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- PDB-5tzh: CRYSTAL STRUCTURE OF HUMAN PHOSPHODIESTERASE 2A IN COMPLEX WITH 3... -

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Basic information

Entry
Database: PDB / ID: 5tzh
TitleCRYSTAL STRUCTURE OF HUMAN PHOSPHODIESTERASE 2A IN COMPLEX WITH 3,3-difluoro-1-[(4-fluorophenyl)carbonyl]-5-{5-methyl-[1,2,4]triazolo[1,5-a]pyrimidin-7-yl}piperidine
ComponentscGMP-dependent 3',5'-cyclic phosphodiesterase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / phosphodiesterase / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


regulation of cGMP-mediated signaling / cellular response to 2,3,7,8-tetrachlorodibenzodioxine / cellular response to macrophage colony-stimulating factor stimulus / cellular response to cGMP / positive regulation of vascular permeability / heart valve development / cellular response to granulocyte macrophage colony-stimulating factor stimulus / negative regulation of vascular permeability / establishment of endothelial barrier / negative regulation of cAMP-mediated signaling ...regulation of cGMP-mediated signaling / cellular response to 2,3,7,8-tetrachlorodibenzodioxine / cellular response to macrophage colony-stimulating factor stimulus / cellular response to cGMP / positive regulation of vascular permeability / heart valve development / cellular response to granulocyte macrophage colony-stimulating factor stimulus / negative regulation of vascular permeability / establishment of endothelial barrier / negative regulation of cAMP-mediated signaling / regulation of mitochondrion organization / aorta development / ventricular septum development / cGMP-stimulated cyclic-nucleotide phosphodiesterase activity / 3',5'-cyclic-nucleotide phosphodiesterase / negative regulation of cGMP-mediated signaling / cGMP-mediated signaling / TPR domain binding / cGMP catabolic process / phosphate ion binding / cGMP effects / 3',5'-cyclic-GMP phosphodiesterase activity / monocyte differentiation / cAMP-mediated signaling / cGMP binding / 3',5'-cyclic-AMP phosphodiesterase activity / regulation of cAMP-mediated signaling / cAMP binding / cellular response to cAMP / cellular response to transforming growth factor beta stimulus / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / synaptic membrane / positive regulation of inflammatory response / cellular response to mechanical stimulus / cellular response to xenobiotic stimulus / presynaptic membrane / G alpha (s) signalling events / mitochondrial inner membrane / mitochondrial outer membrane / mitochondrial matrix / positive regulation of gene expression / perinuclear region of cytoplasm / Golgi apparatus / negative regulation of transcription by RNA polymerase II / magnesium ion binding / endoplasmic reticulum / protein homodimerization activity / zinc ion binding / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Catalytic domain of cyclic nucleotide phosphodiesterase 4b2b / 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain / GAF domain / 3'5'-cyclic nucleotide phosphodiesterase / Domain present in phytochromes and cGMP-specific phosphodiesterases. / 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain / 3'5'-cyclic nucleotide phosphodiesterase, conserved site / 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain