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- PDB-7svp: Structure of compound 34 bound to human Phospholipase D2 catalyti... -

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Basic information

Entry
Database: PDB / ID: 7svp
TitleStructure of compound 34 bound to human Phospholipase D2 catalytic domain
ComponentsPhospholipase D2
KeywordsHYDROLASE/HYDROLASE INHIBITOR / phosphodiesterase / HKD motif / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


Synthesis of PG / phosphatidic acid biosynthetic process / Synthesis of PA / synaptic vesicle recycling / regulation of vesicle-mediated transport / phospholipase D / phospholipid catabolic process / phospholipase D activity / small GTPase-mediated signal transduction / Fc-gamma receptor signaling pathway involved in phagocytosis ...Synthesis of PG / phosphatidic acid biosynthetic process / Synthesis of PA / synaptic vesicle recycling / regulation of vesicle-mediated transport / phospholipase D / phospholipid catabolic process / phospholipase D activity / small GTPase-mediated signal transduction / Fc-gamma receptor signaling pathway involved in phagocytosis / RAC2 GTPase cycle / Role of phospholipids in phagocytosis / cytoskeleton organization / RAC1 GTPase cycle / phosphatidylinositol binding / presynapse / cytoplasmic vesicle / endoplasmic reticulum membrane / plasma membrane
Similarity search - Function
Phospholipase D, eukaryotic type / Phospholipase D family / Phospholipase D Active site motif / Phospholipase D-like domain / PLD-like domain / Phospholipase D. Active site motifs. / Phospholipase D/Transphosphatidylase / Phospholipase D phosphodiesterase active site profile. / PhoX homologous domain, present in p47phox and p40phox. / PX domain profile. ...Phospholipase D, eukaryotic type / Phospholipase D family / Phospholipase D Active site motif / Phospholipase D-like domain / PLD-like domain / Phospholipase D. Active site motifs. / Phospholipase D/Transphosphatidylase / Phospholipase D phosphodiesterase active site profile. / PhoX homologous domain, present in p47phox and p40phox. / PX domain profile. / PX domain / Phox homology / PX domain superfamily / Pleckstrin homology domain. / Pleckstrin homology domain / PH-like domain superfamily
Similarity search - Domain/homology
Chem-CI0 / Phospholipase D2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsMetrick, C.M. / Chodaparambil, J.V.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acs Med.Chem.Lett. / Year: 2022
Title: Discovery of Phospholipase D Inhibitors with Improved Drug-like Properties and Central Nervous System Penetrance.
Authors: May-Dracka, T.L. / Gao, F. / Hopkins, B.T. / Hronowski, X. / Chen, T. / Chodaparambil, J.V. / Metrick, C.M. / Cullivan, M. / Enyedy, I. / Kaliszczak, M. / Kankel, M.W. / Marx, I. / Michell- ...Authors: May-Dracka, T.L. / Gao, F. / Hopkins, B.T. / Hronowski, X. / Chen, T. / Chodaparambil, J.V. / Metrick, C.M. / Cullivan, M. / Enyedy, I. / Kaliszczak, M. / Kankel, M.W. / Marx, I. / Michell-Robinson, M.A. / Murugan, P. / Kumar, P.R. / Rooney, M. / Schuman, E. / Sen, A. / Wang, T. / Ye, T. / Peterson, E.A.
History
DepositionNov 19, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 23, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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
Revision 1.2Oct 25, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Phospholipase D2
A: Phospholipase D2
B: Phospholipase D2
D: Phospholipase D2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)292,9298
Polymers291,3874
Non-polymers1,5424
Water3,549197
1
C: Phospholipase D2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,2322
Polymers72,8471
Non-polymers3861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Phospholipase D2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,2322
Polymers72,8471
Non-polymers3861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Phospholipase D2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,2322
Polymers72,8471
Non-polymers3861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Phospholipase D2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,2322
Polymers72,8471
Non-polymers3861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.721, 132.238, 113.861
Angle α, β, γ (deg.)90.000, 100.649, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
Phospholipase D2 / hPLD2 / Choline phosphatase 2 / PLD1C / Phosphatidylcholine-hydrolyzing phospholipase D2


Mass: 72846.781 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLD2 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: O14939, phospholipase D
#2: Chemical
ChemComp-CI0 / 1-(1-{(2S)-1-[(3R,5R)-3,5-dimethylpiperazin-1-yl]-1-oxopropan-2-yl}piperidin-4-yl)-1,3-dihydro-2H-benzimidazol-2-one


Mass: 385.503 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H31N5O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / 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: 2.28 Å3/Da / Density % sol: 46.01 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.6
Details: 0.08 M sodium cacodylate pH 6.6, 14% PEG 8000, 20% glycerol, 0.16 M calcium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.97 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.9→111 Å / Num. obs: 57790 / % possible obs: 99 % / Redundancy: 3.5 % / Biso Wilson estimate: 60.85 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.28 / Net I/σ(I): 3.82
Reflection shellResolution: 3.05→3.14 Å / Num. unique obs: 2260 / CC1/2: 0.445

