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- PDB-6st3: HIF prolyl hydroxylase 2 (PHD2/ EGLN1) in complex with 4-hydroxy-... -

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Basic information

Entry
Database: PDB / ID: 6st3
TitleHIF prolyl hydroxylase 2 (PHD2/ EGLN1) in complex with 4-hydroxy-N-(4-phenoxybenzyl)-2-(1H-pyrazol-1-yl)pyrimidine-5-carboxamide
ComponentsEgl nine homolog 1
KeywordsOXIDOREDUCTASE / NON-HEME DIOXYGENASE / IRON / 2-OXOGLUTARATE / HYPOXIA-INDUCIBLE FACTOR / HIF / HIF PROLYL HYDROXYLASE DOMAIN 2 / PHD2 / EGLN1 / OXYGENASE / HYPOXIA / DNA-BINDING / METAL-BINDING / TRANSCRIPTION / HELIX-LOOP-HELIX-BETA / DSBH / FACIAL TRIAD / CYTOPLASM / TRANSCRIPTION/EPIGENETIC REGULATION / SIGNALING / DEVELOPMENT / CELL STRUCTURE / BETA-HYDROXYLATION / TRANSCRIPTION ACTIVATOR/INHIBITOR / UBL CONJUGATION / POLYMORPHISM / VITAMIN C / ZINC-FINGER / FAMILIAL ERYTHROCYTOSIS / BREAST CANCER / TRANSCRIPTION 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
FORMIC ACID / Chem-LUW / : / Egl nine homolog 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.426 Å
AuthorsChowdhury, R. / Holt-Martyn, J.P. / Schofield, C.J.
Citation
Journal: Chemmedchem / Year: 2020
Title: Structure-Activity Relationship and Crystallographic Studies on 4-Hydroxypyrimidine HIF Prolyl Hydroxylase Domain Inhibitors.
Authors: Holt-Martyn, J.P. / Chowdhury, R. / Tumber, A. / Yeh, T.L. / Abboud, M.I. / Lippl, K. / Lohans, C.T. / Langley, G.W. / Figg Jr., W. / McDonough, M.A. / Pugh, C.W. / Ratcliffe, P.J. / Schofield, C.J.
#1: Journal: ACS Chem. Biol. / Year: 2013
Title: Selective small molecule probes for the hypoxia inducible factor (HIF) prolyl hydroxylases.
Authors: Chowdhury, R. / Candela-Lena, J.I. / Chan, M.C. / Greenald, D.J. / Yeoh, K.K. / Tian, Y.M. / McDonough, M.A. / Tumber, A. / Rose, N.R. / Conejo-Garcia, A. / Demetriades, M. / Mathavan, S. / ...Authors: Chowdhury, R. / Candela-Lena, J.I. / Chan, M.C. / Greenald, D.J. / Yeoh, K.K. / Tian, Y.M. / McDonough, M.A. / Tumber, A. / Rose, N.R. / Conejo-Garcia, A. / Demetriades, M. / Mathavan, S. / Kawamura, A. / Lee, M.K. / van Eeden, F. / Pugh, C.W. / Ratcliffe, P.J. / Schofield, C.J.
History
DepositionSep 10, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 4, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: 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.year
Revision 1.2Jan 24, 2024Group: 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.pdbx_dist_value / _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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Egl nine homolog 1
B: Egl nine homolog 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,0508
Polymers52,0732
Non-polymers9776
Water2,342130
1
A: Egl nine homolog 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5254
Polymers26,0371
Non-polymers4883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Egl nine homolog 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5254
Polymers26,0371
Non-polymers4883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.870, 80.580, 83.920
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 187 through 215 or (resid 216...
21(chain B and (resid 187 or (resid 188 and (name...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 187 through 215 or (resid 216...A187 - 215
121(chain A and (resid 187 through 215 or (resid 216...A216
131(chain A and (resid 187 through 215 or (resid 216...A189 - 405
141(chain A and (resid 187 through 215 or (resid 216...A189 - 405
151(chain A and (resid 187 through 215 or (resid 216...A189 - 405
161(chain A and (resid 187 through 215 or (resid 216...A189 - 405
171(chain A and (resid 187 through 215 or (resid 216...A189 - 405
211(chain B and (resid 187 or (resid 188 and (name...B187
221(chain B and (resid 187 or (resid 188 and (name...B188
231(chain B and (resid 187 or (resid 188 and (name...B188 - 406
241(chain B and (resid 187 or (resid 188 and (name...B188 - 406
251(chain B and (resid 187 or (resid 188 and (name...B188 - 406
261(chain B and (resid 187 or (resid 188 and (name...B188 - 406

