5IDZ

Structure of Human Enolase 2 in complex with (S)-(1-hydroxy-2-oxopiperidin-3-yl)phosphonate

PDB DOI: https://doi.org/10.2210/pdb5IDZ/pdb

Classification: LYASE/LYASE INHIBITOR
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2016-02-24 Released: 2017-02-22
Deposition Author(s): Leonard, P.G., Muller, F.L.
Funding Organization(s): Cancer Prevention and Research Institute of Texas (CPRIT), American Cancer Society

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.63 Å
R-Value Free: 0.218
R-Value Work: 0.162
R-Value Observed: 0.165

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Pomhex, a cell-permeable Enolase inhibitor for Collateral Lethality targeting of ENO1-deleted Glioblastoma

Lin, Y.H., Satani, N., Hammoudi, N., Felini, F., Leonard, P.G., Maxwell, D., Link, T., Lee, G.R., Bosajou, A., Duoli, S., Marszalek, J.R., Sun, Y.T., McMurray, J., Mandal, P.J., DiFrancesco, M.E., Czako, B., Wang, A., Bornmann, W., DePinho, R.A., Muller, F.L.

To be published.

Macromolecule Content

Total Structure Weight: 97.04 kDa
Atom Count: 6,894
Modelled Residue Count: 870
Deposited Residue Count: 880
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Gamma-enolase	A, B	440	Homo sapiens	Mutation(s): 0 Gene Names: ENO2 EC: 4.2.1.11
UniProt & NIH Common Fund Data Resources
Find proteins for P09104 (Homo sapiens) Explore P09104 Go to UniProtKB: P09104
PHAROS: P09104 GTEx: ENSG00000111674
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P09104
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
6BM Query on 6BM Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain G [auth B] MOL2 format, chain D [auth A] MOL2 format, chain G [auth B]	D [auth A], G [auth B]	[(3S)-1-hydroxy-2-oxopiperidin-3-yl]phosphonic acid C₅ H₁₀ N O₅ P DVZQUMSQEGOYMX-BYPYZUCNSA-N		Interactions Focus chain D [auth A] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain G [auth B]
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B]	E [auth A], H [auth B]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Interactions & Density Focus chain E [auth A] Focus chain H [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain F [auth B] MOL2 format, chain C [auth A] MOL2 format, chain F [auth B]	C [auth A], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.63 Å
R-Value Free: 0.218
R-Value Work: 0.162
R-Value Observed: 0.165
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.1	α = 90
b = 108.74	β = 90
c = 116.46	γ = 90

Software Package:

Software Name	Purpose
iMOSFLM	data reduction
Aimless	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2017-02-22

Deposition Author(s):

Leonard, P.G.

Muller, F.L.

Funding Organization	Location	Grant Number
Cancer Prevention and Research Institute of Texas (CPRIT)	United States	RP140612
American Cancer Society	United States	365082

Revision History (Full details and data files)

Version 1.0: 2017-02-22
Type: Initial release
Version 1.1: 2019-04-24
Changes: Author supporting evidence, Data collection
Version 1.2: 2020-01-08
Changes: Author supporting evidence
Version 1.3: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description

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Help and Resources

5IDZ

Structure of Human Enolase 2 in complex with (S)-(1-hydroxy-2-oxopiperidin-3-yl)phosphonate

Pomhex, a cell-permeable Enolase inhibitor for Collateral Lethality targeting of ENO1-deleted Glioblastoma

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)