superfamily / 3'5'-cyclic nucleotide phosphodiesterase / 3'5'-cyclic nucleotide phosphodiesterase domain signature. ...Catalytic domain of cyclic nucleotide phosphodiesterase 4b2b / 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain / GAF domain / 3'5'-cyclic nucleotide phosphodiesterase / Domain present in phytochromes and cGMP-specific phosphodiesterases. / 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain / 3'5'-cyclic nucleotide phosphodiesterase, conserved site / 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain superfamily / 3'5'-cyclic nucleotide phosphodiesterase / 3'5'-cyclic nucleotide phosphodiesterase domain signature. / 3'5'-cyclic nucleotide phosphodiesterase domain profile. / GAF domain / GAF-like domain superfamily / Metal dependent phosphohydrolases with conserved 'HD' motif. / HD/PDEase domain / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-7OP / cGMP-dependent 3',5'-cyclic phosphodiesterase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
AuthorsXu, R. / Aertgeerts, K.
CitationJournal: J. Med. Chem. / Year: 2017
Title: Design and Synthesis of Novel and Selective Phosphodiesterase 2 (PDE2a) Inhibitors for the Treatment of Memory Disorders.
Authors: Gomez, L. / Massari, M.E. / Vickers, T. / Freestone, G. / Vernier, W. / Ly, K. / Xu, R. / McCarrick, M. / Marrone, T. / Metz, M. / Yan, Y.G. / Yoder, Z.W. / Lemus, R. / Broadbent, N.J. / ...Authors: Gomez, L. / Massari, M.E. / Vickers, T. / Freestone, G. / Vernier, W. / Ly, K. / Xu, R. / McCarrick, M. / Marrone, T. / Metz, M. / Yan, Y.G. / Yoder, Z.W. / Lemus, R. / Broadbent, N.J. / Barido, R. / Warren, N. / Schmelzer, K. / Neul, D. / Lee, D. / Andersen, C.B. / Sebring, K. / Aertgeerts, K. / Zhou, X. / Tabatabaei, A. / Peters, M. / Breitenbucher, J.G.
History
DepositionNov 21, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 22, 2017Group: Database references
Revision 1.2Mar 29, 2017Group: Data collection
Revision 1.3Nov 22, 2017Group: Refinement description / Category: software
Revision 1.4Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: cGMP-dependent 3',5'-cyclic phosphodiesterase
B: cGMP-dependent 3',5'-cyclic phosphodiesterase
C: cGMP-dependent 3',5'-cyclic phosphodiesterase
D: cGMP-dependent 3',5'-cyclic phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,53216
Polymers160,6724
Non-polymers1,86012
Water15,763875
1
A: cGMP-dependent 3',5'-cyclic phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6334
Polymers40,1681
Non-polymers4653
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: cGMP-dependent 3',5'-cyclic phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6334
Polymers40,1681
Non-polymers4653
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: cGMP-dependent 3',5'-cyclic phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6334
Polymers40,1681
Non-polymers4653
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: cGMP-dependent 3',5'-cyclic phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6334
Polymers40,1681
Non-polymers4653
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.838, 72.841, 90.706
Angle α, β, γ (deg.)109.150, 90.930, 91.180
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
cGMP-dependent 3',5'-cyclic phosphodiesterase / Cyclic GMP-stimulated phosphodiesterase / cGSPDE


