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- PDB-9ogw: Identification of ligands for E3 ligases using fragment-based methods -

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Basic information

Entry
Database: PDB / ID: 9ogw
TitleIdentification of ligands for E3 ligases using fragment-based methods
ComponentsE3 ubiquitin-protein ligase CBL-C
KeywordsLIGASE / small molecule / complex crystal structure / CBL-c / TKB (TYROSINE KINASE BINDING) / REGULATOR OF EGFR MEDIATED SIGNAL TRANSDUCTION
Function / homology
Function and homology information


response to glial cell derived neurotrophic factor / epidermal growth factor receptor binding / negative regulation of epidermal growth factor receptor signaling pathway / negative regulation of MAPK cascade / phosphotyrosine residue binding / receptor tyrosine kinase binding / RING-type E3 ubiquitin transferase / SH3 domain binding / ubiquitin protein ligase activity / ubiquitin-dependent protein catabolic process ...response to glial cell derived neurotrophic factor / epidermal growth factor receptor binding / negative regulation of epidermal growth factor receptor signaling pathway / negative regulation of MAPK cascade / phosphotyrosine residue binding / receptor tyrosine kinase binding / RING-type E3 ubiquitin transferase / SH3 domain binding / ubiquitin protein ligase activity / ubiquitin-dependent protein catabolic process / negative regulation of neuron apoptotic process / cell surface receptor signaling pathway / protein stabilization / protein ubiquitination / membrane raft / calcium ion binding / signal transduction / zinc ion binding / plasma membrane
Similarity search - Function
Adaptor protein Cbl, N-terminal helical / Adaptor protein Cbl, EF hand-like / Adaptor protein Cbl, SH2-like domain / Adaptor protein Cbl, PTB domain / Adaptor protein Cbl / CBL proto-oncogene N-terminal domain 1 / CBL proto-oncogene N-terminus, EF hand-like domain / CBL proto-oncogene N-terminus, SH2-like domain / Cbl-type phosphotyrosine-binding (Cbl-PTB) domain profile. / Adaptor protein Cbl, N-terminal domain superfamily ...Adaptor protein Cbl, N-terminal helical / Adaptor protein Cbl, EF hand-like / Adaptor protein Cbl, SH2-like domain / Adaptor protein Cbl, PTB domain / Adaptor protein Cbl / CBL proto-oncogene N-terminal domain 1 / CBL proto-oncogene N-terminus, EF hand-like domain / CBL proto-oncogene N-terminus, SH2-like domain / Cbl-type phosphotyrosine-binding (Cbl-PTB) domain profile. / Adaptor protein Cbl, N-terminal domain superfamily / Zinc finger, C3HC4 type (RING finger) / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / SH2 domain superfamily / EF-hand domain pair / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
: / E3 ubiquitin-protein ligase CBL-C
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsPhan, J. / Fesik, S.W.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: Rsc Chem Biol / Year: 2025
Title: Identification of ligands for E3 ligases with restricted expression using fragment-based methods.
Authors: Waterson, A.G. / Lehmann, B.D. / Lu, Z. / Sensintaffar, J.L. / Olejniczak, E.T. / Zhao, B. / Rietz, T. / Payne, W.G. / Phan, J. / Fesik, S.W.
History
DepositionMay 2, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 22, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase CBL-C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6962
Polymers35,4631
Non-polymers2331
Water3,189177
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)43.998, 63.103, 108.205
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 E3 ubiquitin-protein ligase CBL-C / RING finger protein 57 / RING-type E3 ubiquitin transferase CBL-C / SH3-binding protein CBL-3 / SH3- ...RING finger protein 57 / RING-type E3 ubiquitin transferase CBL-C / SH3-binding protein CBL-3 / SH3-binding protein CBL-C / Signal transduction protein CBL-C


Mass: 35462.648 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CBLC, CBL3, RNF57 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9ULV8, RING-type E3 ubiquitin transferase
#2: Chemical ChemComp-A1CA8 / 2-{[(thiophen-3-yl)methyl]amino}benzoic acid


Mass: 233.286 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H11NO2S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / 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: 2.12 Å3/Da / Density % sol: 41.92 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 10-20% PEG 3350, 0.1 M ammonium formate, pH 6.5 / PH range: 6.5 - 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 1 Å
DetectorType: MAR CCD 300 mm / Detector: CCD / Date: Jan 14, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→40 Å / Num. obs: 28515 / % possible obs: 98.2 % / Redundancy: 7.8 % / CC1/2: 0.99 / Net I/σ(I): 21.5
Reflection shellResolution: 1.8→1.83 Å / Num. unique obs: 1370 / CC1/2: 0.17

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→27.894 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.46 / Phase error: 21.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2269 1979 7.02 %
Rwork0.1861 --
obs0.189 28198 98.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→27.894 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2354 0 16 177 2547
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092437
X-RAY DIFFRACTIONf_angle_d1.0983319
X-RAY DIFFRACTIONf_dihedral_angle_d5.6231423
X-RAY DIFFRACTIONf_chiral_restr0.05358
X-RAY DIFFRACTIONf_plane_restr0.006433
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.8450.35681370.3251811X-RAY DIFFRACTION97
1.845-1.89490.35411370.30531808X-RAY DIFFRACTION97
1.8949-1.95060.32091360.28491807X-RAY DIFFRACTION97
1.9506-2.01360.29761400.261852X-RAY DIFFRACTION98
2.0136-2.08550.28411400.23541851X-RAY DIFFRACTION98
2.0855-2.1690.25981380.20591837X-RAY DIFFRACTION99
2.169-2.26770.23141410.19461861X-RAY DIFFRACTION99
2.2677-2.38720.22741390.1871844X-RAY DIFFRACTION99
2.3872-2.53660.24391420.17291884X-RAY DIFFRACTION99
2.5366-2.73230.20211420.17841893X-RAY DIFFRACTION99
2.7323-3.0070.2381430.17641883X-RAY DIFFRACTION99
3.007-3.44140.22611430.16931897X-RAY DIFFRACTION99
3.4414-4.33320.19291480.14671956X-RAY DIFFRACTION100
4.3332-100.18271530.16642035X-RAY DIFFRACTION99
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)
11.98810.0838-0.00372.9733-0.41211.5042-0.04480.15460.1083-0.07020.0364-0.0971-0.09310.1186-0.01580.142-0.0149-0.00960.1604-0.04390.1369-19.975310.0297-8.5384
21.5282-1.2886-0.91062.84292.39594.37420.20910.2174-0.0717-0.20950.0433-0.07240.34470.4671-0.22180.27630.0765-0.03880.2881-0.05740.2924-17.4249-14.3625-15.1135
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 217 )
2X-RAY DIFFRACTION2chain 'A' and (resid 218 through 322 )

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