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- PDB-8z6c: Crystal structure of HDGFRP2 PWWP domain in complex with 4-(4-bro... -

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Basic information

Entry
Database: PDB / ID: 8z6c
TitleCrystal structure of HDGFRP2 PWWP domain in complex with 4-(4-bromo-1H-pyrazol-3-yl) pyridine
ComponentsHepatoma-derived growth factor-related protein 2
KeywordsSIGNALING PROTEIN / Hepatoma-derived growth factor-related protein 2 / PWWP domain / hit
Function / homology
Function and homology information


histone H3K27me3 reader activity / histone H3K9me2/3 reader activity / skeletal muscle tissue regeneration / muscle cell differentiation / muscle organ development / DNA repair-dependent chromatin remodeling / positive regulation of double-strand break repair via homologous recombination / : / histone reader activity / positive regulation of cell growth ...histone H3K27me3 reader activity / histone H3K9me2/3 reader activity / skeletal muscle tissue regeneration / muscle cell differentiation / muscle organ development / DNA repair-dependent chromatin remodeling / positive regulation of double-strand break repair via homologous recombination / : / histone reader activity / positive regulation of cell growth / DNA recombination / chromatin remodeling / DNA repair / nucleus / cytoplasm
Similarity search - Function
Lens epithelium-derived growth factor, integrase-binding domain / HIV integrase-binding domain superfamily / Lens epithelium-derived growth factor (LEDGF) / TFIIS/LEDGF domain superfamily / domain with conserved PWWP motif / PWWP domain / PWWP domain profile. / PWWP domain
Similarity search - Domain/homology
: / Hepatoma-derived growth factor-related protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsWei, X. / Ruan, K.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22377119 China
CitationJournal: To Be Published
Title: Fragment based discovery of small molecule inhibitors of the HDGFRP2 PWWP domain
Authors: Wei, X. / Ruan, K.
History
DepositionApr 19, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 23, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hepatoma-derived growth factor-related protein 2
B: Hepatoma-derived growth factor-related protein 2
C: Hepatoma-derived growth factor-related protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,12411
Polymers31,9723
Non-polymers1,1528
Water2,756153
1
A: Hepatoma-derived growth factor-related protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,0734
Polymers10,6571
Non-polymers4163
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Hepatoma-derived growth factor-related protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,0734
Polymers10,6571
Non-polymers4163
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Hepatoma-derived growth factor-related protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,9773
Polymers10,6571
Non-polymers3202
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.140, 42.371, 159.201
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Hepatoma-derived growth factor-related protein 2 / HDGF-related protein 2 / HRP-2 / Hepatoma-derived growth factor 2 / HDGF-2


Mass: 10657.184 Da / Num. of mol.: 3 / Fragment: PWWP domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HDGFL2, HDGF2, HDGFRP2, HRP2, UNQ785/PRO1604 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q7Z4V5
#2: Chemical ChemComp-A1D73 / 4-(4-bromanyl-1~{H}-pyrazol-3-yl)pyridine