Mass: 40168.051 Da / Num. of mol.: 4 / Fragment: catalytic domain, UNP RESIDUES 323-663
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDE2A / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): baculovirus insect cell Hi5
References: UniProt: O00408, 3',5'-cyclic-nucleotide phosphodiesterase
#2: Chemical
ChemComp-7OP / [(5S)-3,3-difluoro-5-(5-methyl[1,2,4]triazolo[1,5-a]pyrimidin-7-yl)piperidin-1-yl](4-fluorophenyl)methanone


Mass: 375.348 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C18H16F3N5O
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: Zn
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 875 / 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: 2.19 Å3/Da / Density % sol: 43.82 % / Mosaicity: 0 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.4 / Details: 17-19% PEG3350, 0.2M MgCl2, 0.1M Tris, pH 8.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97741 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 1.6→68.783 Å / Num. obs: 170240 / % possible obs: 95.6 % / Redundancy: 1.9 % / Biso Wilson estimate: 18.71 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.045 / Net I/σ(I): 9.1
Reflection shellResolution: 1.6→1.64 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.623 / CC1/2: 0.626 / % possible all: 84

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation8.18 Å68.78 Å
Translation8.18 Å68.78 Å

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Processing

Software
NameVersionClassification
XSCALE0.5.27data scaling
PHASER2.6.1phasing
PHENIX(1.10.1-2155_1692: ???)refinement
PDB_EXTRACT3.2data extraction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→68.783 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 31.43
RfactorNum. reflection% reflection
Rfree0.2559 8514 5.04 %
Rwork0.2141 --
obs0.2162 168949 94.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 77.47 Å2 / Biso mean: 27.5062 Å2 / Biso min: 7.58 Å2
Refinement stepCycle: final / Resolution: 1.6→68.783 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11029 0 0 875 11904
Biso mean---30.67 -
Num. residues----1346
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00611297
X-RAY DIFFRACTIONf_angle_d0.81915259
X-RAY DIFFRACTIONf_chiral_restr0.0441626
X-RAY DIFFRACTIONf_plane_restr0.0051970
X-RAY DIFFRACTIONf_dihedral_angle_d17.9764171
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6-1.61820.45122020.3794119432174
1.6182-1.63720.4232690.37694851512086
1.6372-1.65720.38122730.35235325559893
1.6572-1.67820.35672850.34935299558494
1.6782-1.70030.39252580.34895256551493
1.7003-1.72360.39932560.33895313556995
1.7236-1.74820.36272760.32595354563094
1.7482-1.77430.34772730.3185350562395
1.7743-1.8020.36272980.31095322562094
1.802-1.83160.32462880.29835369565796
1.8316-1.86310.32792870.28885340562795
1.8631-1.8970.31512860.28055381566796
1.897-1.93350.32182670.28335447571495
1.9335-1.9730.30333030.25915404570796
1.973-2.01590.27942710.2555418568996
2.0159-2.06280.32272880.255426571496
2.0628-2.11440.28553100.23965369567997
2.1144-2.17150.2732780.22695427570596
2.1715-2.23540.25152580.22175467572596
2.2354-2.30760.26262990.2235409570897
2.3076-2.39010.23843200.20275454577497
2.3901-2.48580.24523040.19325381568597
2.4858-2.59890.22163390.19215475581497
2.5989-2.73590.24482980.18915442574097
2.7359-2.90740.22232940.18895475576997
2.9074-3.13180.23082650.18385484574997
3.1318-3.4470.22022090.17745577578697
3.447-3.94570.20653160.16455462577897
3.9457-4.9710.21363410.15645499584098
4.971-68.84620.22653030.19115540584398
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)
11.16020.49750.49442.20150.24962.11010.0482-0.2377-0.17150.1277-0.03020.06710.1944-0.0813-0.00030.1162-0.03210.02170.22430.03510.1516-10.4595-14.1791-1.0163
22.49050.14920.19621.12760.03221.28750.0246-0.0627-0.0204-0.07550.0080.05510.0329-0.0206-0.03510.1048-0.00470.0090.1004-0.00810.0734-0.9018-3.5012-9.7011
32.41540.01280.69441.25310.02881.9646-0.0185-0.38420.32220.1209-0.01230.0328-0.290.22290.02880.1777-0.03510.00540.2065-0.06220.15023.59198.5442.6111
44.6959-0.70322.48880.4114-0.48461.3518-0.0134-0.50090.13910.2296-0.0229-0.1374-0.1419-0.132-0.06660.37340.0630.00320.6452-0.16340.22748.19845.843120.9327
