Structure of PDB 1k9s Chain A Binding Site BS02

Receptor Information

>1k9s Chain A (length=237) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

ATPHINAEMGDFADVVLMPGDPLRAKYIAETFLEDAREVNNVRGMLGFTG
TYKGRKISVMGHGMGIPSCSIYTKELITDFGVKKIIRVGSCGAVLPHVKL
RDVVIGMGACTDSKVNRIRFKDHDFAAIADFDMVRNAVDAAKALGIDARV
GNLFSADLFYSPDGEMFDVMEKYGILGVEMEAAGIYGVAAEFGAKALTIC
TVSDHIRTHEQTTAAERQTTFNDMIKIALESVLLGDK

Ligand information

Ligand ID

FM2

InChI

InChI=1S/C11H15N5O4/c1-16-3-13-5-6(14-15-7(5)11(16)12)10-9(19)8(18)4(2-17)20-10/h3-4,8-10,17-19H,2H2,1H3,(H2,12,14,15)/p+1/t4-,8-,9-,10+/m1/s1

InChIKey

UHYKIYIKTWEXSX-LFAOKBQASA-O

SMILES

Software	SMILES
OpenEye OEToolkits 1.5.0	C[n+]1cnc2c(c1N)[nH]nc2C3C(C(C(O3)CO)O)O
OpenEye OEToolkits 1.5.0	C[n+]1cnc2c(c1N)[nH]nc2[C@H]3[C@@H]([C@@H]([C@H](O3)CO)O)O
ACDLabs 10.04	OC1C(OC(CO)C1O)c3nnc2c(N)[n+](cnc23)C
CACTVS 3.341	C[n+]1cnc2c([nH]nc2[CH]3O[CH](CO)[CH](O)[CH]3O)c1N
CACTVS 3.341	C[n+]1cnc2c([nH]nc2[C@@H]3O[C@H](CO)[C@@H](O)[C@H]3O)c1N

Formula

C11 H16 N5 O4

Name

2-(7-AMINO-6-METHYL-3H-PYRAZOLO[4,3-D]PYRIMIDIN-3-YL)-5-HYDROXYMETHYL-TETRAHYDRO-FURAN-3,4-DIOL;
6-METHYL-FORMYCIN A

PDB chain

1k9s Chain A Residue 9901 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure

Global view

Local view

Structure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]

PDB	1k9s Open and closed conformation of the E. coli purine nucleoside phosphorylase active center and implications for the catalytic mechanism.
Resolution	2.0 Å
Binding residue (original residue number in PDB)	M64 S90 C91 G92 F159 V178 E179 M180 E181 S203
Binding residue (residue number reindexed from 1)	M64 S90 C91 G92 F159 V178 E179 M180 E181 S203
Annotation score	1
Binding affinity	PDBbind-CN: -logKd/Ki=6.52,Ki=0.30uM

Enzymatic activity

Catalytic site (original residue number in PDB)	H4 G20 R24 R43 E75 R87 S90 S203 D204 I206 R217
Catalytic site (residue number reindexed from 1)	H4 G20 R24 R43 E75 R87 S90 S203 D204 I206 R217
Enzyme Commision number	2.4.2.1: purine-nucleoside phosphorylase.

Gene Ontology

	Molecular Function
GO:0003824	catalytic activity
GO:0004731	purine-nucleoside phosphorylase activity
GO:0016757	glycosyltransferase activity
GO:0016763	pentosyltransferase activity
GO:0042802	identical protein binding
GO:0047975	guanosine phosphorylase activity

	Biological Process
GO:0006139	nucleobase-containing compound metabolic process
GO:0006152	purine nucleoside catabolic process
GO:0006974	DNA damage response
GO:0009116	nucleoside metabolic process
GO:0009164	nucleoside catabolic process
GO:0019686	purine nucleoside interconversion
GO:0042278	purine nucleoside metabolic process

	Cellular Component
GO:0005737	cytoplasm
GO:0005829	cytosol
GO:0016020	membrane

View graph for
Molecular Function

View graph for
Biological Process

View graph for
Cellular Component

External links

PDB	RCSB:1k9s, PDBe:1k9s, PDBj:1k9s
PDBsum	1k9s
PubMed	11786017
UniProt	P0ABP8\|DEOD_ECOLI Purine nucleoside phosphorylase DeoD-type (Gene Name=deoD)

[Back to BioLiP]