Structure of PDB 6f4w Chain A Binding Site BS01

Receptor Information

>6f4w Chain A (length=233) Species: 210 (Helicobacter pylori) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

MTPHINAKIGDFYPQCLLCGDPLRVSYIAKKFLQDAKEITNVRNMLGFSG
KYKGRGISLMGHGMGIASCTIYVTELIKTYQVKELLRIGTCGAISPKVGL
KDIIMATGASTDSKTNRVRFLNHDLSATPDFELSLRAYQTAKRLGIDLKV
GNVFSSDFFYSFETHAFDLMAKYNHLAIEMEAAGLYATAMELNAKALCLC
SVSDHLITKEALSPKERVESFDNMIILALEMMS

Ligand information

Ligand ID

FMC

InChI

InChI=1S/C10H13N5O4/c11-10-6-4(12-2-13-10)5(14-15-6)9-8(18)7(17)3(1-16)19-9/h2-3,7-9,16-18H,1H2,(H,14,15)(H2,11,12,13)/t3-,7-,8-,9+/m1/s1

InChIKey

KBHMEHLJSZMEMI-KSYZLYKTSA-N

SMILES

Software	SMILES
CACTVS 3.370	Nc1ncnc2c1[nH]nc2[C@@H]3O[C@H](CO)[C@@H](O)[C@H]3O
CACTVS 3.370	Nc1ncnc2c1[nH]nc2[CH]3O[CH](CO)[CH](O)[CH]3O
ACDLabs 12.01	OC1C(OC(CO)C1O)c3nnc2c3ncnc2N
OpenEye OEToolkits 1.7.0	c1nc2c(c(n1)N)[nH]nc2C3C(C(C(O3)CO)O)O
OpenEye OEToolkits 1.7.0	c1nc2c(c(n1)N)[nH]nc2[C@H]3[C@@H]([C@@H]([C@H](O3)CO)O)O

Formula

C10 H13 N5 O4

Name

(1S)-1-(7-amino-1H-pyrazolo[4,3-d]pyrimidin-3-yl)-1,4-anhydro-D-ribitol

PDB chain

6f4w Chain A Residue 300 [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	6f4w Helicobacter pylori purine nucleoside phosphorylase shows new distribution patterns of open and closed active site conformations and unusual biochemical features.
Resolution	2.293 Å
Binding residue (original residue number in PDB)	M64 C91 G92 F159 E179 E181 D204
Binding residue (residue number reindexed from 1)	M64 C91 G92 F159 E179 E181 D204
Annotation score	1
Binding affinity	MOAD: Kd=2.95uM PDBbind-CN: -logKd/Ki=5.53,Kd=2.95uM

Enzymatic activity

Catalytic site (original residue number in PDB)	H4 G20 R24 R43 E75 R87 T90 S203 D204 L206 R217
Catalytic site (residue number reindexed from 1)	H4 G20 R24 R43 E75 R87 T90 S203 D204 L206 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

	Biological Process
GO:0006139	nucleobase-containing compound metabolic process
GO:0006152	purine nucleoside catabolic process
GO:0009116	nucleoside metabolic process
GO:0009164	nucleoside catabolic process

	Cellular Component
GO:0005829	cytosol

View graph for
Molecular Function

View graph for
Biological Process

View graph for
Cellular Component

External links

PDB	RCSB:6f4w, PDBe:6f4w, PDBj:6f4w
PDBsum	6f4w
PubMed	29430816
UniProt	P56463\|DEOD_HELPY Purine nucleoside phosphorylase DeoD-type (Gene Name=deoD)

[Back to BioLiP]