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- PDB-7s26: ROCK1 IN COMPLEX WITH LIGAND G5018 -

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Basic information

Entry
Database: PDB / ID: 7s26
TitleROCK1 IN COMPLEX WITH LIGAND G5018
ComponentsRho-associated protein kinase 1
KeywordsTRANSFERASE / RHO KINASE / PROTEROS BIOSTRUCTURES GMBH
Function / homology
Function and homology information


regulation of amyloid-beta formation / regulation of angiotensin-activated signaling pathway / apical constriction / Rho-dependent protein serine/threonine kinase activity / podocyte cell migration / regulation of keratinocyte differentiation / positive regulation of phosphatase activity / myoblast migration / positive regulation of connective tissue replacement / membrane to membrane docking ...regulation of amyloid-beta formation / regulation of angiotensin-activated signaling pathway / apical constriction / Rho-dependent protein serine/threonine kinase activity / podocyte cell migration / regulation of keratinocyte differentiation / positive regulation of phosphatase activity / myoblast migration / positive regulation of connective tissue replacement / membrane to membrane docking / negative regulation of membrane protein ectodomain proteolysis / response to transforming growth factor beta / negative regulation of myosin-light-chain-phosphatase activity / regulation of cell junction assembly / positive regulation of dephosphorylation / negative regulation of bicellular tight junction assembly / regulation of synapse maturation / bleb / positive regulation of amyloid-beta clearance / negative regulation of amyloid precursor protein catabolic process / neuron projection arborization / bleb assembly / embryonic morphogenesis / leukocyte tethering or rolling / negative regulation of biomineral tissue development / negative regulation of phosphorylation / actomyosin structure organization / aspartic-type endopeptidase inhibitor activity / regulation of establishment of endothelial barrier / RHO GTPases Activate ROCKs / negative regulation of motor neuron apoptotic process / regulation of stress fiber assembly / regulation of cell motility / Sema4D induced cell migration and growth-cone collapse / aortic valve morphogenesis / response to angiotensin / regulation of establishment of cell polarity / motor neuron apoptotic process / RHOBTB1 GTPase cycle / RND3 GTPase cycle / regulation of synaptic vesicle endocytosis / cortical actin cytoskeleton organization / regulation of neuron differentiation / regulation of focal adhesion assembly / leukocyte cell-cell adhesion / RHOB GTPase cycle / tau-protein kinase activity / leukocyte migration / negative regulation of amyloid-beta formation / EPHA-mediated growth cone collapse / mRNA destabilization / positive regulation of cardiac muscle hypertrophy / RHOC GTPase cycle / Apoptotic cleavage of cellular proteins / positive regulation of focal adhesion assembly / RHOH GTPase cycle / mitotic cytokinesis / Rho protein signal transduction / smooth muscle contraction / RHOA GTPase cycle / epithelial to mesenchymal transition / canonical NF-kappaB signal transduction / regulation of microtubule cytoskeleton organization / positive regulation of autophagy / regulation of cell adhesion / regulation of cell migration / ruffle / EPHB-mediated forward signaling / centriole / blood vessel diameter maintenance / negative regulation of angiogenesis / negative regulation of protein binding / regulation of autophagy / protein localization to plasma membrane / regulation of actin cytoskeleton organization / tau protein binding / Schaffer collateral - CA1 synapse / small GTPase binding / VEGFA-VEGFR2 Pathway / cytoplasmic stress granule / neuron projection development / G alpha (12/13) signalling events / lamellipodium / actin cytoskeleton organization / peptidyl-serine phosphorylation / secretory granule lumen / Potential therapeutics for SARS / positive regulation of MAPK cascade / cytoskeleton / non-specific serine/threonine protein kinase / protein kinase activity / Golgi membrane / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / Neutrophil degranulation / positive regulation of gene expression / signal transduction / extracellular region / ATP binding
Similarity search - Function
Rho-associated protein kinase 1, HR1 / 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 ...Rho-associated protein kinase 1, HR1 / 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
Chem-86K / Rho-associated protein kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.744 Å
AuthorsGanichkin, O. / Harris, S.F. / Steinbacher, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2022
Title: Chemical space docking enables large-scale structure-based virtual screening to discover ROCK1 kinase inhibitors.
Authors: Beroza, P. / Crawford, J.J. / Ganichkin, O. / Gendelev, L. / Harris, S.F. / Klein, R. / Miu, A. / Steinbacher, S. / Klingler, F.M. / Lemmen, C.
History
DepositionSep 3, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 19, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Rho-associated protein kinase 1
B: Rho-associated protein kinase 1
C: Rho-associated protein kinase 1
D: Rho-associated protein kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)185,5529
Polymers184,0364
Non-polymers1,5165
Water1,24369
1
A: Rho-associated protein kinase 1
B: Rho-associated protein kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,1886
Polymers92,0182
Non-polymers1,1694
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5330 Å2
ΔGint-15 kcal/mol
Surface area34290 Å2
MethodPISA
2
C: Rho-associated protein kinase 1
D: Rho-associated protein kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,3653
Polymers92,0182
Non-polymers3461
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3980 Å2
ΔGint-28 kcal/mol
Surface area29510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.141, 101.596, 182.663
Angle α, β, γ (deg.)90.000, 91.980, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Rho-associated protein kinase 1 / Renal carcinoma antigen NY-REN-35 / Rho-associated / coiled-coil-containing protein kinase 1 / ...Renal carcinoma antigen NY-REN-35 / Rho-associated / coiled-coil-containing protein kinase 1 / coiled-coil-containing protein kinase I / ROCK-I / p160 ROCK-1 / p160ROCK


