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- PDB-6p5v: Structure of DCN1 bound to N-((4S,5S)-7-ethyl-4-(4-fluorophenyl)-... -

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Basic information

Entry
Database: PDB / ID: 6p5v
TitleStructure of DCN1 bound to N-((4S,5S)-7-ethyl-4-(4-fluorophenyl)-3-methyl-6-oxo-1-phenyl-4,5,6,7-tetrahydro-1H-pyrazolo[3,4-b]pyridin-5-yl)-3-methylbenzamide
ComponentsLysozyme,DCN1-like protein 1 fusion
KeywordsLIGASE / E3 Ligase
Function / homology
Function and homology information


positive regulation of protein neddylation / ubiquitin-like protein binding / regulation of protein neddylation / protein neddylation / ubiquitin conjugating enzyme binding / cullin family protein binding / regulation of protein ubiquitination / ubiquitin ligase complex / viral release from host cell by cytolysis / peptidoglycan catabolic process ...positive regulation of protein neddylation / ubiquitin-like protein binding / regulation of protein neddylation / protein neddylation / ubiquitin conjugating enzyme binding / cullin family protein binding / regulation of protein ubiquitination / ubiquitin ligase complex / viral release from host cell by cytolysis / peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / Neddylation / host cell cytoplasm / defense response to bacterium / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
Potentiating neddylation domain / Defective-in-cullin neddylation protein / DCN1-like, PONY binding domain / Cullin binding / DCUN1 domain profile. / UBA-like domain / UBA-like superfamily / Endolysin T4 type / T4-type lysozyme / : ...Potentiating neddylation domain / Defective-in-cullin neddylation protein / DCN1-like, PONY binding domain / Cullin binding / DCUN1 domain profile. / UBA-like domain / UBA-like superfamily / Endolysin T4 type / T4-type lysozyme / : / Glycoside hydrolase, family 24 / Phage lysozyme / Lysozyme domain superfamily / Lysozyme-like domain superfamily
Similarity search - Domain/homology
Chem-O37 / Endolysin / DCN1-like protein 1
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.398 Å
AuthorsGuy, R.K. / Kim, H.S. / Hammill, J.T. / Scott, D.C. / Schulman, B.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: J.Med.Chem. / Year: 2019
Title: Discovery of Novel Pyrazolo-pyridone DCN1 Inhibitors Controlling Cullin Neddylation.
Authors: Kim, H.S. / Hammill, J.T. / Scott, D.C. / Chen, Y. / Min, J. / Rector, J. / Singh, B. / Schulman, B.A. / Guy, R.K.
History
DepositionMay 31, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lysozyme,DCN1-like protein 1 fusion
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9123
Polymers44,3071
Non-polymers6052
Water7,548419
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.310, 96.985, 60.072
Angle α, β, γ (deg.)90.000, 106.090, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Lysozyme,DCN1-like protein 1 fusion / DCUN1 domain-containing protein 1 / Defective in cullin neddylation protein 1-like protein 1 / ...DCUN1 domain-containing protein 1 / Defective in cullin neddylation protein 1-like protein 1 / Squamous cell carcinoma-related oncogene


Mass: 44307.352 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus), (gene. exp.) Homo sapiens (human)
Gene: e, T4Tp126, DCUN1D1, DCUN1L1, RP42, SCCRO / Production host: Escherichia coli (E. coli) / References: UniProt: D9IEF7, UniProt: Q96GG9, lysozyme
#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical ChemComp-O37 / N-[(4S,5S)-1-[(1S)-cyclohex-3-en-1-yl]-7-ethyl-4-(4-fluorophenyl)-3-methyl-6-oxo-4,5,6,7-tetrahydro-1H-pyrazolo[3,4-b]pyridin-5-yl]-3-methylbenzamide


Mass: 486.580 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C29H31FN4O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 419 / 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: 2.12 Å3/Da / Density % sol: 42.04 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 7% PEG3350, 0.2M NH4Br

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1.00232 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00232 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 72513 / % possible obs: 94.8 % / Redundancy: 3.6 % / Biso Wilson estimate: 18.43 Å2 / Rmerge(I) obs: 0.032 / Rpim(I) all: 0.019 / Rrim(I) all: 0.038 / Χ2: 0.518 / Net I/σ(I): 9.2 / Num. measured all: 259468
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.4-1.453.30.5869950.7840.3540.6820.39391.8
1.45-1.513.60.41472380.8820.2480.4840.40395.2
1.51-1.583.60.27672730.9350.1670.3240.40895.2
1.58-1.663.50.18272110.9640.1140.2160.42694.3
1.66-1.763.60.12269750.9840.0740.1440.43590.9
1.76-1.93.70.08673360.9920.050.10.47696.5
1.9-2.093.60.05374640.9970.0320.0620.55397.3
2.09-2.393.40.03570430.9980.0220.0420.67492.1
2.39-3.023.80.02775460.9990.0160.0320.81798.4
3.02-503.60.0274320.9990.0120.0240.55395.8

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5V86

5v86


Resolution: 1.398→37.128 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 20.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2049 3450 4.76 %
Rwork0.1712 69019 -
obs0.1728 72469 94.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 70.68 Å2 / Biso mean: 27.3644 Å2 / Biso min: 11.45 Å2
Refinement stepCycle: final / Resolution: 1.398→37.128 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3010 0 85 419 3514
Biso mean--30.6 35.28 -
Num. residues----373
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.3976-1.41680.31661170.28182477259485
1.4168-1.4370.29281220.24052717283993
1.437-1.45850.26571570.21322717287495
1.4585-1.48130.21551580.18272782294095
1.4813-1.50560.24561140.17362769288396
1.5056-1.53150.23651600.17152759291995
1.5315-1.55940.21861260.17232767289395
1.5594-1.58940.23951440.16152786293095
1.5894-1.62180.20761310.15582758288995
1.6218-1.65710.19731420.1562715285794
1.6571-1.69560.23721230.15832427255083
1.6956-1.7380.22541300.16272776290695
1.738-1.7850.2121520.16122817296996
1.785-1.83750.20011300.1652836296697
1.8375-1.89680.22731350.16822802293797
1.8968-1.96460.22131490.1682846299597
1.9646-2.04330.21911280.16112842297098
2.0433-2.13630.22281460.16042836298297
2.1363-2.24890.20921390.15792816295596
2.2489-2.38980.17661270.15072497262486
2.3898-2.57420.22141380.16562872301098
2.5742-2.83320.1941600.17542852301298
2.8332-3.2430.2021290.17712943307299
3.243-4.0850.16941510.16212854300597
4.085-37.14150.20571420.19252756289893

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