6B0Z | pdb_00006b0z

IDH1 R132H mutant in complex with IDH305

PDB DOI: https://doi.org/10.2210/pdb6B0Z/pdb

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

Deposited: 2017-09-15 Released: 2017-11-08
Deposition Author(s): Xie, X., Kulathila, R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.33 Å
R-Value Free:
0.235 (Depositor), 0.238 (DCC)
R-Value Work:
0.189 (Depositor), 0.192 (DCC)
R-Value Observed:
0.191 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Discovery and Evaluation of Clinical Candidate IDH305, a Brain Penetrant Mutant IDH1 Inhibitor.

Cho, Y.S., Levell, J.R., Liu, G., Caferro, T., Sutton, J., Shafer, C.M., Costales, A., Manning, J.R., Zhao, Q., Sendzik, M., Shultz, M., Chenail, G., Dooley, J., Villalba, B., Farsidjani, A., Chen, J., Kulathila, R., Xie, X., Dodd, S., Gould, T., Liang, G., Heimbach, T., Slocum, K., Firestone, B., Pu, M., Pagliarini, R., Growney, J.D.

(2017) ACS Med Chem Lett 8: 1116-1121

PubMed: 29057061 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1021/acsmedchemlett.7b00342
Primary Citation Related Structures:
6B0Z

PubMed Abstract:
Inhibition of mutant IDH1 is being evaluated clinically as a promising treatment option for various cancers with hotspot mutation at Arg ¹³². Having identified an allosteric, induced pocket of IDH1 ^R132H, we have explored 3-pyrimidin-4-yl-oxazolidin-2-ones as mutant IDH1 inhibitors for in vivo modulation of 2-HG production and potential brain penetration. We report here optimization efforts toward the identification of clinical candidate IDH305 ( 13 ), a potent and selective mutant IDH1 inhibitor that has demonstrated brain exposure in rodents. Preclinical characterization of this compound exhibited in vivo correlation of 2-HG reduction and efficacy in a patient-derived IDH1 mutant xenograft tumor model. IDH305 ( 13 ) has progressed into human clinical trials for the treatment of cancers with IDH1 mutation.

Organizational Affiliation

Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States.

Macromolecule Content

Total Structure Weight: 194.33 kDa
Atom Count: 13,796
Modeled Residue Count: 1,617
Deposited Residue Count: 1,668
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isocitrate dehydrogenase [NADP] cytoplasmic	A, B [auth C], C [auth B], D	417	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O75874
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NDP Query on NDP Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth C] SDF format, chain L [auth B] SDF format, chain O [auth D] MOL2 format, chain E [auth A] MOL2 format, chain I [auth C] MOL2 format, chain L [auth B] MOL2 format, chain O [auth D] mmCIF format, chain E [auth A] mmCIF format, chain I [auth C] mmCIF format, chain L [auth B] mmCIF format, chain O [auth D]	E [auth A], I [auth C], L [auth B], O [auth D]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₃₀ N₇ O₁₇ P₃ ACFIXJIJDZMPPO-NNYOXOHSSA-N		Interactions Focus chain E [auth A] Focus chain I [auth C] Focus chain L [auth B] Focus chain O [auth D] Interactions & Density Focus chain E [auth A] Focus chain I [auth C] Focus chain L [auth B] Focus chain O [auth D]
C81 Query on C81 Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain J [auth C] SDF format, chain M [auth B] SDF format, chain R [auth D] SDF format, chain P [auth D] SDF format, chain H [auth A] MOL2 format, chain F [auth A] MOL2 format, chain J [auth C] MOL2 format, chain M [auth B] MOL2 format, chain R [auth D] MOL2 format, chain P [auth D] MOL2 format, chain H [auth A] mmCIF format, chain F [auth A] mmCIF format, chain J [auth C] mmCIF format, chain M [auth B] mmCIF format, chain R [auth D] mmCIF format, chain P [auth D] mmCIF format, chain H [auth A]	F [auth A] H [auth A] J [auth C] M [auth B] P [auth D] F [auth A], H [auth A], J [auth C], M [auth B], P [auth D], R [auth D]	(4R)-4-[(1S)-1-fluoroethyl]-3-[2-({(1S)-1-[4-methyl-2'-(trifluoromethyl)[3,4'-bipyridin]-6-yl]ethyl}amino)pyrimidin-4-yl]-1,3-oxazolidin-2-one C₂₃ H₂₂ F₄ N₆ O₂ DCGDPJCUIKLTDU-SUNYJGFJSA-N		Interactions Focus chain F [auth A] Focus chain H [auth A] Focus chain J [auth C] Focus chain M [auth B] Focus chain P [auth D] Focus chain R [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth A] Focus chain J [auth C] Focus chain M [auth B] Focus chain P [auth D] Focus chain R [auth D]
FLC Query on FLC Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain K [auth C] SDF format, chain N [auth B] SDF format, chain Q [auth D] MOL2 format, chain G [auth A] MOL2 format, chain K [auth C] MOL2 format, chain N [auth B] MOL2 format, chain Q [auth D] mmCIF format, chain G [auth A] mmCIF format, chain K [auth C] mmCIF format, chain N [auth B] mmCIF format, chain Q [auth D]	G [auth A], K [auth C], N [auth B], Q [auth D]	CITRATE ANION C₆ H₅ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-K		Interactions Focus chain G [auth A] Focus chain K [auth C] Focus chain N [auth B] Focus chain Q [auth D] Interactions & Density Focus chain G [auth A] Focus chain K [auth C] Focus chain N [auth B] Focus chain Q [auth D]