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- PDB-6rj5: Crystal structure of PHGDH in complex with compound 39 -

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Basic information

Entry
Database: PDB / ID: 6rj5
TitleCrystal structure of PHGDH in complex with compound 39
ComponentsD-3-phosphoglycerate dehydrogenase
KeywordsOXIDOREDUCTASE / Protein-Ligand complex / Dehydrogenase
Function / homology
Function and homology information


threonine metabolic process / 2-oxoglutarate reductase / gamma-aminobutyric acid metabolic process / glial cell development / phosphoglycerate dehydrogenase / phosphoglycerate dehydrogenase activity / taurine metabolic process / Serine biosynthesis / glycine metabolic process / L-serine biosynthetic process ...threonine metabolic process / 2-oxoglutarate reductase / gamma-aminobutyric acid metabolic process / glial cell development / phosphoglycerate dehydrogenase / phosphoglycerate dehydrogenase activity / taurine metabolic process / Serine biosynthesis / glycine metabolic process / L-serine biosynthetic process / malate dehydrogenase / L-malate dehydrogenase (NAD+) activity / neural tube development / spinal cord development / G1 to G0 transition / glutamine metabolic process / brain development / NAD binding / neuron projection development / regulation of gene expression / electron transfer activity / extracellular exosome / cytosol
Similarity search - Function
D-3-phosphoglycerate dehydrogenase / D-3-phosphoglycerate dehydrogenase, ASB domain / D-3-phosphoglycerate dehydrogenase intervening domain / Allosteric substrate binding domain superfamily / D-isomer specific 2-hydroxyacid dehydrogenases signature 2. / D-isomer specific 2-hydroxyacid dehydrogenases NAD-binding signature. / D-isomer specific 2-hydroxyacid dehydrogenases signature 3. / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site 1 / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain ...D-3-phosphoglycerate dehydrogenase / D-3-phosphoglycerate dehydrogenase, ASB domain / D-3-phosphoglycerate dehydrogenase intervening domain / Allosteric substrate binding domain superfamily / D-isomer specific 2-hydroxyacid dehydrogenases signature 2. / D-isomer specific 2-hydroxyacid dehydrogenases NAD-binding signature. / D-isomer specific 2-hydroxyacid dehydrogenases signature 3. / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site 1 / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-K5N / D-3-phosphoglycerate dehydrogenase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsBader, G. / Wolkerstorfer, B. / Zoephel, A.
CitationJournal: J.Med.Chem. / Year: 2019
Title: Intracellular Trapping of the Selective Phosphoglycerate Dehydrogenase (PHGDH) InhibitorBI-4924Disrupts Serine Biosynthesis.
Authors: Weinstabl, H. / Treu, M. / Rinnenthal, J. / Zahn, S.K. / Ettmayer, P. / Bader, G. / Dahmann, G. / Kessler, D. / Rumpel, K. / Mischerikow, N. / Savarese, F. / Gerstberger, T. / Mayer, M. / ...Authors: Weinstabl, H. / Treu, M. / Rinnenthal, J. / Zahn, S.K. / Ettmayer, P. / Bader, G. / Dahmann, G. / Kessler, D. / Rumpel, K. / Mischerikow, N. / Savarese, F. / Gerstberger, T. / Mayer, M. / Zoephel, A. / Schnitzer, R. / Sommergruber, W. / Martinelli, P. / Arnhof, H. / Peric-Simov, B. / Hofbauer, K.S. / Garavel, G. / Scherbantin, Y. / Mitzner, S. / Fett, T.N. / Scholz, G. / Bruchhaus, J. / Burkard, M. / Kousek, R. / Ciftci, T. / Sharps, B. / Schrenk, A. / Harrer, C. / Haering, D. / Wolkerstorfer, B. / Zhang, X. / Lv, X. / Du, A. / Li, D. / Li, Y. / Quant, J. / Pearson, M. / McConnell, D.B.
History
DepositionApr 26, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 7, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2019Group: Data collection / Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Sep 25, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.3Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: D-3-phosphoglycerate dehydrogenase
B: D-3-phosphoglycerate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,3076
Polymers67,2622
Non-polymers1,0454
Water10,034557
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5630 Å2
ΔGint-66 kcal/mol
Surface area24530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.200, 110.932, 66.057
Angle α, β, γ (deg.)90.000, 91.650, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein D-3-phosphoglycerate dehydrogenase / 3-PGDH / 2-oxoglutarate reductase / Malate dehydrogenase


Mass: 33630.762 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PHGDH, PGDH3 / Production host: Escherichia coli (E. coli)
References: UniProt: O43175, phosphoglycerate dehydrogenase, 2-oxoglutarate reductase, malate dehydrogenase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-K5N / 2-methyl-~{N}-[(1~{R})-1-[4-(methylsulfonylcarbamoyl)phenyl]ethyl]-5-phenyl-pyrazole-3-carboxamide


Mass: 426.489 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H22N4O4S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 557 / 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: 2.35 Å3/Da / Density % sol: 47.71 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.6 / Details: 25 % PEG 8000, 0.1 M MES, 0.2 M Lithium sulphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.89→110.93 Å / Num. obs: 48230 / % possible obs: 97.6 % / Redundancy: 3.9 % / Biso Wilson estimate: 23.84 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.063 / Rrim(I) all: 0.127 / Net I/σ(I): 10.5 / Num. measured all: 187229
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.89-2.323.90.41385225218110.890.2350.4773.997.2
3.28-110.933.80.0453585894090.9970.0260.05224.998

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Processing

Software
NameVersionClassification
Aimless0.3.11data scaling
BUSTER2.11.7refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2G76

2g76


Resolution: 1.89→36.63 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.917 / SU R Cruickshank DPI: 0.151 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.16 / SU Rfree Blow DPI: 0.14 / SU Rfree Cruickshank DPI: 0.136
RfactorNum. reflection% reflectionSelection details
Rfree0.219 1999 4.15 %RANDOM
Rwork0.184 ---
obs0.186 48194 97.2 %-
Displacement parametersBiso max: 113.83 Å2 / Biso mean: 29.02 Å2 / Biso min: 6.45 Å2
Baniso -1Baniso -2Baniso -3
1-3.8571 Å20 Å20.5402 Å2
2---2.1015 Å20 Å2
3----1.7556 Å2
Refine analyzeLuzzati coordinate error obs: 0.23 Å
Refinement stepCycle: final / Resolution: 1.89→36.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4513 0 70 557 5140
Biso mean--34.4 35.71 -
Num. residues----603
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1668SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes797HARMONIC5
X-RAY DIFFRACTIONt_it4637HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion621SEMIHARMONIC5
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_contact5723SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d4637HARMONIC20.009
X-RAY DIFFRACTIONt_angle_deg6272HARMONIC21.07
X-RAY DIFFRACTIONt_omega_torsion2.98
X-RAY DIFFRACTIONt_other_torsion17.27
LS refinement shellResolution: 1.89→1.94 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3182 135 3.94 %
Rwork0.2651 3288 -
all0.2671 3423 -
obs--92.87 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.3737-0.20220.0740.8640.21190.14240.04920.0565-0.0996-0.1351-0.03220.0284-0.00010.0207-0.0169-0.04430.01160.0097-0.0187-0.0124-0.073915.6906-0.6034-2.0364
20.60410.00960.27460.58380.19690.2947-0.0441-0.08570.11620.0595-0.00980.0055-0.0142-0.02350.0539-0.05460.00870.0163-0.0203-0.0044-0.08289.431423.724620.6225
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A5 - 305
2X-RAY DIFFRACTION2{ B|* }B5 - 306

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