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6OHO

6oho


Resolution: 2.9→111 Å / SU ML: 0.527 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 40.9543
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3266 2833 4.93 %
Rwork0.29 54608 -
obs0.2918 57441 99.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 63.88 Å2
Refinement stepCycle: LAST / Resolution: 2.9→111 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17014 0 112 197 17323
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001817598
X-RAY DIFFRACTIONf_angle_d0.469224057
X-RAY DIFFRACTIONf_chiral_restr0.0412712
X-RAY DIFFRACTIONf_plane_restr0.00393084
X-RAY DIFFRACTIONf_dihedral_angle_d11.83556004
LS refinement shellResolution: 2.9→111 Å
RfactorNum. reflection% reflection
Rfree0.2809 153 -
Rwork0.2698 2726 -
obs--96.51 %
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)
12.78662029229-0.2250139733620.4838510256282.30885023778-0.3563381630251.923173762920.1786343202210.5568456615450.20135469955-0.365033444008-0.00633937876465-0.18615957786-0.1486962174450.135636713928-0.1617330907760.3074936907380.03107135648670.04684008983930.3415204797480.03961904986310.394037986469-3.6230714676-39.3490064267-6.61700902722
23.250267719650.2194926077140.520311504274.11271650646-0.4202768528061.482768663970.11635118209-0.3093198501510.85904037690.551168058399-0.121966527398-0.606383515666-0.244579792098-0.02321183810140.08898127970910.425935406976-0.00817898657875-0.02176935134020.195654696723-0.1177693284660.6215541132530.693233039614-37.07196587914.5222028586
31.69249711555-0.535311228877-0.1376374493372.79079859987-0.01093918479071.6651920228-0.0146605239858-0.221818932441-0.5208904450220.4505983119-0.00167997719137-0.2597683744760.3606845665590.06076089825590.0004175422561830.41301632275-0.00837647502522-0.001326250111030.2715504529180.03376162566540.484308230906-2.18274857005-56.10259306212.8490631846
43.172386665211.622970206241.354000409621.137867447210.8872052377243.60040539382-0.4812914571950.3540063490440.1957879541-0.199331582034-0.02688065048050.39192411393-0.1332400395360.1410525525920.4372409582660.5427640880150.04204409301220.1474709513870.5559555037980.0402245465491.0183613407329.270532557-8.4734184015544.4243980749
52.76873081658-0.3785261067131.730553125751.722911500430.2757521007751.831842463790.2429449976350.09664826646160.0593095948774-0.0393763854561-0.1341663745660.3607089612710.351905119740.221230592175-0.05696078702340.4793434270370.01665415549540.1367709543040.644596531213-0.04184012573061.0538164434633.6682449398-17.390335288643.9187390654
61.84178257948-0.01233187287841.438341976141.203312807480.0752065526262.9475708588-0.134395036855-0.269818759337-0.2529678167080.272996544977-0.0971839576131-0.1098225756-0.09692186798110.1922136522620.2110155817390.387804333882-0.01116662004970.02501673730140.7785518534330.09584669876391.0281600757336.804529262-12.778912168764.6315309521
73.07045203703-0.827585390559-0.837028884733.28672739572-0.2531289811812.02748561327-0.265040035473-0.530584475158-0.5276356407590.0681397921353-0.0382751061914-0.08971917709220.202179611076-0.08091928950850.2297070393680.468125188902-0.0285707031638-0.0638285056640.660800316368-0.06305269341570.75029504440930.0545984707-23.469568968968.7156778244
81.041465834250.4064713616580.08667265010151.328094505370.4887722985671.65637628042-0.0548340423741-0.2120177684550.02725032278740.120106414696-0.04999988013760.0500033152779-0.0546441092514-0.1158729023140.1219841060440.4844518961350.007526259234240.08661562713060.389478991877-0.02712508705560.868146545078-6.7843386671-9.3360623379762.3794847229
90.907039913923-0.1237287131570.1170893844481.87075529924-0.3767228517191.258379830340.0431220338548-0.0537073379496-0.127656987315-0.1447413902710.06182748716650.2067085860050.0443017315827-0.05966717077-0.1199047000950.51261687113-0.002724169995720.02802971702470.3693148736870.004202757703870.938296781056-9.33653036852-20.624693727542.828635042
104.70114608478-0.05570744847581.324825002412.232496074750.7495822184652.299821229630.0694421427691-0.5915281737170.299861360410.2041467585640.02134495710070.04711044879450.0633112776417-0.129212623177-0.08601079580920.317883615006-0.0126253722484-0.02041554133050.4342725402880.01466432436090.55459492886547.881032864-43.456568032410.9640262287
114.720347365340.626781521331.021691683012.434123572240.9541822321953.69659314647-0.08745178363960.6215585114990.651441491986-0.25994150211-0.05836383464320.305129504156-0.1419551340090.1420738713130.1438938371190.3744536503790.0168827714193-0.0303610376780.4481323490790.09607422402340.52013182317645.2744395185-41.5148358646-9.78321991229
124.44666467547-0.4808907700240.3118866643560.781150156547-0.2059057180471.517588045790.2793576685350.0732675937135-0.658168490723-0.4144903365730.01501352173720.8069525793940.593649276327-0.00821811449379-0.178408723910.720908424827-0.0502972509976-0.003509273827860.451207810597-0.1214316588290.94329658830942.8886056436-62.7842006009-12.1180948781
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'C' and (resid 320 through 569 )CA320 - 5691 - 228
22chain 'C' and (resid 570 through 680 )CA570 - 680229 - 328
33chain 'C' and (resid 681 through 933 )CA681 - 933329 - 571
44chain 'A' and (resid 321 through 412 )AC321 - 4121 - 92
55chain 'A' and (resid 413 through 530 )AC413 - 53093 - 188
66chain 'A' and (resid 531 through 779 )AC531 - 779189 - 409
77chain 'A' and (resid 780 through 933 )AC780 - 933410 - 555
88chain 'B' and (resid 320 through 568 )BE320 - 5681 - 227
99chain 'B' and (resid 569 through 933 )BE569 - 933228 - 574
1010chain 'D' and (resid 320 through 549 )DG320 - 5491 - 208
1111chain 'D' and (resid 550 through 839 )DG550 - 839209 - 467
1212chain 'D' and (resid 840 through 933 )DG840 - 933468 - 550

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