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- PDB-8y0v: HIF prolyl hydroxylase 2 in complex with inhibitor -

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Basic information

Entry
Database: PDB / ID: 8y0v
TitleHIF prolyl hydroxylase 2 in complex with inhibitor
ComponentsEgl nine homolog 1
KeywordsIMMUNE SYSTEM / Inhibitor
Function / homology
Function and homology information


peptidyl-proline 4-dioxygenase activity / hypoxia-inducible factor-proline dioxygenase activity / hypoxia-inducible factor-proline dioxygenase / peptidyl-proline dioxygenase activity / negative regulation of cyclic-nucleotide phosphodiesterase activity / intracellular oxygen homeostasis / labyrinthine layer development / regulation protein catabolic process at postsynapse / 2-oxoglutarate-dependent dioxygenase activity / heart trabecula formation ...peptidyl-proline 4-dioxygenase activity / hypoxia-inducible factor-proline dioxygenase activity / hypoxia-inducible factor-proline dioxygenase / peptidyl-proline dioxygenase activity / negative regulation of cyclic-nucleotide phosphodiesterase activity / intracellular oxygen homeostasis / labyrinthine layer development / regulation protein catabolic process at postsynapse / 2-oxoglutarate-dependent dioxygenase activity / heart trabecula formation / regulation of modification of postsynaptic structure / cardiac muscle tissue morphogenesis / L-ascorbic acid binding / response to nitric oxide / ventricular septum morphogenesis / regulation of angiogenesis / regulation of neuron apoptotic process / negative regulation of DNA-binding transcription factor activity / ferrous iron binding / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / cellular response to hypoxia / intracellular iron ion homeostasis / response to hypoxia / postsynaptic density / intracellular membrane-bounded organelle / glutamatergic synapse / enzyme binding / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
: / Prolyl 4-hydroxylase alpha subunit, Fe(2+) 2OG dioxygenase domain / 2OG-Fe(II) oxygenase superfamily / Prolyl 4-hydroxylase, alpha subunit / Prolyl 4-hydroxylase alpha subunit homologues. / MYND finger / Zinc finger MYND-type signature. / Zinc finger, MYND-type / Zinc finger MYND-type profile. / Oxoglutarate/iron-dependent dioxygenase / Fe(2+) 2-oxoglutarate dioxygenase domain profile.
Similarity search - Domain/homology
: / : / Egl nine homolog 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsDing, X. / Fan, Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat.Biotechnol. / Year: 2024
Title: Intestinal mucosal barrier repair and immune regulation with an AI-developed gut-restricted PHD inhibitor.
Authors: Fu, Y. / Ding, X. / Zhang, M. / Feng, C. / Yan, Z. / Wang, F. / Xu, J. / Lin, X. / Ding, X. / Wang, L. / Fan, Y. / Li, T. / Yin, Y. / Liang, X. / Xu, C. / Chen, S. / Pulous, F.E. / Gennert, ...Authors: Fu, Y. / Ding, X. / Zhang, M. / Feng, C. / Yan, Z. / Wang, F. / Xu, J. / Lin, X. / Ding, X. / Wang, L. / Fan, Y. / Li, T. / Yin, Y. / Liang, X. / Xu, C. / Chen, S. / Pulous, F.E. / Gennert, D. / Pun, F.W. / Kamya, P. / Ren, F. / Aliper, A. / Zhavoronkov, A.
History
DepositionJan 23, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 18, 2024Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2024Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Egl nine homolog 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0703
Polymers27,5251
Non-polymers5442
Water70339
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.415, 82.415, 63.472
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-622-

HOH

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Components

#1: Protein Egl nine homolog 1 / Hypoxia-inducible factor prolyl hydroxylase 2 / HIF-PH2 / HIF-prolyl hydroxylase 2 / HPH-2 / Prolyl ...Hypoxia-inducible factor prolyl hydroxylase 2 / HIF-PH2 / HIF-prolyl hydroxylase 2 / HPH-2 / Prolyl hydroxylase domain-containing protein 2 / PHD2 / SM-20


Mass: 27525.314 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EGLN1, C1orf12, PNAS-118, PNAS-137 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9GZT9, hypoxia-inducible factor-proline dioxygenase
#2: Chemical ChemComp-A1D5X / ~{tert}-butyl 4-[6-[(6-cyanopyridin-3-yl)methylcarbamoyl]-5-oxidanyl-1,7-naphthyridin-2-yl]piperazine-1-carboxylate


