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- PDB-6adg: Crystal Structures of IDH1 R132H in complex with AG-881 -

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Basic information

Entry
Database: PDB / ID: 6adg
TitleCrystal Structures of IDH1 R132H in complex with AG-881
ComponentsIsocitrate dehydrogenase [NADP] cytoplasmic
KeywordsOXIDOREDUCTASE / IDH1
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
Chem-9UO / Chem-NDP / Isocitrate dehydrogenase [NADP] cytoplasmic
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsMa, R. / Yun, C.H.
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2018
Title: Crystal structures of pan-IDH inhibitor AG-881 in complex with mutant human IDH1 and IDH2
Authors: Ma, R. / Yun, C.H.
History
DepositionAug 1, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 5, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 26, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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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
C: Isocitrate dehydrogenase [NADP] cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,7769
Polymers144,4073
Non-polymers2,3696
Water2,180121
1
A: Isocitrate dehydrogenase [NADP] cytoplasmic
B: Isocitrate dehydrogenase [NADP] cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,2267
Polymers96,2712
Non-polymers1,9545
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8300 Å2
ΔGint-65 kcal/mol
Surface area33500 Å2
MethodPISA
2
C: Isocitrate dehydrogenase [NADP] cytoplasmic
hetero molecules

C: Isocitrate dehydrogenase [NADP] cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,1014
Polymers96,2712
Non-polymers8292
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_365-x-2,-y+1,z1
Buried area6110 Å2
ΔGint-41 kcal/mol
Surface area32610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.965, 197.253, 85.828
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11C-501-

9UO

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Components

#1: Protein Isocitrate dehydrogenase [NADP] cytoplasmic / Cytosolic NADP-isocitrate dehydrogenase


Mass: 48135.684 Da / Num. of mol.: 3 / Mutation: R132H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IDH1 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: O75874, isocitrate dehydrogenase (NADP+)
#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C21H30N7O17P3
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: Mg
#4: Chemical ChemComp-9UO / 6-(6-chloropyridin-2-yl)-N2,N4-bis[(2R)-1,1,1-trifluoropropan-2-yl]-1,3,5-triazine-2,4-diamine


Mass: 414.737 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H13ClF6N6
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 2.69 Å3/Da / Density % sol: 54.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2M Magnesium chloride hexahydrate, 0.1M Tris pH 8.5, 25%(w/v) Polyethylene glycol 3,350, 0.1M Cesium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 30674 / % possible obs: 92.6 % / Redundancy: 3.8 % / Rpim(I) all: 0.105 / Net I/σ(I): 5.4
Reflection shellResolution: 3→3.23 Å / Num. unique obs: 5478 / Rpim(I) all: 0.436

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DE1

5de1


Resolution: 3→43.015 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 0.31 / Phase error: 24.1
RfactorNum. reflection% reflection
Rfree0.2436 1606 5.25 %
Rwork0.2207 --
obs0.2219 30612 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3→43.015 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9312 0 152 121 9585
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0119695
X-RAY DIFFRACTIONf_angle_d1.33413131
X-RAY DIFFRACTIONf_dihedral_angle_d25.773440
X-RAY DIFFRACTIONf_chiral_restr0.0851412
X-RAY DIFFRACTIONf_plane_restr0.0091680
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.09680.35271430.29562582X-RAY DIFFRACTION100
3.0968-3.20750.34711560.26842582X-RAY DIFFRACTION100
3.2075-3.33590.2611290.23492605X-RAY DIFFRACTION100
3.3359-3.48760.24191510.23682597X-RAY DIFFRACTION100
3.4876-3.67140.26481450.22782597X-RAY DIFFRACTION99
3.6714-3.90130.20441570.20482612X-RAY DIFFRACTION100
3.9013-4.20230.23141710.19382597X-RAY DIFFRACTION100
4.2023-4.62470.19641380.18442639X-RAY DIFFRACTION100
4.6247-5.29290.20991320.1962667X-RAY DIFFRACTION100
5.2929-6.66450.24891360.23852698X-RAY DIFFRACTION100
6.6645-43.01950.24751480.22922830X-RAY DIFFRACTION100

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