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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: 26036.582 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: FRAGMENT: CATALYTIC DOMAIN (aa 181-407) / Source: (gene. exp.) Homo sapiens (human) / Gene: EGLN1, C1orf12, PNAS-118, PNAS-137 / Plasmid: PET28A(+) / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9GZT9, hypoxia-inducible factor-proline dioxygenase
#2: Chemical ChemComp-LUW / 4-oxidanyl-~{N}-[(4-phenoxyphenyl)methyl]-2-pyrazol-1-yl-pyrimidine-5-carboxamide


Mass: 387.391 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H17N5O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.62 Å3/Da / Density % sol: 53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.2 M Ammonium acetate, 0.1 M Sodium citrate tribasic dihydrate pH 5.6, 30% PEG 4000, Sitting drop (300 nl), protein-to-well ratio, 1:2, 293K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 21, 2015 / Details: MIRRORS
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.426→83.92 Å / Num. obs: 19127 / % possible obs: 99.3 % / Redundancy: 3.8 % / Biso Wilson estimate: 35.8 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.144 / Rpim(I) all: 0.089 / Rrim(I) all: 0.182 / Net I/σ(I): 6.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.43-2.523.80.9741.519780.5480.5861.20699.5
9.08-83.923.50.054240.990.0330.06498.5

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Processing

Software
NameVersionClassification
Aimless0.7.3data scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BQX

