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- PDB-4w7p: Crystal Structure of ROCK 1 bound to YB-15-QD37 -

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Basic information

Entry
Database: PDB / ID: 4w7p
TitleCrystal Structure of ROCK 1 bound to YB-15-QD37
ComponentsRho-associated protein kinase 1
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / inhibitor / kinase / TRANSFERASE-TRANSFERASE INHIBITOR complex
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 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-3J7 / Rho-associated protein kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsSprague, E.R.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2014
Title: Novel ROCK inhibitors for the treatment of pulmonary arterial hypertension.
Authors: Shaw, D. / Hollingworth, G. / Soldermann, N. / Sprague, E. / Schuler, W. / Vangrevelinghe, E. / Duggan, N. / Thomas, M. / Kosaka, T. / Waters, N. / van Eis, M.J.
History
DepositionAug 22, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 15, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 29, 2014Group: Database references
Revision 1.2Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / entity_src_gen / pdbx_database_status / pdbx_struct_oper_list / refine_hist
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)190,8408
Polymers189,5064
Non-polymers1,3344
Water64936
1
A: Rho-associated protein kinase 1
B: Rho-associated protein kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,4204
Polymers94,7532
Non-polymers6672
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4210 Å2
ΔGint-30 kcal/mol
Surface area35400 Å2
MethodPISA
2
C: Rho-associated protein kinase 1
D: Rho-associated protein kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,4204
Polymers94,7532
Non-polymers6672
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4140 Å2
ΔGint-31 kcal/mol
Surface area34920 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10180 Å2
ΔGint-68 kcal/mol
Surface area68490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.545, 179.659, 89.269
Angle α, β, γ (deg.)90.000, 104.590, 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: 47376.508 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ROCK1 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q13464, non-specific serine/threonine protein kinase
#2: Chemical
ChemComp-3J7 / N~1~-[2-(1H-indazol-5-yl)pyrido[3,4-d]pyrimidin-4-yl]-2-methylpropane-1,2-diamine


Mass: 333.390 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H19N7
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H2O

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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: 2.52 Å3/Da / Density % sol: 51.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M MES PH 5.5, 50 mM CACL2, 7% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.9998 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 29, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9998 Å / Relative weight: 1
ReflectionResolution: 2.8→89.83 Å / Num. obs: 45876 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 3.79 % / Biso Wilson estimate: 70.47 Å2 / Rmerge F obs: 0.125 / Rmerge(I) obs: 0.091 / Rrim(I) all: 0.106 / Χ2: 1.005 / Net I/σ(I): 12.05 / Num. measured all: 173943
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.8-2.870.6250.542.6412973337833820.629100
2.87-2.950.4520.4053.5412647330632970.47199.7
2.95-3.040.3690.3314.3112328320732040.38599.9
3.04-3.130.3070.2754.9312023312731210.3299.8
3.13-3.230.2480.2225.9711745307430650.25999.7
3.23-3.350.1830.1737.4611117290529020.20199.9
3.35-3.470.1510.1429.4110634285928340.16699.1
3.47-3.610.1110.1111.4410428274527380.12899.7
3.61-3.780.0920.09213.549597259325780.10799.4
3.78-3.960.0760.0815.329089251224660.09498.2
3.96-4.170.0610.06717.358897237523620.07999.5
4.17-4.430.0510.05919.278524227622620.06999.4
4.43-4.730.0450.05520.467941213321190.06499.3
4.73-5.110.0450.05520.217354196219520.06499.5
5.11-5.60.0450.05519.926923183818270.06499.4
5.6-6.260.0480.05619.276128161816140.06599.8
6.26-7.230.0430.05220.575471145414510.06199.8
7.23-8.850.0320.04323.984700125012420.0599.4
8.85-12.520.0250.0426.7635579549430.04698.8
12.520.0280.03324.4318675355170.03996.6

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Processing

Software
NameVersionClassification
XDSdata reduction
BUSTER-TNTBUSTER 2.11.2refinement
PDB_EXTRACT3.15data extraction
XSCALEdata scaling
BUSTER2.11.2refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→86.39 Å / Cor.coef. Fo:Fc: 0.9079 / Cor.coef. Fo:Fc free: 0.8663 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.347
RfactorNum. reflection% reflectionSelection details
Rfree0.2462 2294 5 %RANDOM
Rwork0.2056 ---
obs0.2076 45875 99.57 %-
Displacement parametersBiso max: 148.69 Å2 / Biso mean: 52.33 Å2 / Biso min: 10.75 Å2
Baniso -1Baniso -2Baniso -3
1--5.7007 Å20 Å2-1.7595 Å2
2--1.5074 Å20 Å2
3---4.1933 Å2
Refine analyzeLuzzati coordinate error obs: 0.382 Å
Refinement stepCycle: final / Resolution: 2.8→86.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12633 0 100 36 12769
Biso mean--43.5 38.22 -
Num. residues----1545
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d4560SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes345HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1849HARMONIC5
X-RAY DIFFRACTIONt_it13042HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1579SEMIHARMONIC5
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_contact14779SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d13042HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg17619HARMONIC21.14
X-RAY DIFFRACTIONt_omega_torsion2.76
X-RAY DIFFRACTIONt_other_torsion19.83
LS refinement shellResolution: 2.8→2.87 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3082 169 5 %
Rwork0.25 3208 -
all0.253 3377 -
obs--99.57 %
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)
11.36511.31860.74862.30081.22781.5924-0.09550.00580.0343-0.06320.10550.0030.02770.1042-0.01-0.12990.04320.0782-0.0839-0.0154-0.1295-18.285836.658636.9215
21.90751.371-0.04621.933-0.04550.42970.0612-0.03950.0530.0162-0.0050.0274-0.0553-0.0275-0.0563-0.01240.00610.0851-0.10430.0225-0.176-54.3488-6.297828.5765
31.70431.55370.48162.15950.68590.4663-0.08860.0019-0.0364-0.0330.0501-0.02760.08110.06030.0385-0.0312-0.01670.1181-0.0828-0.005-0.14-11.934537.6644-6.2433
41.96351.8111-0.52952.1694-0.54910.9532-0.15030.07010.0193-0.2820.1915-0.0086-0.0313-0.0363-0.0412-0.00780.01370.0868-0.12390.0539-0.1852-47.5915-5.0604-16.8769
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|6 - A|405 }A6 - 405
2X-RAY DIFFRACTION2{ B|6 - B|401 }B6 - 401
3X-RAY DIFFRACTION3{ C|6 - C|401 }C6 - 401
4X-RAY DIFFRACTION4{ D|6 - D|403 }D6 - 403

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