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- PDB-7kwa: Structure of DCN1 bound to N-((4S,5S)-3-(aminomethyl)-7-ethyl-4-(... -

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Basic information

Entry
Database: PDB / ID: 7kwa
TitleStructure of DCN1 bound to N-((4S,5S)-3-(aminomethyl)-7-ethyl-4-(4-fluorophenyl)-6-oxo-1-phenyl-4,5,6,7-tetrahydro-1H-pyrazolo[3,4-b]pyridin-5-yl)-3-(trifluoromethyl)benzamide
ComponentsEndolysin,DCN1-like protein 1
KeywordsLIGASE/Inhibitor / Inhibitor complex / LIGASE / LIGASE-Inhibitor complex
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
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 ...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 / Lysozyme domain superfamily / Phage lysozyme / Lysozyme-like domain superfamily
Similarity search - Domain/homology
Chem-YHP / Endolysin / DCN1-like protein 1
Similarity search - Component
Biological speciesEnterobacteria phage RB59 (virus)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.572 Å
AuthorsKim, H.S. / Hammill, J.T. / Schulman, B.A. / Guy, R.K. / Scott, D.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)5R01CA247365-02 United States
CitationJournal: J.Med.Chem. / Year: 2021
Title: Improvement of Oral Bioavailability of Pyrazolo-Pyridone Inhibitors of the Interaction of DCN1/2 and UBE2M.
Authors: Kim, H.S. / Hammill, J.T. / Scott, D.C. / Chen, Y. / Rice, A.L. / Pistel, W. / Singh, B. / Schulman, B.A. / Guy, R.K.
History
DepositionNov 30, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 14, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)44,8592
Polymers44,3071
Non-polymers5521
Water6,810378
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)35.233, 97.057, 59.837
Angle α, β, γ (deg.)90.000, 106.110, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Endolysin,DCN1-like protein 1 / Lysis protein / Lysozyme / Muramidase / DCNL1 / DCUN1 domain-containing protein 1 / Defective in ...Lysis protein / Lysozyme / Muramidase / DCNL1 / 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 RB59 (virus), (gene. exp.) Homo sapiens (human)
Gene: e, RB59_126, DCUN1D1, DCN1, DCUN1L1, RP42, SCCRO / Production host: Escherichia coli (E. coli) / References: UniProt: A0A097J809, UniProt: Q96GG9, lysozyme
#2: Chemical ChemComp-YHP / N-[(4S,5S)-3-(aminomethyl)-7-ethyl-4-(4-fluorophenyl)-6-oxo-1-phenyl-4,5,6,7-tetrahydro-1H-pyrazolo[3,4-b]pyridin-5-yl]-3-(trifluoromethyl)benzamide


Mass: 551.535 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H25F4N5O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 378 / 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: 2.22 Å3/Da / Density % sol: 44.55 %
Crystal growTemperature: 277 K / Method: evaporation / Details: 6% 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: 0.9786 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 5, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.57→50 Å / Num. obs: 49253 / % possible obs: 91.7 % / Redundancy: 3.5 % / Biso Wilson estimate: 18.63 Å2 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.031 / Rrim(I) all: 0.059 / Χ2: 0.916 / Net I/σ(I): 9 / Num. measured all: 170711
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.57-1.633.20.34945150.9150.2190.4140.38584.7
1.63-1.693.50.29450420.940.180.3450.39693.8
1.69-1.773.60.23650630.9590.1420.2760.43694.5
1.77-1.863.60.17249930.9750.1050.2020.50893.3
1.86-1.983.50.11846600.9860.0720.1380.65487.2
1.98-2.133.70.08851120.9920.0530.1020.89495.7
2.13-2.353.50.06551830.9950.040.0771.16495.7
2.35-2.683.40.05149360.9960.0320.0611.32592.4
2.68-3.383.30.03948340.9980.0250.0461.7889.8
3.38-503.30.02949150.9980.0190.0351.75289.9

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5V86

5v86


Resolution: 1.572→37.082 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 21.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2095 2431 4.94 %
Rwork0.1695 46785 -
obs0.1714 49216 91.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 71.2 Å2 / Biso mean: 27.9416 Å2 / Biso min: 12.18 Å2
Refinement stepCycle: final / Resolution: 1.572→37.082 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2951 0 65 378 3394
Biso mean--48.89 36.24 -
Num. residues----372
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.5723-1.60440.27671360.206249583
1.6044-1.63930.28821600.1807266391
1.6393-1.67740.23131360.172285794
1.6774-1.71940.21491490.1657278295
1.7194-1.76590.22621460.1653286094
1.7659-1.81780.231700.1696272194
1.8178-1.87650.23111660.1613279193
1.8765-1.94360.22291380.1612257086
1.9436-2.02140.21131430.1618268991
2.0214-2.11340.23931360.1611290796
2.1134-2.22480.22321450.1603288896
2.2248-2.36410.19141490.1559284995
2.3641-2.54660.21421580.1633281694
2.5466-2.80280.20751300.1726252885
2.8028-3.20820.21291080.1775287294
3.2082-4.04120.19581400.1613275692
4.0412-37.0820.17981210.1852274189

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