4bqx


Resolution: 2.426→58.123 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.53
RfactorNum. reflection% reflection
Rfree0.2173 946 4.96 %
Rwork0.1924 --
obs0.1936 19083 98.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Bsol: 46.4 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 153.19 Å2 / Biso mean: 49.777 Å2 / Biso min: 20.62 Å2
Refinement stepCycle: final / Resolution: 2.426→58.123 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3202 0 102 130 3434
Biso mean--48.15 46.68 -
Num. residues----419
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1815X-RAY DIFFRACTION6.233TORSIONAL
12B1815X-RAY DIFFRACTION6.233TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.426-2.55370.36371240.3021253499
2.5537-2.71370.25751370.2682257699
2.7137-2.92320.2311270.2278254298
2.9232-3.21740.22571580.2092254999
3.2174-3.68290.20581230.1685260399
3.6829-4.63980.20241340.1516262599
4.6398-58.1230.18651430.1792270898
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)
10.0909-0.09430.13880.1340.01870.321-0.45720.28570.4978-0.06670.3736-0.0645-0.7124-0.1520.00040.7145-0.0684-0.07580.459-0.16390.677510.920346.876423.9922
20.1661-0.0120.08380.1542-0.21230.1331-0.54380.40230.9332-0.42040.08880.3232-0.4025-0.6331-0.00490.5447-0.0489-0.13040.37930.01220.58338.965339.842117.6651
30.27920.1322-0.03761.17610.30870.44740.16240.70180.1199-1.8313-0.251-0.45650.02680.2275-0.00730.4499-0.0010.04930.4588-0.01280.413818.322224.09869.2826
40.6288-0.7432-0.20440.7252-0.96341.25850.0965-0.5448-0.70190.4088-0.1127-0.11350.5649-0.0420.02450.3992-0.00680.04540.39260.01020.468914.713416.233922.0423
51.7170.2359-1.27580.358-0.5583.2612-0.4113-0.10490.2715-0.2863-0.012-0.5291-0.39690.5695-0.84970.446-0.0663-0.16260.3664-0.03030.550220.528735.550722.3582
60.49570.20160.23350.07510.00470.27990.131-0.89670.90310.3364-0.03630.7429-0.561-0.32990.2680.7083-0.0407-0.10350.6783-0.15410.630613.017941.001435.4431
70.3044-0.69750.50710.5597-0.14710.1706-0.01720.27010.0480.21-0.0306-0.03780.42030.6274-0.00120.3212-0.05510.03270.28160.00970.340711.117622.360920.4757
80.06180.24290.39350.1798-0.01920.2018-0.2315-0.13250.12020.5403-0.18890.66840.35180.2681-0.00720.39490.02090.03120.4148-0.00570.36740.985624.122328.4998
90.85810.08190.07470.92910.07970.2286-0.54060.04490.2049-0.2861-0.14780.1061-0.45080.1229-0.01550.4072-0.0375-0.03240.3028-0.01870.27428.461830.437417.5239
100.3998-0.207-0.0060.04990.04180.01260.0539-0.02290.3837-0.3193-0.33790.2341-1.2352-0.6699-0.04530.51770.0199-0.05020.3876-0.08860.4302-3.733331.370418.0303
110.7358-0.11610.84150.0617-0.07710.93320.16810.41931.1728-0.9009-0.16331.2037-1.3064-0.1044-0.34520.42960.0079-0.10350.2789-0.1450.55950.684834.534315.293
121.432-0.49370.93870.6505-0.86953.8318-0.4590.1373-0.10770.2879-0.86230.3209-0.35310.5447-0.5610.46160.07110.02460.1812-0.15810.42054.663934.925327.049
130.2262-0.10350.09980.59450.0199-0.01010.0532-0.0824-0.3561-0.1868-0.07370.4834-0.1794-0.0808-0.01110.2657-0.0199-0.07360.3149-0.09680.3874-2.007925.63318.091
140.3152-0.3870.54330.2839-0.41370.2969-0.25050.26060.0280.23110.2558-0.1255-0.66280.4451-0.00060.399-0.0357-0.04570.3166-0.04560.328711.283927.686223.2354
150.64660.0686-0.20750.3069-0.30230.2593-0.01640.4019-0.07720.87690.4861-0.01190.58170.02440.73230.99660.0865-0.27570.7572-0.19480.408912.163328.811644.2272
160.1789-0.21850.16540.28440.02220.52960.0441-0.14290.2460.31110.05340.2169-0.08470.2674-00.3327-0.001-0.03010.4160.00510.251225.44169.19737.751
170.1263-0.1173-0.12440.44310.31210.03390.4907-0.56040.7880.4175-0.18630.3389-0.62440.49700.2846-0.04-0.00230.31210.02910.376922.198713.6276-0.4327
180.78540.22010.85691.29750.38841.01520.47480.85620.8469-0.66610.0968-0.9084-1.22020.55190.15870.438-0.0470.08180.67270.1570.297228.052314.4313-19.7638
