8VHB

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

PDB DOI: https://doi.org/10.2210/pdb8VHB/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: 1.89 Å
R-Value Free: 0.206
R-Value Work: 0.167
R-Value Observed: 0.169

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: 199.58 kDa
Atom Count: 14,601
Modelled Residue Count: 1,653
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 8 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 HA [auth D] SDF format, chain P [auth B] MOL2 format, chain HA [auth D] MOL2 format, chain P [auth B]	HA [auth D], P [auth B]	(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 HA [auth D] Focus chain P [auth B] Interactions & Density Focus chain HA [auth D] Focus chain P [auth B]
NDP (Subject of Investigation/LOI) Query on NDP Download Ideal Coordinates CCD File SDF format, chain BA [auth C] SDF format, chain F [auth A] MOL2 format, chain BA [auth C] MOL2 format, chain F [auth A]	BA [auth C], F [auth A]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₃₀ N₇ O₁₇ P₃ ACFIXJIJDZMPPO-NNYOXOHSSA-N		Interactions Focus chain BA [auth C] Focus chain F [auth A] Interactions & Density Focus chain BA [auth C] Focus chain F [auth A]
AKG (Subject of Investigation/LOI) Query on AKG Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain E [auth A] MOL2 format, chain AA [auth C] MOL2 format, chain E [auth A]	AA [auth C], E [auth A]	2-OXOGLUTARIC ACID C₅ H₆ O₅ KPGXRSRHYNQIFN-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain E [auth A] Interactions & Density Focus chain AA [auth C] Focus chain E [auth A]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain MA [auth D] MOL2 format, chain MA [auth D]	MA [auth D]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain MA [auth D] Interactions & Density Focus chain MA [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain EA [auth C] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain JA [auth D] SDF format, chain KA [auth D] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain X [auth B] MOL2 format, chain EA [auth C] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain JA [auth D] MOL2 format, chain KA [auth D] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain X [auth B]	EA [auth C] G [auth A] H [auth A] JA [auth D] KA [auth D] EA [auth C], G [auth A], H [auth A], JA [auth D], KA [auth D], R [auth B], S [auth B], X [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain EA [auth C] Focus chain G [auth A] Focus chain H [auth A] Focus chain JA [auth D] Focus chain KA [auth D] Focus chain R [auth B] Focus chain S [auth B] Focus chain X [auth B] Interactions & Density Focus chain EA [auth C] Focus chain G [auth A] Focus chain H [auth A] Focus chain JA [auth D] Focus chain KA [auth D] Focus chain R [auth B] Focus chain S [auth B] Focus chain X [auth B]
SCN Query on SCN Download Ideal Coordinates CCD File SDF format, chain CA [auth C] SDF format, chain DA [auth C] SDF format, chain I [auth A] SDF format, chain IA [auth D] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain LA [auth D] SDF format, chain NA [auth D] SDF format, chain Q [auth B] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain Y [auth B] MOL2 format, chain CA [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth D] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth D] MOL2 format, chain NA [auth D] MOL2 format, chain Q [auth B] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain Y [auth B]	CA [auth C] DA [auth C] I [auth A] IA [auth D] J [auth A] CA [auth C], DA [auth C], I [auth A], IA [auth D], J [auth A], K [auth A], L [auth A], LA [auth D], NA [auth D], Q [auth B], T [auth B], U [auth B], V [auth B], W [auth B], Y [auth B]	THIOCYANATE ION C N S ZMZDMBWJUHKJPS-UHFFFAOYSA-M		Interactions Focus chain CA [auth C] Focus chain DA [auth C] Focus chain I [auth A] Focus chain IA [auth D] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain LA [auth D] Focus chain NA [auth D] Focus chain Q [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain Y [auth B] Interactions & Density Focus chain CA [auth C] Focus chain DA [auth C] Focus chain I [auth A] Focus chain IA [auth D] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain LA [auth D] Focus chain NA [auth D] Focus chain Q [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain Y [auth B]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain GA [auth C] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain PA [auth D] MOL2 format, chain GA [auth C] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain PA [auth D]	GA [auth C], N [auth A], O [auth A], PA [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain GA [auth C] Focus chain N [auth A] Focus chain O [auth A] Focus chain PA [auth D] Interactions & Density Focus chain GA [auth C] Focus chain N [auth A] Focus chain O [auth A] Focus chain PA [auth D]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain FA [auth C] SDF format, chain M [auth A] SDF format, chain OA [auth D] SDF format, chain Z [auth B] MOL2 format, chain FA [auth C] MOL2 format, chain M [auth A] MOL2 format, chain OA [auth D] MOL2 format, chain Z [auth B]	FA [auth C], M [auth A], OA [auth D], Z [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain FA [auth C] Focus chain M [auth A] Focus chain OA [auth D] Focus chain Z [auth B] Interactions & Density Focus chain FA [auth C] Focus chain M [auth A] Focus chain OA [auth D] Focus chain Z [auth B]