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- PDB-7pad: The crystal structure of DW-0254 in complex with PDE6D -

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Basic information

Entry
Database: PDB / ID: 7pad
TitleThe crystal structure of DW-0254 in complex with PDE6D
ComponentsRetinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta
KeywordsPROTEIN BINDING / inhibitor / complex
Function / homology
Function and homology information


ARL13B-mediated ciliary trafficking of INPP5E / GTPase inhibitor activity / visual perception / cytoplasmic vesicle membrane / cilium / small GTPase binding / RAS processing / cytoplasmic vesicle / cytoskeleton / cytosol / cytoplasm
Similarity search - Function
Retinal rod rhodopsin-sensitive cGMP 3', 5'-cyclic phosphodiesterase, delta subunit / GMP phosphodiesterase, delta subunit / GMP phosphodiesterase, delta subunit superfamily / GMP-PDE, delta subunit / Immunoglobulin E-set
Similarity search - Domain/homology
NICKEL (II) ION / Chem-O7W / Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å
AuthorsBeaumont, E. / Williams, D.
Funding support1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)5R01CA202756
CitationJournal: Blood Cancer J / Year: 2022
Title: Validation of a small molecule inhibitor of PDE6D-RAS interaction with favorable anti-leukemic effects.
Authors: Canovas Nunes, S. / De Vita, S. / Anighoro, A. / Autelitano, F. / Beaumont, E. / Klingbeil, P. / McGuinness, M. / Duvert, B. / Harris, C. / Yang, L. / Pokharel, S.P. / Chen, C.W. / Ermann, M. ...Authors: Canovas Nunes, S. / De Vita, S. / Anighoro, A. / Autelitano, F. / Beaumont, E. / Klingbeil, P. / McGuinness, M. / Duvert, B. / Harris, C. / Yang, L. / Pokharel, S.P. / Chen, C.W. / Ermann, M. / Williams, D.A. / Xu, H.
History
DepositionJul 29, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 8, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1595
Polymers19,3531
Non-polymers8064
Water2,558142
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area640 Å2
ΔGint-0 kcal/mol
Surface area8050 Å2
Unit cell
Length a, b, c (Å)44.507, 39.277, 44.803
Angle α, β, γ (deg.)90.000, 106.070, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules B

#1: Protein Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta / GMP-PDE delta / Protein p17


Mass: 19352.996 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDE6D, PDED / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL / References: UniProt: O43924

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Non-polymers , 5 types, 146 molecules

#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-O7W / ~{N}-[(4-ethylphenyl)methyl]-3-[5-[2-(1~{H}-indol-3-yl)ethyl]-1,3,4-oxadiazol-2-yl]-~{N}-methyl-propanamide


Mass: 416.515 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H28N4O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 1.94 Å3/Da / Density % sol: 36.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M Hepes pH7.0, 20 mM MgCl2, 20 mM NiCl2, 15 % PEG3350
PH range: 6.8-7.3

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.49→43.05 Å / Num. obs: 23686 / % possible obs: 97 % / Redundancy: 2.8 % / CC1/2: 0.996 / Rmerge(I) obs: 0.063 / Rrim(I) all: 0.088 / Net I/σ(I): 9.2
Reflection shellResolution: 1.49→1.52 Å / Rmerge(I) obs: 0.653 / Mean I/σ(I) obs: 2 / Num. unique obs: 1162 / CC1/2: 0.699 / Rpim(I) all: 0.61 / Rrim(I) all: 0.896 / % possible all: 99.4

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Processing

Software
NameVersionClassification
BUSTER2.11.7 (6-FEB-2020)refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimless0.7.4data scaling
DIMPLEphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5NAL

5nal


Resolution: 1.49→43.05 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.933 / SU R Cruickshank DPI: 0.08 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.083 / SU Rfree Blow DPI: 0.081 / SU Rfree Cruickshank DPI: 0.079
RfactorNum. reflection% reflectionSelection details
Rfree0.2098 1120 4.73 %RANDOM
Rwork0.1836 ---
obs0.1848 23674 96.7 %-
Displacement parametersBiso max: 111.01 Å2 / Biso mean: 19.97 Å2 / Biso min: 9.64 Å2
Baniso -1Baniso -2Baniso -3
1--0.0731 Å20 Å26.5394 Å2
2--1.2785 Å20 Å2
3----1.2054 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: final / Resolution: 1.49→43.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1218 0 70 142 1430
Biso mean--33.33 30.86 -
Num. residues----149
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d501SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes241HARMONIC5
X-RAY DIFFRACTIONt_it1369HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion166SEMIHARMONIC5
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_contact1270SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1386HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg1896HARMONIC21.01
X-RAY DIFFRACTIONt_omega_torsion3.95
X-RAY DIFFRACTIONt_other_torsion15.6
LS refinement shellResolution: 1.49→1.5 Å / Rfactor Rfree error: 0 / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.2392 24 5.06 %
Rwork0.2665 450 -
all0.265 474 -
obs--99 %

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