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- PDB-9hfp: ROCK2 IN COMPLEX WITH CPD7 -

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Basic information

Entry
Database: PDB / ID: 9hfp
TitleROCK2 IN COMPLEX WITH CPD7
ComponentsRho-associated protein kinase 2
KeywordsTRANSFERASE / KINASE / complex structure / inhibitor
Function / homology
Function and homology information


positive regulation of connective tissue growth factor production / cellular response to acetylcholine / positive regulation of centrosome duplication / regulation of angiotensin-activated signaling pathway / negative regulation of protein localization to lysosome / regulation of keratinocyte differentiation / positive regulation of connective tissue replacement / positive regulation of fibroblast growth factor production / response to transforming growth factor beta / positive regulation of amyloid precursor protein catabolic process ...positive regulation of connective tissue growth factor production / cellular response to acetylcholine / positive regulation of centrosome duplication / regulation of angiotensin-activated signaling pathway / negative regulation of protein localization to lysosome / regulation of keratinocyte differentiation / positive regulation of connective tissue replacement / positive regulation of fibroblast growth factor production / response to transforming growth factor beta / positive regulation of amyloid precursor protein catabolic process / regulation of cell junction assembly / negative regulation of bicellular tight junction assembly / regulation of nervous system process / positive regulation of protein localization to early endosome / regulation of cellular response to hypoxia / host-mediated perturbation of viral process / negative regulation of nitric oxide biosynthetic process / embryonic morphogenesis / negative regulation of biomineral tissue development / regulation of cell motility / cellular response to testosterone stimulus / regulation of establishment of endothelial barrier / RHO GTPases Activate ROCKs / regulation of stress fiber assembly / actomyosin structure organization / Sema4D induced cell migration and growth-cone collapse / response to angiotensin / aortic valve morphogenesis / cortical actin cytoskeleton organization / RHOBTB1 GTPase cycle / regulation of establishment of cell polarity / tau-protein kinase activity / regulation of focal adhesion assembly / positive regulation of amyloid-beta formation / RHOB GTPase cycle / EPHA-mediated growth cone collapse / RHOC GTPase cycle / positive regulation of cardiac muscle hypertrophy / mRNA destabilization / mitotic cytokinesis / centrosome duplication / RHOH GTPase cycle / smooth muscle contraction / RHOA GTPase cycle / endopeptidase activator activity / epithelial to mesenchymal transition / Rho protein signal transduction / regulation of cell adhesion / positive regulation of stress fiber assembly / EPHB-mediated forward signaling / positive regulation of endothelial cell migration / negative regulation of angiogenesis / blood vessel diameter maintenance / response to ischemia / protein localization to plasma membrane / regulation of actin cytoskeleton organization / regulation of circadian rhythm / small GTPase binding / tau protein binding / VEGFA-VEGFR2 Pathway / cytoplasmic ribonucleoprotein granule / rhythmic process / G alpha (12/13) signalling events / positive regulation of protein phosphorylation / actin cytoskeleton organization / protease binding / Potential therapeutics for SARS / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / cytoskeleton / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / positive regulation of MAPK cascade / positive regulation of cell migration / protein phosphorylation / 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
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. / : / HR1 rho-binding domain / REM-1 domain profile. / Zinc finger phorbol-ester/DAG-type 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. / : / 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 / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.92 Å
AuthorsScheufler, C. / Griessner, A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Med.Chem. / Year: 2025
Title: Discovery and Optimization of Selective Inhibitors of Large Tumor Suppressor Kinases LATS1 and 2 for In Vivo Investigation of the Hippo-YAP Pathway in Tissue Regeneration.
Authors: Namoto, K. / Vangrevelinghe, E. / Machauer, R. / Behnke, D. / Buschmann, N. / Lachal, J. / Schipp, K. / Sorge, M. / Barker, K. / Fabbiani, F. / Piechon, P. / Connor, L.E. / Laurent, S. / ...Authors: Namoto, K. / Vangrevelinghe, E. / Machauer, R. / Behnke, D. / Buschmann, N. / Lachal, J. / Schipp, K. / Sorge, M. / Barker, K. / Fabbiani, F. / Piechon, P. / Connor, L.E. / Laurent, S. / Lohmann, F. / Unterreiner, V. / George, E.L. / Redmond, E. / Wang, L. / Scheufler, C. / Sohal, B. / Sailer, A.W. / Glatthar, R. / Tchorz, J.S. / Maibaum, J.
History
DepositionNov 18, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 9, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)45,7802
Polymers45,4721
Non-polymers3081
Water00
1
A: Rho-associated protein kinase 2
hetero molecules