190.2467-0.3175-0.01915.6279-1.2171.6104-0.4550.8152-0.3795-0.58140.22330.73660.3156-0.48370.17650.4739-0.02770.03490.5581-0.05260.310121.39392.9577-20.3681
200.8623-0.02470.23170.5324-0.03220.284-0.15170.4352-0.0082-0.017-0.0669-0.0691-0.02420.4268-0.00010.3012-0.01170.02930.45250.01910.378131.42545.3058-5.3068
21-0.0139-0.01810.01840.2181-0.20070.076-0.3446-0.4359-0.23370.77510.21810.00910.43230.32480.00030.41010.0330.02960.3741-0.00740.439723.7634-3.75965.3826
220.24880.23740.27070.1315-0.0128-0.06960.4970.548-0.0711-0.2477-0.4140.15060.07040.49120.00010.3560.0678-0.01090.3897-0.03110.318119.16295.3764-16.0593
230.48320.20070.44670.1992-0.38480.6027-0.04440.1927-0.5042-0.35670.49070.43710.4024-0.38460.04020.3718-0.0554-0.01370.3529-0.09120.40398.83350.6561-9.7944
241.55310.15150.35080.28390.39040.3188-0.19720.35880.13040.17590.18-0.3147-0.1247-0.09510.00540.24350.02790.02170.27730.05710.322819.390711.4639-9.2079
250.46-0.2355-0.24660.6930.74170.413-0.0944-0.09690.10431.0337-0.07570.1494-0.75820.1783-0.00330.38190.0174-0.01340.28150.01250.38437.597613.4009-5.1155
260.3293-0.25160.25910.57170.32490.38280.8506-0.19420.79980.2649-0.30230.2491-0.93020.2037-0.00020.36270.01720.03140.31360.06090.493613.707216.4122-4.5009
271.0212-0.18850.33480.26010.01230.8628-0.19260.0309-0.31830.10070.3433-0.09760.3005-0.14720.00670.3267-0.01150.04970.22930.00630.246915.4074.3318-1.1461
281.14850.8305-0.06510.2921-0.10380.13260.0591-0.01920.3460.47060.09070.0710.0342-0.21550.52140.14750.0114-0.04630.33440.06760.37497.783611.3472-11.1899
290.8436-0.23720.11290.50920.74020.69240.0250.3343-0.14270.16160.01720.4141-0.16630.2573-0.00050.2911-0.011-0.01450.30830.01780.279520.50234.27-10.2966
300.6885-0.1403-0.08640.55480.47460.4921-0.36780.2282-0.07320.3014-0.17230.1130.16950.5549-0.01220.5049-00.08360.31520.03290.358118.9286-15.3316-4.3078
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 188:204)A188 - 204
2X-RAY DIFFRACTION2(chain A and resid 205:215)A205 - 215
3X-RAY DIFFRACTION3(chain A and resid 216:232)A216 - 232
4X-RAY DIFFRACTION4(chain A and resid 233:266)A233 - 266
5X-RAY DIFFRACTION5(chain A and resid 267:283)A267 - 283
6X-RAY DIFFRACTION6(chain A and resid 284:293)A284 - 293
7X-RAY DIFFRACTION7(chain A and resid 294:306)A294 - 306
8X-RAY DIFFRACTION8(chain A and resid 307:320)A307 - 320
9X-RAY DIFFRACTION9(chain A and resid 321:335)A321 - 335
10X-RAY DIFFRACTION10(chain A and resid 336:350)A336 - 350
11X-RAY DIFFRACTION11(chain A and resid 351:361)A351 - 361
12X-RAY DIFFRACTION12(chain A and resid 362:371)A362 - 371
13X-RAY DIFFRACTION13(chain A and resid 372:381)A372 - 381
14X-RAY DIFFRACTION14(chain A and resid 382:392)A382 - 392
15X-RAY DIFFRACTION15(chain A and resid 393:403)A393 - 403
16X-RAY DIFFRACTION16(chain B and resid 188:204)B188 - 204
17X-RAY DIFFRACTION17(chain B and resid 205:215)B205 - 215
18X-RAY DIFFRACTION18(chain B and resid 216:232)B216 - 232
19X-RAY DIFFRACTION19(chain B and resid 233:266)B233 - 266
20X-RAY DIFFRACTION20(chain B and resid 267:283)B267 - 283
21X-RAY DIFFRACTION21(chain B and resid 284:293)B284 - 293
22X-RAY DIFFRACTION22(chain B and resid 294:306)B294 - 306
23X-RAY DIFFRACTION23(chain B and resid 307:320)B307 - 320
24X-RAY DIFFRACTION24(chain B and resid 321:335)B321 - 335
25X-RAY DIFFRACTION25(chain B and resid 336:350)B336 - 350
26X-RAY DIFFRACTION26(chain B and resid 351:361)B351 - 361
27X-RAY DIFFRACTION27(chain B and resid 362:371)B362 - 371
28X-RAY DIFFRACTION28(chain B and resid 372:381)B372 - 381
29X-RAY DIFFRACTION29(chain B and resid 382:392)B382 - 392
30X-RAY DIFFRACTION30(chain B and resid 393:403)B393 - 403

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