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- PDB-5v18: Structure of PHD2 in complex with 1,2,4-Triazolo-[1,5-a]pyridine -

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Basic information

Entry
Database: PDB / ID: 5v18
TitleStructure of PHD2 in complex with 1,2,4-Triazolo-[1,5-a]pyridine
ComponentsEgl nine homolog 1
KeywordsOxidoreductase/Inhibitor / HIF Prolylhydroxylase Domain-2 / Inhibitor / momodentate binding / Oxidoreductase-Inhibitor complex
Function / homology
Function and homology information


hypoxia-inducible factor-proline dioxygenase activity / hypoxia-inducible factor-proline dioxygenase / peptidyl-proline 4-dioxygenase activity / peptidyl-proline dioxygenase activity / peptidyl-proline hydroxylation to 4-hydroxy-L-proline / negative regulation of cyclic-nucleotide phosphodiesterase activity / regulation protein catabolic process at postsynapse / intracellular oxygen homeostasis / labyrinthine layer development / cardiac muscle tissue morphogenesis ...hypoxia-inducible factor-proline dioxygenase activity / hypoxia-inducible factor-proline dioxygenase / peptidyl-proline 4-dioxygenase activity / peptidyl-proline dioxygenase activity / peptidyl-proline hydroxylation to 4-hydroxy-L-proline / negative regulation of cyclic-nucleotide phosphodiesterase activity / regulation protein catabolic process at postsynapse / intracellular oxygen homeostasis / labyrinthine layer development / cardiac muscle tissue morphogenesis / 2-oxoglutarate-dependent dioxygenase activity / heart trabecula formation / regulation of modification of postsynaptic structure / L-ascorbic acid binding / response to nitric oxide / ventricular septum morphogenesis / regulation of angiogenesis / ferrous iron binding / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / negative regulation of DNA-binding transcription factor activity / cellular response to hypoxia / intracellular iron ion homeostasis / postsynaptic density / response to hypoxia / intracellular membrane-bounded organelle / glutamatergic synapse / enzyme binding / positive regulation of transcription by RNA polymerase II / nucleus / cytoplasm / cytosol
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. / q2cbj1_9rhob like domain / MYND finger / Zinc finger, MYND-type / Zinc finger MYND-type signature. / Zinc finger MYND-type profile. / Oxoglutarate/iron-dependent dioxygenase ...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. / q2cbj1_9rhob like domain / MYND finger / Zinc finger, MYND-type / Zinc finger MYND-type signature. / Zinc finger MYND-type profile. / Oxoglutarate/iron-dependent dioxygenase / Fe(2+) 2-oxoglutarate dioxygenase domain profile. / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-8UY / : / Egl nine homolog 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.15 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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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)27,1625
Polymers26,6931
Non-polymers4684
Water57632
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.528, 72.528, 45.642
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

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Components

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


Mass: 26693.379 Da / Num. of mol.: 1 / Fragment: UNP residues 80-315
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 (E. coli)
References: UniProt: Q9GZT9, 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-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
#4: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 2.25 Å3/Da / Density % sol: 45.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 25% PEG 335, 200 mM ASO4, 100 mM Bis-Tris pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 21, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 12901 / % possible obs: 98.1 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.046 / Χ2: 1.178 / Net I/σ(I): 18.6 / Num. measured all: 50034
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsΧ2Diffraction-ID% possible all
2.15-2.192.50.6171.02186.6
2.19-2.232.70.4431.016193.3
2.23-2.272.90.4261.201197.2
2.27-2.323.40.4391.09199.7
2.32-2.374.10.3431.082199.7
2.37-2.424.20.2811.1191100
2.42-2.484.20.2381.1371100
2.48-2.554.20.181.1381100
2.55-2.624.20.1531.21100
2.62-2.714.20.1271.2171100
2.71-2.814.20.0991.1751100
2.81-2.924.20.0761.2741100
2.92-3.054.20.0711.361100
3.05-3.214.10.061.2961100
3.21-3.414.10.0531.297199.7
3.41-3.684.10.0421.256199.8
3.68-4.054.10.0381.242199.7
4.05-4.6340.0421.109196.4
4.63-5.8340.0390.96198.5
5.83-503.80.0341.158191.4

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
REFMAC5.8.0135refinement
PDB_EXTRACT3.22data extraction
DENZOdata reduction
PHASERphasing
RefinementResolution: 2.15→25.64 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.953 / SU B: 13.234 / SU ML: 0.151 / SU R Cruickshank DPI: 0.2446 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.245 / ESU R Free: 0.196
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.235 645 5 %RANDOM
Rwork0.1905 ---
obs0.1926 12238 98.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 159.22 Å2 / Biso mean: 68.713 Å2 / Biso min: 43.93 Å2
Baniso -1Baniso -2Baniso -3
1--0.58 Å2-0 Å20 Å2
2---0.58 Å20 Å2
3---1.16 Å2
Refinement stepCycle: final / Resolution: 2.15→25.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1701 0 28 32 1761
Biso mean--78.84 69.16 -
Num. residues----215
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0191768
X-RAY DIFFRACTIONr_bond_other_d0.0020.021653
X-RAY DIFFRACTIONr_angle_refined_deg1.2311.9722386
X-RAY DIFFRACTIONr_angle_other_deg0.933807
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5695211
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.22923.73583
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.57815302
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.9861513
X-RAY DIFFRACTIONr_chiral_restr0.0710.2252
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211981
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02403
LS refinement shellResolution: 2.148→2.203 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 41 -
Rwork0.291 815 -
all-856 -
obs--88.07 %
Refinement TLS params.Method: refined / Origin x: 23.9592 Å / Origin y: 64.0893 Å / Origin z: 0.9243 Å
111213212223313233
T0.0366 Å2-0.036 Å2-0.0005 Å2-0.1235 Å2-0.0324 Å2--0.0153 Å2
L3.2822 °20.8242 °20.3616 °2-3.0325 °2-0.8158 °2--2.4464 °2
S-0.0088 Å °-0.2169 Å °0.1681 Å °-0.0658 Å °0.0224 Å °0.0382 Å °0.2815 Å °-0.2098 Å °-0.0136 Å °

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