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- PDB-5v1b: Structure of PHD1 in complex with 1,2,4-Triazolo-[1,5-a]pyridine -

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Basic information

Entry
Database: PDB / ID: 5v1b
TitleStructure of PHD1 in complex with 1,2,4-Triazolo-[1,5-a]pyridine
ComponentsEgl nine homolog 2
KeywordsOxidoreductase/Inhibitor / HIF Prolylhydroxylase Domain-1 / Inhibitor / momodentate binding / Oxidoreductase-Inhibitor complex
Function / homology
Function and homology information


hypoxia-inducible factor-proline dioxygenase / peptidyl-proline 4-dioxygenase activity / peptidyl-proline dioxygenase activity / peptidyl-proline hydroxylation to 4-hydroxy-L-proline / Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor / 2-oxoglutarate-dependent dioxygenase activity / L-ascorbic acid binding / oxygen sensor activity / estrogen receptor signaling pathway / regulation of neuron apoptotic process ...hypoxia-inducible factor-proline dioxygenase / peptidyl-proline 4-dioxygenase activity / peptidyl-proline dioxygenase activity / peptidyl-proline hydroxylation to 4-hydroxy-L-proline / Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor / 2-oxoglutarate-dependent dioxygenase activity / L-ascorbic acid binding / oxygen sensor activity / estrogen receptor signaling pathway / regulation of neuron apoptotic process / cell redox homeostasis / regulation of cell growth / ferrous iron binding / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / positive regulation of protein catabolic process / cellular response to hypoxia / response to hypoxia / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
2OG-Fe(II) oxygenase superfamily / Prolyl 4-hydroxylase, alpha subunit / Prolyl 4-hydroxylase alpha subunit homologues. / q2cbj1_9rhob like domain / Oxoglutarate/iron-dependent dioxygenase / Fe(2+) 2-oxoglutarate dioxygenase domain profile. / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-8UY / : / Prolyl hydroxylase EGLN2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.49 Å
AuthorsSkene, R.J.
CitationJournal: J. Med. Chem. / Year: 2017
Title: 1,2,4-Triazolo-[1,5-a]pyridine HIF Prolylhydroxylase Domain-1 (PHD-1) Inhibitors With a Novel Monodentate Binding Interaction.
Authors: Ahmed, S. / Ayscough, A. / Barker, G.R. / Canning, H.E. / Davenport, R. / Downham, R. / Harrison, D. / Jenkins, K. / Kinsella, N. / Livermore, D.G. / Wright, S. / Ivetac, A.D. / Skene, R. / ...Authors: Ahmed, S. / Ayscough, A. / Barker, G.R. / Canning, H.E. / Davenport, R. / Downham, R. / Harrison, D. / Jenkins, K. / Kinsella, N. / Livermore, D.G. / Wright, S. / Ivetac, A.D. / Skene, R. / Wilkens, S.J. / Webster, N.A. / Hendrick, A.G.
History
DepositionMar 1, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 21, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 26, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Egl nine homolog 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0345
Polymers26,5651
Non-polymers4684
Water1,65792
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.717, 112.082, 66.223
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Egl nine homolog 2 / Estrogen-induced tag 6 / HPH-3 / Hypoxia-inducible factor prolyl hydroxylase 1 / HPH-1 / Prolyl ...Estrogen-induced tag 6 / HPH-3 / Hypoxia-inducible factor prolyl hydroxylase 1 / HPH-1 / Prolyl hydroxylase domain-containing protein 1 / PHD1


Mass: 26565.438 Da / Num. of mol.: 1 / Fragment: UNP residues 167-403
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EGLN2, EIT6 / Production host: Escherichia coli (E. coli)
References: UniProt: Q96KS0, hypoxia-inducible factor-proline dioxygenase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#4: Chemical ChemComp-8UY / 4-([1,2,4]triazolo[1,5-a]pyridin-5-yl)benzonitrile


Mass: 220.229 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H8N4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 2.33 Å3/Da / Density % sol: 47.21 %
Crystal growTemperature: 273 K / Method: vapor diffusion, sitting drop / Details: 28% PEG 3350, Bis-Tris 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.49→50 Å / Num. obs: 8476 / % possible obs: 96.6 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.045 / Rrim(I) all: 0.11 / Χ2: 1.002 / Net I/σ(I): 7.3 / Num. measured all: 34505
Reflection shellΧ2: 1.02

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
REFMAC5.8.0135refinement
PDB_EXTRACT3.22data extraction
DENZOdata reduction
PHASERphasing
RefinementResolution: 2.49→43.34 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.945 / WRfactor Rfree: 0.2036 / WRfactor Rwork: 0.1623 / FOM work R set: 0.7591 / SU B: 30.645 / SU ML: 0.272 / SU R Cruickshank DPI: 0.6936 / SU Rfree: 0.2837 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.694 / ESU R Free: 0.284 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2363 447 5 %RANDOM
Rwork0.1894 ---
obs0.1917 8475 99.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 167.68 Å2 / Biso mean: 69.198 Å2 / Biso min: 43.56 Å2
Baniso -1Baniso -2Baniso -3
1--0.42 Å2-0 Å2-0 Å2
2---2.01 Å2-0 Å2
3---2.43 Å2
Refinement stepCycle: final / Resolution: 2.49→43.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1771 0 28 92 1891
Biso mean--96.38 64.61 -
Num. residues----226
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0191841
X-RAY DIFFRACTIONr_angle_refined_deg1.3021.9652494
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3115223
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.6821.76585
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.85115288
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2561521
X-RAY DIFFRACTIONr_chiral_restr0.0830.2261
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211436
LS refinement shellResolution: 2.493→2.557 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.528 30 -
Rwork0.45 569 -
all-599 -
obs--90.76 %
Refinement TLS params.Method: refined / Origin x: 18.592 Å / Origin y: 18.167 Å / Origin z: -2.172 Å
111213212223313233
T0.0492 Å20.0096 Å20.0285 Å2-0.1257 Å2-0.003 Å2--0.0325 Å2
L2.6538 °2-0.3594 °2-0.1616 °2-2.0436 °2-0.1715 °2--1.5673 °2
S0.095 Å °-0.0119 Å °0.1079 Å °-0.0149 Å °-0.1062 Å °0.0106 Å °0.011 Å °-0.0684 Å °0.0112 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A171 - 403
2X-RAY DIFFRACTION1A501 - 504
3X-RAY DIFFRACTION1A601 - 692

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