Mass: 224.057 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H6BrN3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / 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: 2.22 Å3/Da / Density % sol: 44.66 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop
Details: 0.01 M magnesium sulfate heptahydrate, 0.05 M sodium cacodylate trihydrate (pH 6.5), 2 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 20, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.93→42.37 Å / Num. obs: 21227 / % possible obs: 95.1 % / Redundancy: 12.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.115 / Net I/σ(I): 14.2
Reflection shellResolution: 1.93→1.98 Å / Rmerge(I) obs: 0.906 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 1428 / CC1/2: 0.898 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19refinement
XDSJun 30, 2023data reduction
Aimlessdata scaling
MOLREPphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.93→37.4 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2358 1003 4.75 %
Rwork0.189 --
obs0.1912 21126 94.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.93→37.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2183 0 61 153 2397
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082336
X-RAY DIFFRACTIONf_angle_d0.9393180
X-RAY DIFFRACTIONf_dihedral_angle_d7.172297
X-RAY DIFFRACTIONf_chiral_restr0.058288
X-RAY DIFFRACTIONf_plane_restr0.009419
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.93-2.030.27441500.22562893X-RAY DIFFRACTION99
2.03-2.160.25191450.19242959X-RAY DIFFRACTION100
2.16-2.330.2802790.21871985X-RAY DIFFRACTION66
2.33-2.560.27931900.21242950X-RAY DIFFRACTION100
2.56-2.930.26031340.21483043X-RAY DIFFRACTION100
2.93-3.690.23991500.18293072X-RAY DIFFRACTION100
3.69-37.40.19091550.16613221X-RAY DIFFRACTION100
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)
15.78440.3828-1.23241.69991.42393.53610.0103-0.09470.15760.00780.1141-0.18320.0090.1443-0.0940.08350.0165-0.01090.1756-0.00310.144418.62356.77111.4579
28.6940.7485-5.36343.5744-0.35867.94380.1843-0.47740.17730.44790.04350.0166-0.21730.0511-0.18960.32630.00980.02910.37170.00290.211915.05817.835616.1344
35.39691.64870.95534.13781.27983.89580.16520.2816-0.1859-0.04110.0676-0.2670.19880.1877-0.23820.10070.0466-0.01710.1467-0.00870.169118.34643.2991-0.6861
47.7239-2.8881-0.62778.29013.82153.95930.1724-0.1055-0.4524-0.01630.00430.51010.1818-0.1243-0.09830.1192-0.0223-0.04760.12630.0080.20277.34911.5956-3.0191
55.0491-0.7811-0.3634.6832-0.75374.0687-0.07370.1498-0.2660.1030.08420.4977-0.0836-0.48670.01050.29180.02350.08770.20310.00540.2296-0.75785.813534.9313
63.3755-0.63345.2710.1371-0.88298.5232-0.1745-0.08730.5748-0.00551.14222.0352-0.1205-1.5753-0.66970.36970.0644-0.00060.91530.34050.7915-13.68059.771931.4335
74.98340.27-1.01525.4749-1.08621.612-0.0322-0.04650.03870.12630.1578-0.1772-0.0313-0.0738-0.07640.31240.02910.05470.1984-0.03450.17580.79295.468934.4127
83.6920.1049-1.57252.67592.14295.41560.13870.22680.3964-0.62720.0106-0.4336-0.67570.2874-0.1280.3268-0.02730.10360.22870.02310.23858.459213.505731.3685
96.02110.6972-1.42693.2640.91895.034-0.7148-0.502-0.35630.69410.35790.30450.1293-0.37290.30290.35770.09380.08860.3256-0.00040.265819.6053-13.080121.3082
102.5662-1.4729-1.99072.36922.25322.52810.0527-0.1744-0.26231.042-0.4248-0.08940.43731.18580.11630.73080.02220.02970.9420.04940.510121.4137-7.129935.5652
118.1342-1.1677-3.39033.95882.32116.7115-0.4894-0.5252-0.34480.32460.3870.35480.55490.01840.07770.32130.06140.06140.29920.04220.292519.7758-13.348321.3761
125.7162-0.491-2.42765.84092.36148.1432-0.2982-0.1811-0.10790.07150.4008-0.4043-0.17120.2678-0.09910.24150.01040.08930.243-0.01360.228727.6861-15.732612.1456
137.3251.594-2.00693.4369-0.87868.8224-1.4066-1.85380.1891.30150.6119-0.67450.51830.89080.59130.7320.3909-0.08040.6742-0.00360.497431.926-19.650724.2701
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 25 )
2X-RAY DIFFRACTION2chain 'A' and (resid 26 through 39 )
3X-RAY DIFFRACTION3chain 'A' and (resid 40 through 76 )
4X-RAY DIFFRACTION4chain 'A' and (resid 77 through 93 )
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 25 )
6X-RAY DIFFRACTION6chain 'B' and (resid 26 through 38 )
7X-RAY DIFFRACTION7chain 'B' and (resid 39 through 68 )
8X-RAY DIFFRACTION8chain 'B' and (resid 69 through 93 )
9X-RAY DIFFRACTION9chain 'C' and (resid 3 through 25 )
10X-RAY DIFFRACTION10chain 'C' and (resid 26 through 38 )
11X-RAY DIFFRACTION11chain 'C' and (resid 39 through 68 )
12X-RAY DIFFRACTION12chain 'C' and (resid 69 through 86 )
13X-RAY DIFFRACTION13chain 'C' and (resid 87 through 92 )

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