Mass: 46009.078 Da / Num. of mol.: 4 / Fragment: KINASE DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ROCK1 / Production host: unidentified baculovirus
References: UniProt: Q13464, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Chemical ChemComp-86K / 2-[methyl(phenyl)amino]-1-[4-(1H-pyrrolo[2,3-b]pyridin-3-yl)-3,6-dihydropyridin-1(2H)-yl]ethan-1-one


Mass: 346.426 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H22N4O / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 69 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.96 Å3/Da / Density % sol: 58.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 15-17% PEG 5K MME, 0.1 M HEPES/NaOH pH 7.5, 5% (v/v) tacsimate pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.000045 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Feb 24, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.000045 Å / Relative weight: 1
ReflectionResolution: 2.74→88.77 Å / Num. obs: 54767 / % possible obs: 99.9 % / Redundancy: 4.3 % / Biso Wilson estimate: 116.21 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.028 / Rrim(I) all: 0.06 / Net I/σ(I): 14.4 / Num. measured all: 237848 / Scaling rejects: 7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.74-2.894.10.7633284779440.7510.4180.8721.799.9
8.68-88.774.30.044778618050.9970.0230.0534.199.3

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Processing

Software
NameVersionClassification
BUSTER2.11.8 (16-JUL-2021)refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.744→49.18 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.916 / SU R Cruickshank DPI: 0.778 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.67 / SU Rfree Blow DPI: 0.324 / SU Rfree Cruickshank DPI: 0.336
Details: HYDROGENS WERE FULLY REFINED WITH ZERO OCCUPANCY AT NUCLEAR POSITION. REFINEMENT NOTES. NUMBER OF REFINEMENT NOTES : 1 NOTE 1 : IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
RfactorNum. reflection% reflectionSelection details
Rfree0.2685 733 1.34 %RANDOM
Rwork0.2469 ---
obs0.2472 54745 99.9 %-
Displacement parametersBiso max: 217.19 Å2 / Biso mean: 124.5 Å2 / Biso min: 61.57 Å2
Baniso -1Baniso -2Baniso -3
1-8.858 Å20 Å2-9.6217 Å2
2---0.9119 Å20 Å2
3----7.9461 Å2
Refine analyzeLuzzati coordinate error obs: 0.44 Å
Refinement stepCycle: final / Resolution: 2.744→49.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11283 0 108 69 11460
Biso mean--117.6 92.4 -
Num. residues----1379
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d4110SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes2068HARMONIC5
X-RAY DIFFRACTIONt_it11669HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1408SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact8650SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d11735HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg15901HARMONIC20.9
X-RAY DIFFRACTIONt_omega_torsion2.78
X-RAY DIFFRACTIONt_other_torsion18.83
LS refinement shellResolution: 2.744→2.77 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.4713 19 1.25 %
Rwork0.3329 1502 -
obs--99.8 %

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