Structure of PDB 1nm9 Chain A Binding Site BS05

Receptor Information
>1nm9 Chain A (length=496) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QYSSNTQQGRTSIVHLFEWRWVDIALECERYLAPKGFGGVQVSPPNENVA
IHNPFRPAWERYQPVSYKLCTRSGNEDEFRNMVTRCNNVGVRIYVDAVIN
HMCGNAVSAGTSSTCGSYFNPGSRDFPAVPYSGWDFNDGKCKTGSGDIEN
YNDATQVRDCRLSGLLDLALGKDYVRSKIAEYMNHLIDIGVAGFRIDASK
HMWPGDIKAILDKLHNLNSNWFPEGSKPFIYQEVIDLGGEPIKSSDYFGN
GRVTEFKYGAKLGTVIRKWNGEKMSYLKNWGEGWGFMPSDRALVFVDNHD
NQRGHGAGGASILTFWDARLYKMAVGFMLAHPYGFTRVMSSYRWPRYFEN
GKDVNDWVGPPNDNGVTKEVTINPDTTCGNDWVCEHRWRQIRNMVNFRNV
VDGQPFTNWYDNGSNQVAFGRGNRGFIVFNNDDWTFSLTLQTGLPAGTYC
DVISGDKINGNCTGIKIYVSDDGKAHFSISNSAEDPFIAIHAESKL
Ligand information
Ligand IDHMC
InChIInChI=1S/C7H12O5/c8-2-3-1-4(9)6(11)7(12)5(3)10/h1,4-12H,2H2/t4-,5+,6-,7-/m0/s1
InChIKeyPJPGMULJEYSZBS-VZFHVOOUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C1=C(C(C(C(C1O)O)O)O)CO
ACDLabs 10.04OC1C(=CC(O)C(O)C1O)CO
OpenEye OEToolkits 1.5.0C1=C([C@H]([C@@H]([C@H]([C@H]1O)O)O)O)CO
CACTVS 3.341OCC1=C[CH](O)[CH](O)[CH](O)[CH]1O
CACTVS 3.341OCC1=C[C@H](O)[C@H](O)[C@@H](O)[C@@H]1O
FormulaC7 H12 O5
Name5-HYDROXYMETHYL-CHONDURITOL
ChEMBLCHEMBL1233349
DrugBankDB03092
ZINC
PDB chain1nm9 Chain A Residue 504 [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]
PDB1nm9 Human salivary alpha-amylase Trp58 situated at subsite -2 is critical for enzyme activity.
Resolution2.1 Å
Binding residue
(original residue number in PDB)		Y62 H101 D197 E233 H299 D300
Binding residue
(residue number reindexed from 1)		Y62 H101 D197 E233 H299 D300
Annotation score1
Enzymatic activity
Enzyme Commision number 3.2.1.1: alpha-amylase.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0004556 alpha-amylase activity
GO:0005509 calcium ion binding
GO:0016160 amylase activity
GO:0016798 hydrolase activity, acting on glycosyl bonds
GO:0031404 chloride ion binding
GO:0043169 cation binding
GO:0046872 metal ion binding
Biological Process
GO:0005975 carbohydrate metabolic process
GO:0009311 oligosaccharide metabolic process
Cellular Component
GO:0005576 extracellular region
GO:0005615 extracellular space
GO:0070062 extracellular exosome

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:1nm9, PDBe:1nm9, PDBj:1nm9
PDBsum1nm9
PubMed15182367
UniProtP0DUB6|AMY1A_HUMAN Alpha-amylase 1A (Gene Name=AMY1A)

[Back to BioLiP]