Structure of PDB 3ern Chain A Binding Site BS02

Receptor Information

>3ern Chain A (length=157) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

EMRIGHGFDVHAFGGEGPIIIGGVRIPYEKGLLAHSDGDVALHALTDALL
GAAALGDIGKLFPDTDPAFKGADSRELLREAWRRIQAKGYTLGNVDVTII
AQAPKMLPHIPQMRVFIAEDLGCHMDDVNVKATTTEKLGFTGRGEGIACE
AVALLIK

Ligand information

Ligand ID

CAR

InChI

InChI=1S/C9H14N3O8P/c10-5-1-2-12(9(15)11-5)8-7(14)6(13)4(20-8)3-19-21(16,17)18/h1-2,4,6-8,13-14H,3H2,(H2,10,11,15)(H2,16,17,18)/t4-,6-,7+,8-/m1/s1

InChIKey

IERHLVCPSMICTF-CCXZUQQUSA-N

SMILES

Software	SMILES
CACTVS 3.341	NC1=NC(=O)N(C=C1)[CH]2O[CH](CO[P](O)(O)=O)[CH](O)[CH]2O
OpenEye OEToolkits 1.5.0	C1=CN(C(=O)N=C1N)C2C(C(C(O2)COP(=O)(O)O)O)O
CACTVS 3.341	NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@@H]2O
ACDLabs 10.04	O=C1N=C(N)C=CN1C2OC(C(O)C2O)COP(=O)(O)O
OpenEye OEToolkits 1.5.0	C1=CN(C(=O)N=C1N)[C@H]2[C@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O

Formula

C9 H14 N3 O8 P

Name

CYTOSINE ARABINOSE-5'-PHOSPHATE

PDB chain

3ern Chain A Residue 900 [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	3ern A structure-based approach to ligand discovery for 2C-methyl-D-erythritol-2,4-cyclodiphosphate synthase: a target for antimicrobial therapy
Resolution	2.1 Å
Binding residue (original residue number in PDB)	A100 K104 M105 L106 A131 T132 T133
Binding residue (residue number reindexed from 1)	A101 K105 M106 L107 A132 T133 T134
Annotation score	3
Binding affinity	MOAD: Kd=18.91mM PDBbind-CN: -logKd/Ki=1.72,Kd=18.91mM BindingDB: Kd=18910000nM

Enzymatic activity

Enzyme Commision number

4.6.1.12: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase.

Gene Ontology

	Molecular Function
GO:0005515	protein binding
GO:0008270	zinc ion binding
GO:0008685	2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase activity
GO:0016829	lyase activity
GO:0030145	manganese ion binding
GO:0042802	identical protein binding
GO:0046872	metal ion binding

	Biological Process
GO:0006744	ubiquinone biosynthetic process
GO:0008299	isoprenoid biosynthetic process
GO:0016114	terpenoid biosynthetic process
GO:0019288	isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway

View graph for
Molecular Function

View graph for
Biological Process

External links

PDB	RCSB:3ern, PDBe:3ern, PDBj:3ern
PDBsum	3ern
PubMed	19320487
UniProt	P62617\|ISPF_ECOLI 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (Gene Name=ispF)

[Back to BioLiP]