	CO[C@@H]1[C@@H](CC[C@@](C)(O)[C@H]1[C@@]2(C)O[C@@H]2CC=C(C)C)OC(=O)NC(=O)CCl

Formula

C19 H30 Cl N O6

Name

(1R,2S,3S,4R)-4-hydroxy-2-methoxy-4-methyl-3-[(2R,3R)-2-methyl-3-(3-methylbut-2-en-1-yl)oxiran-2-yl]cyclohexyl (chloroacetyl)carbamate;
TNP-470 (Open form)

PDB chain

5yr4 Chain A Residue 410 [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	5yr4 Discovery of natural product ovalicin sensitive type 1 methionine aminopeptidases: molecular and structural basis.
Resolution	1.82 Å
Binding residue (original residue number in PDB)	P192 Y195 H212 Y300 C301 M309 H310 E336
Binding residue (residue number reindexed from 1)	P103 Y106 H123 Y211 C212 M220 H221 E247
Annotation score	1
Binding affinity	PDBbind-CN: -logKd/Ki=6.34,Ki=0.46uM

Enzyme Commision number

3.4.11.18: methionyl aminopeptidase.

	Molecular Function
GO:0070006	metalloaminopeptidase activity

	Biological Process
GO:0006508	proteolysis

PDB	RCSB:5yr4, PDBe:5yr4, PDBj:5yr4
PDBsum	5yr4
PubMed	30837307
UniProt	P53582\|MAP11_HUMAN Methionine aminopeptidase 1 (Gene Name=METAP1)

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Structure of PDB 5yr4 Chain A Binding Site BS04