Mass: 489.526 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H27N7O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.26 Å3/Da / Density % sol: 45.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2M Ammonium phosphate monobasic, 0.1M Tris (8.3 8.7), 40% MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 5, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.5→47.43 Å / Num. obs: 8584 / % possible obs: 99.9 % / Redundancy: 7.2 % / CC1/2: 0.98 / Net I/σ(I): 9.2
Reflection shellResolution: 2.5→2.6 Å / Num. unique obs: 984 / CC1/2: 0.699

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→47.43 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.905 / SU B: 11.321 / SU ML: 0.25 / Cross valid method: FREE R-VALUE / ESU R: 0.574 / ESU R Free: 0.331
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2907 410 4.78 %
Rwork0.2255 8168 -
all0.228 --
obs-8578 99.825 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 70 Å2
Baniso -1Baniso -2Baniso -3
1-0.977 Å20.488 Å20 Å2
2--0.977 Å2-0 Å2
3----3.169 Å2
Refinement stepCycle: LAST / Resolution: 2.5→47.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1558 0 37 39 1634
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0121640
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161476
X-RAY DIFFRACTIONr_angle_refined_deg0.7441.6612210
X-RAY DIFFRACTIONr_angle_other_deg0.2691.5763434
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1835195
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.2615
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.19510269
X-RAY DIFFRACTIONr_dihedral_angle_6_deg11.591075
X-RAY DIFFRACTIONr_chiral_restr0.0350.2227
X-RAY DIFFRACTIONr_chiral_restr_other0.0220.21
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021874
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02341
X-RAY DIFFRACTIONr_nbd_refined0.1970.2288
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1770.21382
X-RAY DIFFRACTIONr_nbtor_refined0.1780.2798
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0850.2809
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1280.241
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1670.24
X-RAY DIFFRACTIONr_nbd_other0.2040.212
X-RAY DIFFRACTIONr_mcbond_it2.2177.472786
X-RAY DIFFRACTIONr_mcbond_other2.2187.468785
X-RAY DIFFRACTIONr_mcangle_it3.67811.188979
X-RAY DIFFRACTIONr_mcangle_other3.67611.192980
X-RAY DIFFRACTIONr_scbond_it2.0857.486854
X-RAY DIFFRACTIONr_scbond_other2.0627.491853
X-RAY DIFFRACTIONr_scangle_it3.44811.161231
X-RAY DIFFRACTIONr_scangle_other3.44611.161232
X-RAY DIFFRACTIONr_lrange_it5.61286.6311814
X-RAY DIFFRACTIONr_lrange_other5.57286.6111811
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.5650.338240.249600X-RAY DIFFRACTION99.5215
2.565-2.6350.34400.277563X-RAY DIFFRACTION100
2.635-2.7110.378290.287572X-RAY DIFFRACTION99.5033
2.711-2.7950.312300.277544X-RAY DIFFRACTION100
2.795-2.8860.382410.287535X-RAY DIFFRACTION99.8267
2.886-2.9870.333280.269502X-RAY DIFFRACTION99.8117
2.987-3.0990.292340.188494X-RAY DIFFRACTION99.811
3.099-3.2250.373350.262465X-RAY DIFFRACTION99.8004
3.225-3.3680.348180.254470X-RAY DIFFRACTION100
3.368-3.5310.28260.231441X-RAY DIFFRACTION100
3.531-3.7210.407130.251442X-RAY DIFFRACTION100
3.721-3.9450.298160.218396X-RAY DIFFRACTION100
3.945-4.2160.229150.214379X-RAY DIFFRACTION99.7468
4.216-4.550.1960.178365X-RAY DIFFRACTION99.7312
4.55-4.980.209130.17322X-RAY DIFFRACTION100
4.98-5.560.263170.199295X-RAY DIFFRACTION100
5.56-6.4060.364120.216261X-RAY DIFFRACTION100
6.406-7.810.19540.242233X-RAY DIFFRACTION100
7.81-10.8980.44530.164183X-RAY DIFFRACTION100
10.898-47.430.20660.267106X-RAY DIFFRACTION98.2456

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