51.4516-0.2577-0.01182.1033-0.34972.00160.03980.0834-0.2397-0.0942-0.0378-0.21950.27930.31920.00680.17020.04520.00430.1281-0.0170.150824.9705-12.798-37.5818
61.8027-0.0592-0.04321.11990.11531.3984-0.0088-0.02030.096-0.0240.0162-0.0017-0.1086-0.0629-0.00620.1370.00450.00920.0805-0.00270.084316.34161.3703-33.8983
71.37790.30651.11980.60290.40221.2753-0.07540.51030.2158-0.24040.07670.1073-0.1834-0.09350.02720.28790.00440.00050.34190.06640.14737.90813.2564-54.4934
82.1908-0.3008-0.35821.455-0.63843.10450.06880.1429-0.2388-0.1395-0.14-0.34420.28020.780.04850.1680.04820.02770.2773-0.02250.253554.244-42.6626-37.0472
94.5599-0.3368-0.08680.7328-0.10831.76190.05970.0253-0.19360.09610.006-0.01280.0454-0.1281-0.07610.144-0.0217-0.00630.0645-0.01140.141238.6627-39.9654-25.4356
106.7394-1.36574.74572.1735-1.03725.2791-0.1522-0.54440.26350.17680.103-0.2698-0.48220.34210.06780.1445-0.04020.02670.2802-0.06510.17250.4092-32.8303-22.9245
110.94110.1059-0.46981.52480.51161.17950.38620.06640.3838-0.07570.0505-0.2801-1.05270.0609-0.19990.4767-0.06840.140.1595-0.03840.264447.9914-23.8154-36.716
125.98991.0159-0.64161.537-0.65740.2914-0.03630.2871-0.2901-0.1265-0.12310.14120.2082-0.98950.0410.2459-0.0334-0.08230.5665-0.09710.210130.9419-40.8819-46.9321
132.60.23980.00651.94190.28922.25450.3510.12770.2245-0.2604-0.33220.1911-0.4436-0.81590.01530.35210.08890.00030.4645-0.05610.17233.4753-29.4919-47.0342
145.00372.58093.27721.91061.65453.2199-0.03330.18680.0909-0.3306-0.00580.0542-0.2357-0.10760.01210.33130.04930.02240.4847-0.02270.145434.2731-35.0566-60.4001
151.10870.0851-0.09351.12920.11941.28820.0994-0.5165-0.40440.03620.00390.34710.2321-0.4816-0.02260.1707-0.0799-0.00710.38210.10260.277417.7353-39.77961.0426
163.87260.65810.67550.84710.40581.49020.04550.0864-0.3091-0.05020.02650.02280.08370.048-0.07170.1320.0013-0.02620.08270.01650.178433.2051-38.7608-11.0516
175.18582.23794.2543.10712.18134.1382-0.07470.4556-0.2099-0.1160.17930.2266-0.1842-0.1255-0.06790.1516-0.00690.01850.21620.02740.177721.3933-32.653-14.8895
186.1536-4.0212.34415.0006-0.89612.1564-0.0855-0.29610.3010.0110.081-0.2168-0.0761-0.1012-0.0070.1425-0.0020.02920.21990.01390.097124.3845-16.7407-4.8982
192.0075-1.0591.21413.1118-1.69111.97120.0573-0.3272-0.05530.08310.00520.0973-0.04630.0617-0.0620.10530.01030.02060.27520.00760.111723.1347-25.7032-0.6419
202.0194-1.23720.35491.55840.32361.52260.0893-0.3891-0.05250.05980.0648-0.1051-0.01390.1006-0.12280.1704-0.0062-0.01110.38470.04350.136839.0813-28.78929.0554
215.5473-1.87594.20321.0005-1.27033.36340.0358-0.19370.05210.1091-0.0071-0.028-0.0115-0.2121-0.03960.25040.02150.00880.54280.02090.152837.2541-27.635722.1278
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 576 through 635 )A576 - 635
2X-RAY DIFFRACTION2chain 'A' and (resid 636 through 768 )A636 - 768
3X-RAY DIFFRACTION3chain 'A' and (resid 769 through 878 )A769 - 878
4X-RAY DIFFRACTION4chain 'A' and (resid 879 through 916 )A879 - 916
5X-RAY DIFFRACTION5chain 'B' and (resid 578 through 695 )B578 - 695
6X-RAY DIFFRACTION6chain 'B' and (resid 696 through 840 )B696 - 840
7X-RAY DIFFRACTION7chain 'B' and (resid 841 through 916 )B841 - 916
8X-RAY DIFFRACTION8chain 'C' and (resid 590 through 695 )C590 - 695
9X-RAY DIFFRACTION9chain 'C' and (resid 696 through 750 )C696 - 750
10X-RAY DIFFRACTION10chain 'C' and (resid 751 through 768 )C751 - 768
11X-RAY DIFFRACTION11chain 'C' and (resid 769 through 815 )C769 - 815
12X-RAY DIFFRACTION12chain 'C' and (resid 816 through 839 )C816 - 839
13X-RAY DIFFRACTION13chain 'C' and (resid 840 through 878 )C840 - 878
14X-RAY DIFFRACTION14chain 'C' and (resid 879 through 916 )C879 - 916
15X-RAY DIFFRACTION15chain 'D' and (resid 590 through 695 )D590 - 695
16X-RAY DIFFRACTION16chain 'D' and (resid 696 through 750 )D696 - 750
17X-RAY DIFFRACTION17chain 'D' and (resid 751 through 768 )D751 - 768
18X-RAY DIFFRACTION18chain 'D' and (resid 769 through 792 )D769 - 792
19X-RAY DIFFRACTION19chain 'D' and (resid 793 through 815 )D793 - 815
20X-RAY DIFFRACTION20chain 'D' and (resid 816 through 878 )D816 - 878
21X-RAY DIFFRACTION21chain 'D' and (resid 879 through 916 )D879 - 916

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