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- PDB-6p5w: Structure of DCN1 bound to 3-methyl-N-((4S,5S)-3-methyl-6-oxo-1-p... -

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Basic information

Entry
Database: PDB / ID: 6p5w
TitleStructure of DCN1 bound to 3-methyl-N-((4S,5S)-3-methyl-6-oxo-1-phenyl-4-(p-tolyl)-4,5,6,7-tetrahydro-1H-pyrazolo[3,4-b]pyridin-5-yl)benzamide
ComponentsLysozyme,DCN1-like protein 1 chimera
KeywordsLIGASE / E3 Ligase / HYDROLASE
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 / cytosol / cytoplasm
Similarity search - Function
Cullin, PONY binding domain / Potentiating neddylation domain / Defective-in-cullin neddylation protein / DCN1-like, PONY binding domain / Cullin binding / DCUN1 domain profile. / UBA-like domain / UBA-like superfamily / Lysozyme - #40 / Endolysin T4 type ...Cullin, PONY binding domain / Potentiating neddylation domain / Defective-in-cullin neddylation protein / DCN1-like, PONY binding domain / Cullin binding / DCUN1 domain profile. / UBA-like domain / UBA-like superfamily / Lysozyme - #40 / Endolysin T4 type / T4-type lysozyme / : / Glycoside hydrolase, family 24 / Phage lysozyme / Lysozyme domain superfamily / Recoverin; domain 1 / Lysozyme / Lysozyme-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-O0A / Endolysin / DCN1-like protein 1
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 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: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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 chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7582
Polymers44,3071
Non-polymers4511
Water5,891327
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area18670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.710, 95.567, 58.989
Angle α, β, γ (deg.)90.000, 106.030, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Lysozyme,DCN1-like protein 1 chimera / 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 / Plasmid: pRSF DUET / Production host: Escherichia coli (E. coli) / References: UniProt: D9IEF7, UniProt: Q96GG9, lysozyme
#2: Chemical ChemComp-O0A / 3-methyl-N-[(4S,5S)-3-methyl-4-(4-methylphenyl)-6-oxo-1-phenyl-4,5,6,7-tetrahydro-1H-pyrazolo[3,4-b]pyridin-5-yl]benzamide


Mass: 450.532 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H26N4O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 327 / 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: 6% PEG3350, 0.2M NH4Br

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.97857 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 30, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.69→50 Å / Num. obs: 40350 / % possible obs: 97.7 % / Redundancy: 3 % / Biso Wilson estimate: 23.28 Å2 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.057 / Rrim(I) all: 0.101 / Χ2: 4.211 / Net I/σ(I): 28.1 / Num. measured all: 123063
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.69-1.752.50.18438820.9310.1330.2281.76194.8
1.75-1.822.80.15439750.9520.1090.192.28596.5
1.82-1.93.10.13940070.9580.0950.1693.22897.1
1.9-23.10.11839990.9670.080.1434.61497.5
2-2.133.20.10340220.9730.0690.1246.08597.9
2.13-2.293.20.09440730.9740.0640.1145.90198.3
2.29-2.523.20.08240480.9790.0560.0994.66898.5
2.52-2.893.20.07641090.9830.0520.0924.18198.8
2.89-3.643.10.07440920.980.0520.0913.78499.1
3.64-503.10.08441430.9610.0570.1024.37798.5

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Processing

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

5v86


Resolution: 1.69→33.011 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 20.68
RfactorNum. reflection% reflection
Rfree0.2217 2025 5.02 %
Rwork0.1756 --
obs0.1779 40323 97.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 66.03 Å2 / Biso mean: 29.5509 Å2 / Biso min: 4.14 Å2
Refinement stepCycle: final / Resolution: 1.69→33.011 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2962 0 34 327 3323
Biso mean--38.88 36.52 -
Num. residues----370
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.69-1.73220.23161500.16412580273092
1.7322-1.77910.2221360.16282645278196
1.7791-1.83140.22031390.15672737287697
1.8314-1.89050.21011430.15762677282097
1.8905-1.95810.19381400.16142744288497
1.9581-2.03650.21581510.15822753290498
2.0365-2.12910.2151470.15912708285598
2.1291-2.24140.2391380.15192756289498
2.2414-2.38170.22661480.15542756290498
2.3817-2.56560.20421550.16542760291599
2.5656-2.82360.22191360.18022797293399
2.8236-3.23190.22651210.18182800292199
3.2319-4.07070.2221750.16912763293899
4.0707-33.0170.22861460.20972822296898

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