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- PDB-4umx: IDH1 R132H in complex with cpd 1 -

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Basic information

Entry
Database: PDB / ID: 4umx
TitleIDH1 R132H in complex with cpd 1
ComponentsISOCITRATE DEHYDROGENASE [NADP] CYTOPLASMIC
KeywordsOXIDOREDUCTASE / ISOCITRATE DEHYDROGENASE INHIBITOR
Function / homology
Function and homology information


Abnormal conversion of 2-oxoglutarate to 2-hydroxyglutarate / NADPH regeneration / regulation of phospholipid catabolic process / regulation of phospholipid biosynthetic process / NFE2L2 regulating TCA cycle genes / isocitrate metabolic process / isocitrate dehydrogenase (NADP+) / isocitrate dehydrogenase (NADP+) activity / 2-oxoglutarate metabolic process / NADP metabolic process ...Abnormal conversion of 2-oxoglutarate to 2-hydroxyglutarate / NADPH regeneration / regulation of phospholipid catabolic process / regulation of phospholipid biosynthetic process / NFE2L2 regulating TCA cycle genes / isocitrate metabolic process / isocitrate dehydrogenase (NADP+) / isocitrate dehydrogenase (NADP+) activity / 2-oxoglutarate metabolic process / NADP metabolic process / glyoxylate cycle / response to steroid hormone / female gonad development / peroxisomal matrix / tricarboxylic acid cycle / glutathione metabolic process / Peroxisomal protein import / NAD binding / peroxisome / tertiary granule lumen / NADP binding / secretory granule lumen / ficolin-1-rich granule lumen / response to oxidative stress / cadherin binding / Neutrophil degranulation / magnesium ion binding / protein homodimerization activity / mitochondrion / extracellular exosome / extracellular region / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Isocitrate dehydrogenase NADP-dependent / Isopropylmalate Dehydrogenase / Isopropylmalate Dehydrogenase / Isocitrate/isopropylmalate dehydrogenase, conserved site / Isocitrate and isopropylmalate dehydrogenases signature. / Isopropylmalate dehydrogenase-like domain / Isocitrate/isopropylmalate dehydrogenase / Isocitrate/isopropylmalate dehydrogenase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Chem-VVS / Isocitrate dehydrogenase [NADP] cytoplasmic
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsMathieu, M. / Marquette, J.P.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Selective Inhibition of Mutant Isocitrate Dehydrogenase 1 (Idh1) Via Disruption of a Metal Binding Network by an Allosteric Small Molecule.
Authors: Deng, G. / Shen, J. / Yin, M. / Mcmanus, J. / Mathieu, M. / Gee, P. / He, T. / Shi, C. / Bedel, O. / Mclean, L.R. / Le-Strat, F. / Zhang, Y. / Marquette, J. / Gao, Q. / Zhang, B. / Rak, A. / ...Authors: Deng, G. / Shen, J. / Yin, M. / Mcmanus, J. / Mathieu, M. / Gee, P. / He, T. / Shi, C. / Bedel, O. / Mclean, L.R. / Le-Strat, F. / Zhang, Y. / Marquette, J. / Gao, Q. / Zhang, B. / Rak, A. / Hoffmann, D. / Rooney, E. / Vassort, A. / Englaro, W. / Li, Y. / Patel, V. / Adrian, F. / Gross, S. / Wiederschain, D. / Cheng, H. / Licht, S.
History
DepositionMay 22, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 19, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 26, 2014Group: Database references
Revision 1.2Jan 14, 2015Group: Refinement description
Revision 1.3Jan 21, 2015Group: Database references
Revision 1.4Aug 23, 2017Group: Data collection / Structure summary / Category: diffrn_detector / entity / Item: _diffrn_detector.type / _entity.pdbx_mutation
Revision 1.5Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ISOCITRATE DEHYDROGENASE [NADP] CYTOPLASMIC
B: ISOCITRATE DEHYDROGENASE [NADP] CYTOPLASMIC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,2176
Polymers96,2712
Non-polymers1,9454
Water13,799766
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7950 Å2
ΔGint-47.4 kcal/mol
Surface area36090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.408, 81.408, 305.917
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein ISOCITRATE DEHYDROGENASE [NADP] CYTOPLASMIC / IDH / CYTOSOLIC NADP-ISOCITRATE DEHYDROGENASE / IDP / NADP(+)- SPECIFIC ICDH / OXALOSUCCINATE DECARBOXYLASE


Mass: 48135.684 Da / Num. of mol.: 2 / Mutation: R132H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: O75874, isocitrate dehydrogenase (NADP+)
#2: Chemical ChemComp-VVS / 2,6-bis(1H-imidazol-1-ylmethyl)-4-(2,4,4-trimethylpentan-2-yl)phenol


Mass: 366.500 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H30N4O
#3: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 766 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.63 Å3/Da / Density % sol: 49.5 % / Description: NONE
Crystal growpH: 8 / Details: PEG 8K 26%, TRIS 100MM PH 8, MALONATE NA 200MM

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98011
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 9, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 1.88→305.9 Å / Num. obs: 85717 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 14 % / Biso Wilson estimate: 28.07 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 17.8
Reflection shellResolution: 1.88→1.88 Å / Redundancy: 9.8 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 3.3 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.11.2refinement
XDSdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3MAR

3mar


Resolution: 1.88→78.67 Å / Cor.coef. Fo:Fc: 0.9514 / Cor.coef. Fo:Fc free: 0.9359 / SU R Cruickshank DPI: 0.125 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.134 / SU Rfree Blow DPI: 0.121 / SU Rfree Cruickshank DPI: 0.117
RfactorNum. reflection% reflectionSelection details
Rfree0.2112 4249 5 %RANDOM
Rwork0.1825 ---
obs-84917 100 %-
Displacement parametersBiso mean: 32.89 Å2
Baniso -1Baniso -2Baniso -3
1--0.5899 Å20 Å20 Å2
2---0.5899 Å20 Å2
3---1.1798 Å2
Refine analyzeLuzzati coordinate error obs: 0.498 Å
Refinement stepCycle: LAST / Resolution: 1.88→78.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6479 0 129 766 7374
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.016753HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.029126HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2406SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes176HARMONIC2
X-RAY DIFFRACTIONt_gen_planes996HARMONIC5
X-RAY DIFFRACTIONt_it6753HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.37
X-RAY DIFFRACTIONt_other_torsion17.17
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion875SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact8464SEMIHARMONIC4
LS refinement shellResolution: 1.88→1.93 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2548 313 5.07 %
Rwork0.1992 5861 -
all0.202 6174 -
obs--100 %

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