3C56

Experimental Data Snapshot

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

(2008) Chemistry 14: 8521-8529

PubMed Abstract:
We report the synthesis and biochemical evaluation of selective inhibitors of class II (zinc-dependent) fructose bisphosphate aldolases. The most active compound is a simplified analogue of fructose bisphosphate, bearing a well-positioned metal chelating group. It is a powerful and highly selective competitive inhibitor of isolated class II aldolases. We report crystallographic studies of this inhibitor bound in the active site of the Helicobacter pylori enzyme. The compound also shows activity against Mycobacterium tuberculosis isolates.

Organizational Affiliation

LCBB-ICMMO, UMR 8182, Université Paris-Sud, Orsay, France.

Macromolecule Content

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fructose-bisphosphate aldolase	A, B	307	Helicobacter pylori	Mutation(s): 0 Gene Names: fba EC: 4.1.2.13
UniProt
Find proteins for P56109 (Helicobacter pylori (strain ATCC 700392 / 26695)) Explore P56109 Go to UniProtKB: P56109
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P56109
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PH4 Query on PH4 Download Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain D [auth A] MOL2 format, chain F [auth B] MOL2 format, chain D [auth A] mmCIF format, chain F [auth B] mmCIF format, chain D [auth A]	D [auth A], F [auth B]	3-{hydroxy[(phosphonooxy)acetyl]amino}propyl dihydrogen phosphate C₅ H₁₃ N O₁₀ P₂ IISKWLQYGVRJHI-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth B] mmCIF format, chain C [auth A] mmCIF format, chain E [auth B]	C [auth A], E [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
PH4	PDBBind: 3C56	Ki: 13 (nM) from 1 assay(s)
PH4	BindingDB: 3C56	Ki: 13 (nM) from 1 assay(s)

Experimental Data & Validation

Unit Cell:

Software Package:

Entry History

Deposition Author(s):

Coincon, M.

Version 1.0: 2008-08-26
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2018-01-24
Changes: Structure summary
Version 1.3: 2019-07-24
Changes: Data collection, Refinement description
Version 1.4: 2024-02-21
Changes: Data collection, Database references, Derived calculations
Version 1.5: 2024-04-03
Changes: Refinement description