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- PDB-9jcu: TDI01 binding WT ROCK2 KD -

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Basic information

Entry
Database: PDB / ID: 9jcu
TitleTDI01 binding WT ROCK2 KD
ComponentsRho-associated protein kinase 2
KeywordsSIGNALING PROTEIN / inhibitor / kinase / complex
Function / homology
Function and homology information


positive regulation of connective tissue growth factor production / cellular response to acetylcholine / positive regulation of fibroblast growth factor production / positive regulation of centrosome duplication / regulation of angiotensin-activated signaling pathway / negative regulation of protein localization to lysosome / regulation of keratinocyte differentiation / Rho-dependent protein serine/threonine kinase activity / positive regulation of connective tissue replacement / response to transforming growth factor beta ...positive regulation of connective tissue growth factor production / cellular response to acetylcholine / positive regulation of fibroblast growth factor production / positive regulation of centrosome duplication / regulation of angiotensin-activated signaling pathway / negative regulation of protein localization to lysosome / regulation of keratinocyte differentiation / Rho-dependent protein serine/threonine kinase activity / positive regulation of connective tissue replacement / response to transforming growth factor beta / positive regulation of amyloid precursor protein catabolic process / regulation of cell junction assembly / regulation of nervous system process / positive regulation of protein localization to early endosome / host-mediated perturbation of viral process / cellular response to testosterone stimulus / regulation of cellular response to hypoxia / embryonic morphogenesis / negative regulation of nitric oxide biosynthetic process / regulation of cell motility / negative regulation of biomineral tissue development / regulation of establishment of endothelial barrier / response to angiotensin / regulation of stress fiber assembly / RHO GTPases Activate ROCKs / actomyosin structure organization / Sema4D induced cell migration and growth-cone collapse / aortic valve morphogenesis / cortical actin cytoskeleton organization / RHOBTB1 GTPase cycle / regulation of establishment of cell polarity / negative regulation of bicellular tight junction assembly / tau-protein kinase activity / regulation of focal adhesion assembly / RHOB GTPase cycle / positive regulation of amyloid-beta formation / EPHA-mediated growth cone collapse / positive regulation of cardiac muscle hypertrophy / RHOC GTPase cycle / mRNA destabilization / centrosome duplication / mitotic cytokinesis / RHOH GTPase cycle / smooth muscle contraction / epithelial to mesenchymal transition / RHOA GTPase cycle / endopeptidase activator activity / regulation of cell adhesion / Rho protein signal transduction / positive regulation of stress fiber assembly / EPHB-mediated forward signaling / positive regulation of endothelial cell migration / blood vessel diameter maintenance / negative regulation of angiogenesis / response to ischemia / protein localization to plasma membrane / regulation of actin cytoskeleton organization / regulation of circadian rhythm / small GTPase binding / VEGFA-VEGFR2 Pathway / tau protein binding / cytoplasmic ribonucleoprotein granule / positive regulation of protein phosphorylation / rhythmic process / G alpha (12/13) signalling events / actin cytoskeleton organization / protease binding / Potential therapeutics for SARS / cytoskeleton / protein phosphorylation / non-specific serine/threonine protein kinase / positive regulation of MAPK cascade / positive regulation of cell migration / negative regulation of gene expression / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / positive regulation of gene expression / structural molecule activity / RNA binding / zinc ion binding / ATP binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
: / Rho-associated protein kinase 2, HR1 domain / ROCK, Rho binding domain / Rho-associated protein kinase 1/2 / Rho Binding / Rho-binding (RhoBD) domain profile. / MRCK kinase PH domain / : / HR1 rho-binding domain / REM-1 domain profile. ...: / Rho-associated protein kinase 2, HR1 domain / ROCK, Rho binding domain / Rho-associated protein kinase 1/2 / Rho Binding / Rho-binding (RhoBD) domain profile. / MRCK kinase PH domain / : / HR1 rho-binding domain / REM-1 domain profile. / Zinc finger phorbol-ester/DAG-type profile. / Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains) / Protein kinase C-like, phorbol ester/diacylglycerol-binding domain / C1-like domain superfamily / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / PH-like domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
: / Rho-associated protein kinase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.02 Å
AuthorsYan, H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82003102 China
CitationJournal: To Be Published
Title: Structure of one TDI01 compound complex with ROCK2 kinase domain
Authors: Yan, H.
History
DepositionAug 30, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 3, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Rho-associated protein kinase 2
B: Rho-associated protein kinase 2
C: Rho-associated protein kinase 2
D: Rho-associated protein kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,6558
Polymers179,5534
Non-polymers2,1024
Water00
1
A: Rho-associated protein kinase 2
B: Rho-associated protein kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,8274
Polymers89,7762
Non-polymers1,0512
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3950 Å2
ΔGint-29 kcal/mol
Surface area35870 Å2
MethodPISA
2
C: Rho-associated protein kinase 2
D: Rho-associated protein kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,8274
Polymers89,7762
Non-polymers1,0512
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3800 Å2
ΔGint-30 kcal/mol
Surface area35330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)147.114, 144.409, 134.523
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

#1: Protein
Rho-associated protein kinase 2 / Rho kinase 2 / Rho-associated / coiled-coil-containing protein kinase 2 / coiled-coil-containing ...Rho kinase 2 / Rho-associated / coiled-coil-containing protein kinase 2 / coiled-coil-containing protein kinase II / ROCK-II / p164 ROCK-2


