8VHE

Crystal Structure of Human IDH1 R132Q in Complex with NADPH-TCEP Adduct

PDB DOI: https://doi.org/10.2210/pdb8VHE/pdb

Classification: OXIDOREDUCTASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2023-12-31 Released: 2024-04-24
Deposition Author(s): Mealka, M., Sohl, C.D., Huxford, T.
Funding Organization(s): American Cancer Society, National Institutes of Health/National Cancer Institute (NIH/NCI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.16 Å
R-Value Free: 0.223
R-Value Work: 0.171
R-Value Observed: 0.174

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Active site remodeling in tumor-relevant IDH1 mutants drive distinct kinetic features and possible resistance mechanisms

Mealka, M., Sohl, C.D., Huxford, T.

To be published.

Macromolecule Content

Total Structure Weight: 199.29 kDa
Atom Count: 14,414
Modelled Residue Count: 1,660
Deposited Residue Count: 1,720
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isocitrate dehydrogenase [NADP] cytoplasmic	A, B, C, D	430	Homo sapiens	Mutation(s): 1 Gene Names: IDH1, PICD EC: 1.1.1.42
UniProt & NIH Common Fund Data Resources
Find proteins for O75874 (Homo sapiens) Explore O75874 Go to UniProtKB: O75874
PHAROS: O75874 GTEx: ENSG00000138413
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O75874
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1AAX (Subject of Investigation/LOI) Query on A1AAX Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain K [auth B] SDF format, chain R [auth C] SDF format, chain X [auth D] MOL2 format, chain E [auth A] MOL2 format, chain K [auth B] MOL2 format, chain R [auth C] MOL2 format, chain X [auth D]	E [auth A], K [auth B], R [auth C], X [auth D]	3,3',3''-({(4R)-1-[(2R,3R,4S,5R)-5-({[(S)-{[(S)-{[(2R,3R,4R,5R)-5-(6-amino-9H-purin-9-yl)-3-hydroxy-4-(phosphonooxy)oxolan-2-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}methyl)-3,4-dihydroxyoxolan-2-yl]-3-carbamoyl-1,4-dihydropyridin-4-yl}-lambda~5~-phosphanetriyl)tripropanoic acid C₃₀ H₄₅ N₇ O₂₃ P₄ JKBBAKXQOZUNQB-OUZSCQEMSA-N		Interactions Focus chain E [auth A] Focus chain K [auth B] Focus chain R [auth C] Focus chain X [auth D] Interactions & Density Focus chain E [auth A] Focus chain K [auth B] Focus chain R [auth C] Focus chain X [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain L [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain S [auth C] SDF format, chain W [auth D] SDF format, chain Z [auth D] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain L [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain S [auth C] MOL2 format, chain W [auth D] MOL2 format, chain Z [auth D]	F [auth A] G [auth A] H [auth A] L [auth B] N [auth B] F [auth A], G [auth A], H [auth A], L [auth B], N [auth B], O [auth B], S [auth C], W [auth D], Z [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain S [auth C] Focus chain W [auth D] Focus chain Z [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain S [auth C] Focus chain W [auth D] Focus chain Z [auth D]
SCN Query on SCN Download Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain T [auth C] SDF format, chain Y [auth D] MOL2 format, chain M [auth B] MOL2 format, chain T [auth C] MOL2 format, chain Y [auth D]	M [auth B], T [auth C], Y [auth D]	THIOCYANATE ION C N S ZMZDMBWJUHKJPS-UHFFFAOYSA-M		Interactions Focus chain M [auth B] Focus chain T [auth C] Focus chain Y [auth D] Interactions & Density Focus chain M [auth B] Focus chain T [auth C] Focus chain Y [auth D]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain J [auth A] SDF format, chain Q [auth B] SDF format, chain V [auth C] MOL2 format, chain BA [auth D] MOL2 format, chain J [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain V [auth C]	BA [auth D], J [auth A], Q [auth B], V [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain BA [auth D] Focus chain J [auth A] Focus chain Q [auth B] Focus chain V [auth C] Interactions & Density Focus chain BA [auth D] Focus chain J [auth A] Focus chain Q [auth B] Focus chain V [auth C]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain I [auth A] SDF format, chain P [auth B] SDF format, chain U [auth C] MOL2 format, chain AA [auth D] MOL2 format, chain I [auth A] MOL2 format, chain P [auth B] MOL2 format, chain U [auth C]	AA [auth D], I [auth A], P [auth B], U [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AA [auth D] Focus chain I [auth A] Focus chain P [auth B] Focus chain U [auth C] Interactions & Density Focus chain AA [auth D] Focus chain I [auth A] Focus chain P [auth B] Focus chain U [auth C]