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- PDB-9x59: Crystal structure of RhoGDI2 in complex with Compound 2102 -

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Basic information

Entry
Database: PDB / ID: 9x59
TitleCrystal structure of RhoGDI2 in complex with Compound 2102
ComponentsRho GDP-dissociation inhibitor 2
KeywordsSIGNALING PROTEIN / Inhibitor / Complex / Rho GDP-dissociation inhibitor 2
Function / homology
Function and homology information


cellular response to redox state / Rho GDP-dissociation inhibitor activity / negative regulation of trophoblast cell migration / regulation of Rho protein signal transduction / CDC42 GTPase cycle / RHOH GTPase cycle / RHOG GTPase cycle / RHOA GTPase cycle / RAC3 GTPase cycle / Rho protein signal transduction ...cellular response to redox state / Rho GDP-dissociation inhibitor activity / negative regulation of trophoblast cell migration / regulation of Rho protein signal transduction / CDC42 GTPase cycle / RHOH GTPase cycle / RHOG GTPase cycle / RHOA GTPase cycle / RAC3 GTPase cycle / Rho protein signal transduction / RAC1 GTPase cycle / GTPase activator activity / small GTPase binding / cytoplasmic vesicle / cytoskeleton / GTPase activity / extracellular exosome / membrane / cytoplasm / cytosol
Similarity search - Function
Rho protein GDP-dissociation inhibitor / Rho GDP-dissociation inhibitor domain superfamily / RHO protein GDP dissociation inhibitor / Immunoglobulin E-set
Similarity search - Domain/homology
: / Rho GDP-dissociation inhibitor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsLiu, M. / Ruan, K.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22377119 China
CitationJournal: Acs Chem.Biol. / Year: 2025
Title: Fragment-Based Discovery of a Small-Molecule RhoGDI2 Ligand, HR3119, that Inhibits Cancer Cell Migration.
Authors: Liu, M. / Wan, S. / Guo, S. / Liu, J. / Li, W. / Wang, L. / Li, F. / Zhang, J. / Liu, X. / Liu, D. / Yao, X. / Gao, J. / Ruan, K. / He, W.
History
DepositionOct 12, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 29, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Rho GDP-dissociation inhibitor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4242
Polymers16,1581
Non-polymers2651
Water2,720151
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.969, 51.969, 97.446
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Rho GDP-dissociation inhibitor 2 / Rho GDI 2 / Ly-GDI / Rho-GDI beta


Mass: 16158.364 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARHGDIB, GDIA2, GDID4, RAP1GN1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P52566
#2: Chemical ChemComp-A1EY2 / (~{R})-(4-phenylphenyl)-thiophen-2-yl-methanamine


Mass: 265.373 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H15NS / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / 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: 2.04 Å3/Da / Density % sol: 39.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 30% PEG 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9786 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 25, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.65→40 Å / Num. obs: 16953 / % possible obs: 99.5 % / Redundancy: 7.1 % / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.038 / Rrim(I) all: 0.102 / Χ2: 0.931 / Net I/σ(I): 7.8 / Num. measured all: 121027
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.65-1.687.50.4818400.9020.9740.1820.5150.808100
1.68-1.717.40.4278210.9130.9770.1640.4590.85199.9
1.71-1.747.30.3798380.9170.9780.1460.4070.912100
1.74-1.787.20.3368230.940.9840.1310.3620.979100
1.78-1.8270.3058250.9360.9830.1220.3291.01799.8
1.82-1.866.70.268370.9560.9890.1060.2811.06799.8
1.86-1.970.2318250.9640.9910.0940.251.09299.5
1.9-1.967.40.218360.9680.9920.0820.2261.18599.9
1.96-2.017.50.188450.9790.9950.0690.1931.09799.5
2.01-2.087.50.178230.9840.9960.0660.1831.14499.8
2.08-2.157.40.1548220.9840.9960.060.1661.14599.4
2.15-2.247.20.1458510.9880.9970.0560.1551.06299.3
2.24-2.346.70.1338400.9840.9960.0550.1451.05899.6
2.34-2.466.90.1258590.9860.9970.0510.1350.99999.7
2.46-2.627.50.1188450.9870.9970.0450.1260.94399.8
2.62-2.827.40.1088460.9880.9970.0420.1160.863100
2.82-3.117.10.0988730.9910.9980.0390.1050.7799.7
3.11-3.556.40.0878650.9910.9980.0370.0950.69599.2
3.55-4.487.10.0768880.9930.9980.030.0820.55498.9
4.48-406.60.0699510.9950.9990.0280.0750.40796.5

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Processing

Software
NameVersionClassification
PHENIX(1.19rc3_4028: ???)refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→36.75 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 18.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2123 821 4.94 %
Rwork0.1638 --
obs0.1661 16624 99.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.65→36.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1097 0 19 151 1267
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061145
X-RAY DIFFRACTIONf_angle_d0.8271552
X-RAY DIFFRACTIONf_dihedral_angle_d7.162149
X-RAY DIFFRACTIONf_chiral_restr0.055170
X-RAY DIFFRACTIONf_plane_restr0.007195
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.750.25831370.17432567X-RAY DIFFRACTION99
1.75-1.890.18381410.1482551X-RAY DIFFRACTION99
1.89-2.080.20581410.14132619X-RAY DIFFRACTION100
2.08-2.380.23531300.15812612X-RAY DIFFRACTION100
2.38-30.21591340.18262651X-RAY DIFFRACTION100
3-36.750.2021380.16642803X-RAY DIFFRACTION98

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