5EU9 | pdb_00005eu9

Structure of Human Enolase 2 in complex with ((3S,5S)-1,5-dihydroxy-3-methyl-2-oxopyrrolidin-3-yl)phosphonic acid

PDB DOI: https://doi.org/10.2210/pdb5EU9/pdb

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

Deposited: 2015-11-18 Released: 2016-11-23
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: 2.05 Å
R-Value Free:
0.192 (Depositor), 0.190 (DCC)
R-Value Work:
0.154 (Depositor), 0.160 (DCC)
R-Value Observed:
0.154 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

SF2312, a natural phosphonate inhibitor of Enolase

Leonard, P.G., Maxwell, D., Satani, N., Peng, Z., Link, T., Lee, G., Bosajou, A., Sun, D., Lin, Y.E., DiFrancesco, M.E., Czako, B., Wang, Y.A., Bornmann, W., DePhinho, R.A., Muller, F.L.

To be published.

Macromolecule Content

Total Structure Weight: 388.17 kDa
Atom Count: 29,111
Modeled Residue Count: 3,468
Deposited Residue Count: 3,520
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, C, D, E A, B, C, D, E, F, G, H	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
5TX Query on 5TX Download Ideal Coordinates CCD File SDF format, chain DA [auth F] SDF format, chain HA [auth G] SDF format, chain K [auth A] SDF format, chain LA [auth H] SDF format, chain N [auth B] SDF format, chain R [auth C] SDF format, chain V [auth D] SDF format, chain Z [auth E] MOL2 format, chain DA [auth F] MOL2 format, chain HA [auth G] MOL2 format, chain K [auth A] MOL2 format, chain LA [auth H] MOL2 format, chain N [auth B] MOL2 format, chain R [auth C] MOL2 format, chain V [auth D] MOL2 format, chain Z [auth E] mmCIF format, chain DA [auth F] mmCIF format, chain HA [auth G] mmCIF format, chain K [auth A] mmCIF format, chain LA [auth H] mmCIF format, chain N [auth B] mmCIF format, chain R [auth C] mmCIF format, chain V [auth D] mmCIF format, chain Z [auth E]	DA [auth F] HA [auth G] K [auth A] LA [auth H] N [auth B] DA [auth F], HA [auth G], K [auth A], LA [auth H], N [auth B], R [auth C], V [auth D], Z [auth E]	((3S,5S)-1,5-dihydroxy-3-methyl-2-oxopyrrolidin-3-yl)phosphonic acid C₅ H₁₀ N O₆ P VVBLYPMICKYZTP-UCORVYFPSA-N		Interactions Focus chain DA [auth F] Focus chain HA [auth G] Focus chain K [auth A] Focus chain LA [auth H] Focus chain N [auth B] Focus chain R [auth C] Focus chain V [auth D] Focus chain Z [auth E] Interactions & Density Focus chain DA [auth F] Focus chain HA [auth G] Focus chain K [auth A] Focus chain LA [auth H] Focus chain N [auth B] Focus chain R [auth C] Focus chain V [auth D] Focus chain Z [auth E]
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain CA [auth F] SDF format, chain GA [auth G] SDF format, chain KA [auth H] SDF format, chain Q [auth C] SDF format, chain U [auth D] SDF format, chain Y [auth E] MOL2 format, chain CA [auth F] MOL2 format, chain GA [auth G] MOL2 format, chain KA [auth H] MOL2 format, chain Q [auth C] MOL2 format, chain U [auth D] MOL2 format, chain Y [auth E] mmCIF format, chain CA [auth F] mmCIF format, chain GA [auth G] mmCIF format, chain KA [auth H] mmCIF format, chain Q [auth C] mmCIF format, chain U [auth D] mmCIF format, chain Y [auth E]	CA [auth F] GA [auth G] KA [auth H] Q [auth C] U [auth D] CA [auth F], GA [auth G], KA [auth H], Q [auth C], U [auth D], Y [auth E]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain CA [auth F] Focus chain GA [auth G] Focus chain KA [auth H] Focus chain Q [auth C] Focus chain U [auth D] Focus chain Y [auth E] Interactions & Density Focus chain CA [auth F] Focus chain GA [auth G] Focus chain KA [auth H] Focus chain Q [auth C] Focus chain U [auth D] Focus chain Y [auth E]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain AA [auth F] SDF format, chain BA [auth F] SDF format, chain EA [auth G] SDF format, chain FA [auth G] SDF format, chain I [auth A] SDF format, chain IA [auth H] SDF format, chain J [auth A] SDF format, chain JA [auth H] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain O [auth C] SDF format, chain P [auth C] SDF format, chain S [auth D] SDF format, chain T [auth D] SDF format, chain W [auth E] SDF format, chain X [auth E] MOL2 format, chain AA [auth F] MOL2 format, chain BA [auth F] MOL2 format, chain EA [auth G] MOL2 format, chain FA [auth G] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth H] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth H] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain O [auth C] MOL2 format, chain P [auth C] MOL2 format, chain S [auth D] MOL2 format, chain T [auth D] MOL2 format, chain W [auth E] MOL2 format, chain X [auth E] mmCIF format, chain AA [auth F] mmCIF format, chain BA [auth F] mmCIF format, chain EA [auth G] mmCIF format, chain FA [auth G] mmCIF format, chain I [auth A] mmCIF format, chain IA [auth H] mmCIF format, chain J [auth A] mmCIF format, chain JA [auth H] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain O [auth C] mmCIF format, chain P [auth C] mmCIF format, chain S [auth D] mmCIF format, chain T [auth D] mmCIF format, chain W [auth E] mmCIF format, chain X [auth E]	AA [auth F] BA [auth F] EA [auth G] FA [auth G] I [auth A] AA [auth F], BA [auth F], EA [auth G], FA [auth G], I [auth A], IA [auth H], J [auth A], JA [auth H], L [auth B], M [auth B], O [auth C], P [auth C], S [auth D], T [auth D], W [auth E], X [auth E]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AA [auth F] Focus chain BA [auth F] Focus chain EA [auth G] Focus chain FA [auth G] Focus chain I [auth A] Focus chain IA [auth H] Focus chain J [auth A] Focus chain JA [auth H] Focus chain L [auth B] Focus chain M [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain S [auth D] Focus chain T [auth D] Focus chain W [auth E] Focus chain X [auth E] Interactions & Density Focus chain AA [auth F] Focus chain BA [auth F] Focus chain EA [auth G] Focus chain FA [auth G] Focus chain I [auth A] Focus chain IA [auth H] Focus chain J [auth A] Focus chain JA [auth H] Focus chain L [auth B] Focus chain M [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain S [auth D] Focus chain T [auth D] Focus chain W [auth E] Focus chain X [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free: 0.192 (Depositor), 0.190 (DCC)
R-Value Work: 0.154 (Depositor), 0.160 (DCC)
R-Value Observed: 0.154 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 119.251	α = 90
b = 110.31	β = 90
c = 136.93	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2016-11-23

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: 2016-11-23
Type: Initial release
Version 1.1: 2017-11-22
Changes: Refinement description
Version 1.2: 2019-04-24
Changes: Author supporting evidence, Data collection
Version 1.3: 2020-01-08
Changes: Author supporting evidence
Version 1.4: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description