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- PDB-9x55: Crystal structure of RhoGDI2 in complex with Compound 3054a -

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Basic information

Entry
Database: PDB / ID: 9x55
TitleCrystal structure of RhoGDI2 in complex with Compound 3054a
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: 2.37 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)16,5352
Polymers16,1581
Non-polymers3771
Water61334
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.958, 53.958, 94.868
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-A1EY4 / (3~{S})-~{N}-[(~{R})-(4-phenylphenyl)-thiophen-2-yl-methyl]piperidine-3-carboxamide


Mass: 376.514 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H24N2OS / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 2.03 Å3/Da / Density % sol: 39.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 30% PEG1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.37→40 Å / Num. obs: 6119 / % possible obs: 99.7 % / Redundancy: 17.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.101 / Net I/σ(I): 26.3
Reflection shellResolution: 2.37→2.41 Å / Redundancy: 12.5 % / Rmerge(I) obs: 0.476 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 283 / CC1/2: 0.99 / % possible all: 100

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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: 2.37→38.15 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 20.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2603 259 5.18 %
Rwork0.2051 --
obs0.2077 4998 81.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.37→38.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1092 0 27 34 1153
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031149
X-RAY DIFFRACTIONf_angle_d0.5791557
X-RAY DIFFRACTIONf_dihedral_angle_d6.147153
X-RAY DIFFRACTIONf_chiral_restr0.044171
X-RAY DIFFRACTIONf_plane_restr0.004194
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.37-2.980.3345900.26381778X-RAY DIFFRACTION63
2.99-38.150.24491690.19112961X-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)
13.19241.8987-0.14554.8073-4.31596.26740.0370.14870.1005-0.29080.44320.75620.2994-0.753-0.45460.1928-0.015-0.04740.4049-0.0050.2511-12.490712.56170.0301
22.4220.7628-0.30991.88481.03663.75530.0908-0.15810.16620.31450.10870.9931-0.1869-1.1151-0.12820.3394-0.05420.0730.5728-0.01020.4428-15.58449.978410.5735
32.39371.1036-0.07433.3761-1.91585.04830.04230.1004-0.01480.0075-0.01240.1003-0.0221-0.1493-0.00330.13220.06190.01350.1899-0.03130.2011-4.666513.98655.1876
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 64 through 91 )
2X-RAY DIFFRACTION2chain 'A' and (resid 92 through 102 )
3X-RAY DIFFRACTION3chain 'A' and (resid 103 through 200 )

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