Mass: 44888.141 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ROCK2, KIAA0619 / Cell line (production host): sf9 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: O75116, non-specific serine/threonine protein kinase
#2: Chemical
ChemComp-A1EBC / [3,3-bis(fluoranyl)azetidin-1-yl]-[1-methyl-6-[4-[[4-(1~{H}-pyrazol-4-yl)phenyl]amino]furo[3,2-d]pyrimidin-2-yl]indol-2-yl]methanone


Mass: 525.509 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C28H21F2N7O2 / Feature type: SUBJECT OF INVESTIGATION
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: 4.01 Å3/Da / Density % sol: 69.31 %
Crystal growTemperature: 288 K / Method: lipidic cubic phase / pH: 6.2 / Details: PEG 300, potassium phosphate / PH range: 6.0-6.7

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Data collection

DiffractionMean temperature: 288 K / Serial crystal experiment: N
Diffraction sourceSource: LIQUID ANODE / Type: Excillum MetalJet D2 70 kV / Wavelength: 3 Å
DetectorType: CS-PAD CXI-1 / Detector: PIXEL / Date: Nov 12, 2018
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 3 Å / Relative weight: 1
ReflectionResolution: 3.02→43.89 Å / Num. obs: 56063 / % possible obs: 98.38 % / Redundancy: 1.62 % / Biso Wilson estimate: 72.93 Å2 / CC1/2: 1 / Net I/σ(I): 12
Reflection shellResolution: 3.02→3.11 Å / Num. unique obs: 18 / CC1/2: 0.98

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.02→43.89 Å / SU ML: 0.3553 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.9088
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2202 2764 4.93 %
Rwork0.1837 53299 -
obs0.1856 56063 98.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 67.78 Å2
Refinement stepCycle: LAST / Resolution: 3.02→43.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12522 0 156 0 12678
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00513011
X-RAY DIFFRACTIONf_angle_d1.251517620
X-RAY DIFFRACTIONf_chiral_restr0.05181851
X-RAY DIFFRACTIONf_plane_restr0.00672268
X-RAY DIFFRACTIONf_dihedral_angle_d15.4764794
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.02-3.070.3471190.32062163X-RAY DIFFRACTION80.75
3.07-3.130.37421420.27522623X-RAY DIFFRACTION98.47
3.13-3.190.35361020.2612649X-RAY DIFFRACTION98.25
3.19-3.250.30461360.25372620X-RAY DIFFRACTION98.36
3.25-3.320.32681460.24132637X-RAY DIFFRACTION98.44
3.32-3.40.31761230.23442644X-RAY DIFFRACTION98.68
3.4-3.480.27411500.22462642X-RAY DIFFRACTION99.08
3.48-3.580.29581600.21732643X-RAY DIFFRACTION99.26
3.58-3.680.2431300.19242696X-RAY DIFFRACTION99.61
3.68-3.80.20881180.1762693X-RAY DIFFRACTION99.4
3.8-3.940.1971790.17042649X-RAY DIFFRACTION99.82
3.89-4.180.17991450.17992884X-RAY DIFFRACTION99.02
3.94-4.10.22171400.16432680X-RAY DIFFRACTION99.51
4.1-4.280.20391470.15622667X-RAY DIFFRACTION99.72
4.28-4.510.19781630.14472682X-RAY DIFFRACTION99.82
4.51-4.790.16861500.14462699X-RAY DIFFRACTION99.93
4.79-5.160.17491430.15382727X-RAY DIFFRACTION99.9
5.16-5.680.19371080.1652758X-RAY DIFFRACTION100
5.68-6.50.19351110.17872772X-RAY DIFFRACTION99.65
6.5-8.180.21491520.17882771X-RAY DIFFRACTION99.86
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)
11.557376709040.02751699090340.1104738313492.318148471.073433563972.1190602848-0.1025416464220.31099791288-0.189208808118-0.197607363794-0.1108073479350.0334164725978-0.0492664612049-0.1520548361310.2272761305380.365555693707-0.0279574866638-0.03251855569650.597448522222-0.1015510972590.486534419373163.4479995728.616905539310.2245387328
22.03560526848-0.103336041147-0.09847366365033.049936830382.249297468062.841728463870.03726647276850.05888302887270.113864182468-0.117594582282-0.102401957502-0.130730890409-0.0638931849081-0.4535184206820.05611112103270.424670425906-0.005026700426360.1094526369950.737735724791-0.1018288207150.502620412864165.773725218-26.5852116448-9.74091400178
33.038006288770.5318126297471.683775719310.8030072647090.4918563285052.27072409668-0.189689125129-0.1019367108010.103867611530.131714020279-0.0521046418743-0.00469327123119-0.147288401648-0.1857995910730.2292016562350.488115613935-0.00481670128327-0.03108818594270.32158958276-0.07239507333190.450770488339124.015809782-23.1226862853-76.3491311559
43.10433858550.8885131475571.98333840691.685988104410.5276883339312.85761492163-0.2478825887430.0851326339078-0.0947105151388-0.1476836842670.0302992162782-0.0198737799676-0.2873597334970.1509384492090.2032896829340.5435671419540.056135419093-0.05563549521850.2701183877280.02806097657220.464235221412177.641884603-11.1657538949-55.5714901121
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth seq-ID: 27 - 417

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDLabel seq-ID
11(chain A and resseq 27:417)AA1 - 389
22(chain B and resseq 27:417)BB1 - 389
33(chain C and resseq 27:417)CC1 - 389
44(chain D and resseq 27:417)DD1 - 387

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