A: Rho-associated protein kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,5604
Polymers90,9432
Non-polymers6172
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/31
Buried area3330 Å2
ΔGint-27 kcal/mol
Surface area33880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.968, 90.968, 338.333
Angle α, β, γ (deg.)90, 90, 120
Int Tables number180
Space group name H-MP6222

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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: 45471.727 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ROCK2, KIAA0619 / Production host: unidentified baculovirus
References: UniProt: O75116, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-A1IUI / ~{N}-[4-[(3~{R})-piperidin-3-yl]oxyphenyl]-1~{H}-pyrrolo[2,3-b]pyridin-4-amine


Mass: 308.378 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H20N4O / 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: 4.44 Å3/Da / Density % sol: 72.32 % / Description: NONE
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: The purified protein was used in crystallisation trials employing both, a standard screen with approximately 1200 different conditions, as well as crystallisation conditions identified using ...Details: The purified protein was used in crystallisation trials employing both, a standard screen with approximately 1200 different conditions, as well as crystallisation conditions identified using literature data. Conditions initially obtained have been optimised using standard strategies, systematically varying parameters critically influencing crystallisation, such as temperature, protein concentration, drop ratio, and others. These conditions were also refined by systematically varying pH or precipitant concentrations.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99988 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 9, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99988 Å / Relative weight: 1
ReflectionResolution: 2.92→41.2 Å / Num. obs: 18434 / % possible obs: 97 % / Redundancy: 2.77 % / Rmerge(I) obs: 0.062 / Rrim(I) all: 0.075 / Net I/σ(I): 13.4
Reflection shellResolution: 2.92→3.17 Å / Redundancy: 2.82 % / Rmerge(I) obs: 0.435 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 3935 / Rrim(I) all: 0.532 / % possible all: 98.3

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Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
XDSdata reduction
XSCALEdata scaling
BUSTERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: NONE

Resolution: 2.92→41.2 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.902 / SU R Cruickshank DPI: 0.43 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.452 / SU Rfree Blow DPI: 0.266 / SU Rfree Cruickshank DPI: 0.265
RfactorNum. reflection% reflectionSelection details
Rfree0.2204 609 -RANDOM
Rwork0.2053 ---
obs0.2059 18434 97 %-
Displacement parametersBiso mean: 82.36 Å2
Baniso -1Baniso -2Baniso -3
1--9.8064 Å20 Å20 Å2
2---9.8064 Å20 Å2
3---19.6129 Å2
Refine analyzeLuzzati coordinate error obs: 0.4 Å
Refinement stepCycle: LAST / Resolution: 2.92→41.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3065 0 23 0 3088
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0093169HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.954305HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1052SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes544HARMONIC5
X-RAY DIFFRACTIONt_it3169HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion397SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact2513SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.91
X-RAY DIFFRACTIONt_other_torsion18.66
LS refinement shellResolution: 2.92→2.95 Å
RfactorNum. reflection% reflection
Rfree0.2505 25 -
Rwork0.2894 --
obs0.2876 615 99.17 %
Refinement TLS params.Origin x: 10.4607 Å / Origin y: 17.1483 Å / Origin z: 29.2729 Å
111213212223313233
T-0.0476 Å2-0.2462 Å2-0.0376 Å2-0.0201 Å20.0747 Å2---0.0008 Å2
L1.2137 °2-0.363 °20.2555 °2-0.9796 °2-1.4442 °2--3.1726 °2
S0.1746 Å °-0.0712 Å °-0.1983 Å °-0.0712 Å °-0.1822 Å °0.1596 Å °-0.1983 Å °0.1596 Å °0.0075 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* L|1 }A23 - 417
2X-RAY DIFFRACTION1{ A|* L|1 }L1

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