Structure of PDB 2nmt Chain A Binding Site BS02

Receptor Information
>2nmt Chain A (length=422) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AMKDHKFWRTQPVKDFDEKVVEEGPIDKPKTPEDISDKPLPLLSSFEWCS
IDVDNKKQLEDVFVLLNENYVEDRDAGFRFNYTKEFFNWALKSPGWKKDW
HIGVRVKETQKLVAFISAIPVTLGVRGKQVPSVEINFLCVHKQLRSKRLT
PVLIKEITRRVNKCDIWHALYTAGIVLPAPVSTCRYTHRPLNWKKLYEVD
FTGLPDGHTEEDMIAENALPAKTKTAGLRKLKKEDIDQVFELFKRYQSRF
ELIQIFTKEEFEHNFIGEESLPLDKQVIFSYVVEQPDGKITDFFSFYSLP
FTILNNTKYKDLGIGYLYYYATDADFQFKDRFDPKATKALKTRLCELIYD
ACILAKNANMDVFNALTSQDNTLFLDDLKFGPGDGFLNFYLFNYRAKPIT
GGLNPDNSNDIKRRSNVGVVML
Ligand information
Ligand IDMIM
InChIInChI=1S/C33H52N6O4/c1-25-35-20-22-39(25)21-8-6-11-27-13-15-28(16-14-27)23-31(41)37-30(24-40)33(43)38-29(12-5-7-18-34)32(42)36-19-17-26-9-3-2-4-10-26/h13-16,20,22,26,29-30,40H,2-12,17-19,21,23-24,34H2,1H3,(H,36,42)(H,37,41)(H,38,43)/t29-,30-/m0/s1
InChIKeyWHLPIOSHBKQGHA-KYJUHHDHSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0Cc1nccn1CCCCc2ccc(cc2)CC(=O)N[C@@H](CO)C(=O)N[C@@H](CCCCN)C(=O)NCCC3CCCCC3
CACTVS 3.341Cc1nccn1CCCCc2ccc(CC(=O)N[C@@H](CO)C(=O)N[C@@H](CCCCN)C(=O)NCCC3CCCCC3)cc2
ACDLabs 10.04O=C(NCCC1CCCCC1)C(NC(=O)C(NC(=O)Cc2ccc(cc2)CCCCn3ccnc3C)CO)CCCCN
OpenEye OEToolkits 1.5.0Cc1nccn1CCCCc2ccc(cc2)CC(=O)NC(CO)C(=O)NC(CCCCN)C(=O)NCCC3CCCCC3
CACTVS 3.341Cc1nccn1CCCCc2ccc(CC(=O)N[CH](CO)C(=O)N[CH](CCCCN)C(=O)NCCC3CCCCC3)cc2
FormulaC33 H52 N6 O4
Name[CYCLOHEXYLETHYL]-[[[[4-[2-METHYL-1-IMIDAZOLYL-BUTYL]PHENYL]ACETYL]-SERYL]-LYSINYL]-AMINE
ChEMBLCHEMBL6269
DrugBankDB02477
ZINCZINC000014880363
PDB chain2nmt Chain A Residue 700 [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]
PDB2nmt Structure of N-myristoyltransferase with bound myristoylCoA and peptide substrate analogs.
Resolution2.9 Å
Binding residue
(original residue number in PDB)		V104 D106 D108 F113 Y115 G207 Y219 H221 P223 F234 T235 G416 D417 G418 L455
Binding residue
(residue number reindexed from 1)		V71 D73 D75 F80 Y82 G174 Y186 H188 P190 F201 T202 G383 D384 G385 L422
Annotation score1
Binding affinityBindingDB: IC50=24nM
Enzymatic activity
Catalytic site (original residue number in PDB) N169 F170 L171 T205 L455
Catalytic site (residue number reindexed from 1) N136 F137 L138 T172 L422
Enzyme Commision number 2.3.1.97: glycylpeptide N-tetradecanoyltransferase.
Gene Ontology
Molecular Function
GO:0004379 glycylpeptide N-tetradecanoyltransferase activity
GO:0016746 acyltransferase activity
Biological Process
GO:0006499 N-terminal protein myristoylation
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:2nmt, PDBe:2nmt, PDBj:2nmt
PDBsum2nmt
PubMed9846880
UniProtP14743|NMT_YEAST Glycylpeptide N-tetradecanoyltransferase (Gene Name=NMT1)

[Back to BioLiP]