6M61

Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) with inhibitor heptelidic acid

PDB DOI: https://doi.org/10.2210/pdb6M61/pdb

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

Deposited: 2020-03-12 Released: 2020-12-30
Deposition Author(s): Yan, Y., Zang, X., Cooper, S.J., Lin, H., Zhou, J., Tang, Y.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.82 Å
R-Value Free:
0.228 (Depositor), 0.230 (DCC)
R-Value Work:
0.192 (Depositor), 0.190 (DCC)
R-Value Observed:
0.193 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Biosynthesis of the fungal glyceraldehyde-3-phosphate dehydrogenase inhibitor heptelidic acid and mechanism of self-resistance

Yan, Y., Zang, X., Cooper, S.J., Lin, H., Zhou, J., Tang, Y.

(2020) Chem Sci 11: 9554-9562

DOI: https://doi.org/10.1039/D0SC03805A

Macromolecule Content

Total Structure Weight: 148.08 kDa
Atom Count: 11,441
Modelled Residue Count: 1,334
Deposited Residue Count: 1,344
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glyceraldehyde-3-phosphate dehydrogenase	A [auth O], B [auth Q], C [auth P], D [auth R]	336	Homo sapiens	Mutation(s): 0 Gene Names: GAPDH, GAPD, CDABP0047, OK/SW-cl.12 EC: 1.2.1.12 (PDB Primary Data), 2.6.99 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P04406 (Homo sapiens) Explore P04406 Go to UniProtKB: P04406
PHAROS: P04406 GTEx: ENSG00000111640
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P04406
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD Download Ideal Coordinates CCD File SDF format, chain K [auth O] SDF format, chain S [auth Q] MOL2 format, chain K [auth O] MOL2 format, chain S [auth Q] mmCIF format, chain K [auth O] mmCIF format, chain S [auth Q]	K [auth O], S [auth Q]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain K [auth O] Focus chain S [auth Q] Interactions & Density Focus chain K [auth O] Focus chain S [auth Q]
F4F (Subject of Investigation/LOI) Query on F4F Download Ideal Coordinates CCD File SDF format, chain J [auth O] SDF format, chain R [auth Q] MOL2 format, chain J [auth O] MOL2 format, chain R [auth Q] mmCIF format, chain J [auth O] mmCIF format, chain R [auth Q]	J [auth O], R [auth Q]	(5aS,6R,9S,9aS)-9-methyl-9-oxidanyl-1-oxidanylidene-6-propan-2-yl-3,5a,6,7,8,9a-hexahydro-2-benzoxepine-4-carboxylic acid C₁₅ H₂₂ O₅ TVCGWSMBKPHYFK-BLTAXRJOSA-N		Interactions Focus chain J [auth O] Focus chain R [auth Q] Interactions & Density Focus chain J [auth O] Focus chain R [auth Q]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain G [auth O] MOL2 format, chain G [auth O] mmCIF format, chain G [auth O]	G [auth O]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain G [auth O] Interactions & Density Focus chain G [auth O]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain Z [auth R] MOL2 format, chain Z [auth R] mmCIF format, chain Z [auth R]	Z [auth R]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain Z [auth R] Interactions & Density Focus chain Z [auth R]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain H [auth O] SDF format, chain I [auth O] SDF format, chain Q SDF format, chain W [auth P] SDF format, chain X [auth P] MOL2 format, chain H [auth O] MOL2 format, chain I [auth O] MOL2 format, chain Q MOL2 format, chain W [auth P] MOL2 format, chain X [auth P] mmCIF format, chain H [auth O] mmCIF format, chain I [auth O] mmCIF format, chain Q mmCIF format, chain W [auth P] mmCIF format, chain X [auth P]	H [auth O], I [auth O], Q, W [auth P], X [auth P]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain H [auth O] Focus chain I [auth O] Focus chain Q Focus chain W [auth P] Focus chain X [auth P] Interactions & Density Focus chain H [auth O] Focus chain I [auth O] Focus chain Q Focus chain W [auth P] Focus chain X [auth P]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain E [auth O] SDF format, chain F [auth O] SDF format, chain L [auth Q] SDF format, chain M [auth Q] SDF format, chain N [auth Q] SDF format, chain O [auth Q] SDF format, chain P [auth Q] SDF format, chain T [auth P] SDF format, chain U [auth P] SDF format, chain V [auth P] SDF format, chain Y [auth R] MOL2 format, chain E [auth O] MOL2 format, chain F [auth O] MOL2 format, chain L [auth Q] MOL2 format, chain M [auth Q] MOL2 format, chain N [auth Q] MOL2 format, chain O [auth Q] MOL2 format, chain P [auth Q] MOL2 format, chain T [auth P] MOL2 format, chain U [auth P] MOL2 format, chain V [auth P] MOL2 format, chain Y [auth R] mmCIF format, chain E [auth O] mmCIF format, chain F [auth O] mmCIF format, chain L [auth Q] mmCIF format, chain M [auth Q] mmCIF format, chain N [auth Q] mmCIF format, chain O [auth Q] mmCIF format, chain P [auth Q] mmCIF format, chain T [auth P] mmCIF format, chain U [auth P] mmCIF format, chain V [auth P] mmCIF format, chain Y [auth R]	E [auth O] F [auth O] L [auth Q] M [auth Q] N [auth Q] E [auth O], F [auth O], L [auth Q], M [auth Q], N [auth Q], O [auth Q], P [auth Q], T [auth P], U [auth P], V [auth P], Y [auth R]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth O] Focus chain F [auth O] Focus chain L [auth Q] Focus chain M [auth Q] Focus chain N [auth Q] Focus chain O [auth Q] Focus chain P [auth Q] Focus chain T [auth P] Focus chain U [auth P] Focus chain V [auth P] Focus chain Y [auth R] Interactions & Density Focus chain E [auth O] Focus chain F [auth O] Focus chain L [auth Q] Focus chain M [auth Q] Focus chain N [auth Q] Focus chain O [auth Q] Focus chain P [auth Q] Focus chain T [auth P] Focus chain U [auth P] Focus chain V [auth P] Focus chain Y [auth R]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.82 Å
R-Value Free: 0.228 (Depositor), 0.230 (DCC)
R-Value Work: 0.192 (Depositor), 0.190 (DCC)
R-Value Observed: 0.193 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.358	α = 90
b = 135.078	β = 90
c = 146.227	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2020-12-30

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2020-12-30
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Database references, Refinement description
Version 1.2: 2024-11-20
Changes: Structure summary