8VHA

Crystal Structure of Human IDH1 R132Q in complex with NADPH and Alpha-Ketoglutarate

PDB DOI: https://doi.org/10.2210/pdb8VHA/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: 2.28 Å
R-Value Free: 0.222
R-Value Work: 0.167
R-Value Observed: 0.170

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: 197.85 kDa
Atom Count: 13,764
Modelled Residue Count: 1,649
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 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EE1 (Subject of Investigation/LOI) Query on EE1 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain M [auth C] MOL2 format, chain E [auth A] MOL2 format, chain M [auth C]	E [auth A], M [auth C]	(3~{S})-3-[(4~{S})-3-aminocarbonyl-1-[(2~{R},3~{R},4~{S},5~{R})-5-[[[[(2~{R},3~{R},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3-oxidanyl-4-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxymethyl]-3,4-bis(oxidanyl)oxolan-2-yl]-4~{H}-pyridin-4-yl]-2-oxidanylidene-pentanedioic acid C₂₆ H₃₄ N₇ O₂₂ P₃ WSGZIHXYYXDDDT-PJNAXEGASA-N		Interactions Focus chain E [auth A] Focus chain M [auth C] Interactions & Density Focus chain E [auth A] Focus chain M [auth C]
NDP (Subject of Investigation/LOI) Query on NDP Download Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain O [auth D] MOL2 format, chain H [auth B] MOL2 format, chain O [auth D]	H [auth B], O [auth D]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₃₀ N₇ O₁₇ P₃ ACFIXJIJDZMPPO-NNYOXOHSSA-N		Interactions Focus chain H [auth B] Focus chain O [auth D] Interactions & Density Focus chain H [auth B] Focus chain O [auth D]
AKG (Subject of Investigation/LOI) Query on AKG Download Ideal Coordinates CCD File SDF format, chain J [auth B] MOL2 format, chain J [auth B]	J [auth B]	2-OXOGLUTARIC ACID C₅ H₆ O₅ KPGXRSRHYNQIFN-UHFFFAOYSA-N		Interactions Focus chain J [auth B] Interactions & Density Focus chain J [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain P [auth D] MOL2 format, chain P [auth D]	P [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain P [auth D] Interactions & Density Focus chain P [auth D]
NO3 Query on NO3 Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain I [auth B] SDF format, chain L [auth C] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain L [auth C]	F [auth A], I [auth B], L [auth C]	NITRATE ION N O₃ NHNBFGGVMKEFGY-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain I [auth B] Focus chain L [auth C] Interactions & Density Focus chain F [auth A] Focus chain I [auth B] Focus chain L [auth C]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain K [auth B] SDF format, chain N [auth C] SDF format, chain Q [auth D] MOL2 format, chain G [auth A] MOL2 format, chain K [auth B] MOL2 format, chain N [auth C] MOL2 format, chain Q [auth D]	G [auth A], K [auth B], N [auth C], Q [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain K [auth B] Focus chain N [auth C] Focus chain Q [auth D] Interactions & Density Focus chain G [auth A] Focus chain K [auth B] Focus chain N [auth C] Focus chain Q [auth D]