Structure of PDB 5e2a Chain A Binding Site BS02

Receptor Information
>5e2a Chain A (length=227) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VPRGSTSEVIEDEKQFYSKAKTYWKQIPPTVDGMLGGYGHISSIDINSSR
KFLQRFLREGPNKTGTSCALDCGAGIGRITKRLLLPLFREVDMVDITEDF
LVQAKTYLGEEGKRVRNYFCCGLQDFTPEPDSYDVIWIQWVIGHLTDQHL
AEFLRRCKGSLRPNGIIVIKDNMAQEGVILDDVDSSVCRDLDVVRRIICS
AGLSLLAEERQENLPDEIYHVYSFALR
Ligand information
Ligand IDSAH
InChIInChI=1S/C14H20N6O5S/c15-6(14(23)24)1-2-26-3-7-9(21)10(22)13(25-7)20-5-19-8-11(16)17-4-18-12(8)20/h4-7,9-10,13,21-22H,1-3,15H2,(H,23,24)(H2,16,17,18)/t6-,7+,9+,10+,13+/m0/s1
InChIKeyZJUKTBDSGOFHSH-WFMPWKQPSA-N
SMILES
SoftwareSMILES
CACTVS 3.341N[CH](CCSC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23)C(O)=O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)CSCCC(C(=O)O)N)O)O)N
CACTVS 3.341N[C@@H](CCSC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23)C(O)=O
ACDLabs 10.04O=C(O)C(N)CCSCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CSCC[C@@H](C(=O)O)N)O)O)N
FormulaC14 H20 N6 O5 S
NameS-ADENOSYL-L-HOMOCYSTEINE
ChEMBLCHEMBL418052
DrugBankDB01752
ZINCZINC000004228232
PDB chain5e2a Chain A Residue 301 [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]
PDB5e2a Structural basis for substrate recognition by the human N-terminal methyltransferase 1.
Resolution1.75 Å
Binding residue
(original residue number in PDB)		W20 M30 G69 G71 R74 I75 D91 I92 T93 F96 G118 L119 Q135 W136 V137 H140
Binding residue
(residue number reindexed from 1)		W24 M34 G73 G75 R78 I79 D95 I96 T97 F100 G122 L123 Q139 W140 V141 H144
Annotation score5
Enzymatic activity
Enzyme Commision number 2.1.1.244: protein N-terminal methyltransferase.
Gene Ontology
Molecular Function
GO:0005515 protein binding
GO:0008168 methyltransferase activity
GO:0008276 protein methyltransferase activity
GO:0042054 histone methyltransferase activity
GO:0071885 N-terminal protein N-methyltransferase activity
Biological Process
GO:0006338 chromatin remodeling
GO:0006480 N-terminal protein amino acid methylation
GO:0007051 spindle organization
GO:0007059 chromosome segregation
GO:0018012 N-terminal peptidyl-alanine trimethylation
GO:0018013 N-terminal peptidyl-glycine methylation
GO:0018016 N-terminal peptidyl-proline dimethylation
GO:0032259 methylation
GO:0035572 N-terminal peptidyl-serine dimethylation
GO:0035573 N-terminal peptidyl-serine trimethylation
Cellular Component
GO:0005634 nucleus
GO:0005654 nucleoplasm
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:5e2a, PDBe:5e2a, PDBj:5e2a
PDBsum5e2a
PubMed26543161
UniProtQ9BV86|NTM1A_HUMAN N-terminal Xaa-Pro-Lys N-methyltransferase 1 (Gene Name=NTMT1)

[Back to BioLiP]