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- PDB-6v8c: Design, Synthesis, and Mechanism of Fluorine-substituted Cyclohex... -

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Basic information

Entry
Database: PDB / ID: 6v8c
TitleDesign, Synthesis, and Mechanism of Fluorine-substituted Cyclohexene Analogues of GAMA-Aminobutyric Acid (GABA) as Selective Ornithine Aminotransferase Inactivators
ComponentsOrnithine aminotransferase, mitochondrial
KeywordsTRANSFERASE / Human Ornithine Aminotransferase (hOAT) / Mechanism Based Inactivator / PLP Hepatocellular Carcinoma (HCC)
Function / homology
Function and homology information


L-arginine catabolic process to proline via ornithine / ornithine aminotransferase activity / ornithine aminotransferase / L-arginine catabolic process to L-glutamate / L-proline biosynthetic process / Glutamate and glutamine metabolism / visual perception / pyridoxal phosphate binding / mitochondrial matrix / mitochondrion ...L-arginine catabolic process to proline via ornithine / ornithine aminotransferase activity / ornithine aminotransferase / L-arginine catabolic process to L-glutamate / L-proline biosynthetic process / Glutamate and glutamine metabolism / visual perception / pyridoxal phosphate binding / mitochondrial matrix / mitochondrion / nucleoplasm / identical protein binding / cytoplasm
Similarity search - Function
Ornithine aminotransferase / : / : / Aminotransferases class-III pyridoxal-phosphate attachment site. / Aminotransferase class-III / Aminotransferase class-III / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / 3-aminocyclohexa-1,3-diene-1-carboxylic acid / Ornithine aminotransferase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsZhu, W. / Doubleday, P.T. / Catlin, D.S. / Weerawarna, P. / Butrin, A. / Shen, S. / Kelleher, N.L. / Liu, D. / Silverman, R.B.
Funding support1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)DA030604
CitationJournal: To Be Published
Title: Design, Synthesis, and Mechanism of Fluorine-substituted Cyclohexene Analogues of GAMA-Aminobutyric Acid (GABA) as Selective Ornithine Aminotransferase Inactivators
Authors: Zhu, W. / Doubleday, P.T. / Catlin, D.S. / Weerawarna, P. / Butrin, A. / Shen, S. / Kelleher, N.L. / Liu, D. / Silverman, R.B.
History
DepositionDec 10, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2020Provider: repository / Type: Initial release
Revision 2.0Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Non-polymer description / Refinement description
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.formula / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 3.0Dec 25, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / pdbx_entry_details ...atom_site / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_validate_close_contact / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_entry_details.has_protein_modification / _pdbx_nonpoly_scheme.auth_seq_num

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ornithine aminotransferase, mitochondrial
B: Ornithine aminotransferase, mitochondrial
C: Ornithine aminotransferase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,7409
Polymers134,5813
Non-polymers1,1596
Water14,592810
1
A: Ornithine aminotransferase, mitochondrial
hetero molecules

A: Ornithine aminotransferase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,4936
Polymers89,7212
Non-polymers7734
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555-x+y,y,-z+1/31
Buried area11440 Å2
ΔGint-63 kcal/mol
Surface area25830 Å2
MethodPISA
2
B: Ornithine aminotransferase, mitochondrial
hetero molecules

B: Ornithine aminotransferase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,4936
Polymers89,7212
Non-polymers7734
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_565x,x-y+1,-z1
Buried area11430 Å2
ΔGint-63 kcal/mol
Surface area25520 Å2
MethodPISA
3
C: Ornithine aminotransferase, mitochondrial
hetero molecules

C: Ornithine aminotransferase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,4936
Polymers89,7212
Non-polymers7734
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_554-y,-x,-z-1/31
Buried area11480 Å2
ΔGint-64 kcal/mol
Surface area25920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)193.782, 193.782, 57.200
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number151
Space group name H-MP3112
Components on special symmetry positions
IDModelComponents
11A-644-

HOH

21A-832-

HOH

31A-851-

HOH

41A-855-

HOH

51B-811-

HOH

61B-864-

HOH

71B-882-

HOH

81B-885-

HOH

91C-811-

HOH

101C-835-

HOH

111C-846-

HOH

121C-850-

HOH

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Components

#1: Protein Ornithine aminotransferase, mitochondrial / Ornithine delta-aminotransferase / Ornithine--oxo-acid aminotransferase


Mass: 44860.320 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: OAT / Production host: Escherichia coli (E. coli) / References: UniProt: P04181, ornithine aminotransferase
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical ChemComp-QRM / 3-aminocyclohexa-1,3-diene-1-carboxylic acid


Mass: 139.152 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C7H9NO2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 810 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.3 Å3/Da / Density % sol: 46.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 16.5% PEG 1000 240 mM NaCl 25% glycerol.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.98 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Mar 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.9→27.99 Å / Num. obs: 92236 / % possible obs: 96.22 % / Redundancy: 18.4 % / CC1/2: 0.989 / Net I/σ(I): 1.34
Reflection shellResolution: 1.9→1.92 Å / Num. unique obs: 2515 / CC1/2: 0.932

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Processing

Software
NameVersionClassification
PHENIX1.17.1refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
MOLREPdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OAT

1oat


Resolution: 1.9→27.97 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 40.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2675 4653 5.04 %RANDOM
Rwork0.2386 ---
obs0.2401 92236 96.22 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 91.14 Å2 / Biso mean: 24.5382 Å2 / Biso min: 3.5 Å2
Refinement stepCycle: final / Resolution: 1.9→27.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9475 0 75 810 10360
Biso mean--17.85 29.98 -
Num. residues----1212
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)
12.3776-0.5143-1.14723.3059-0.62472.49150.1027-0.09670.7696-0.03590.2099-0.5865-0.53610.3436-0.22220.32750.01240.13530.26210.01410.5469-14.125142.686-21.688
21.63110.60980.69871.01510.29472.6190.21660.02480.45270.01320.0067-0.195-0.42370.1036-0.1830.36170.05930.16680.2410.01470.5321-19.47644.6959-14.2498
32.53810.70910.80671.43150.40462.62480.2814-0.6511-0.27390.3617-0.21880.4220.3662-0.195-0.07350.2764-0.1080.03480.45390.07120.3075-17.459373.725624.1145
42.7388-0.0386-0.06150.61620.09720.62790.1112-0.1289-0.4543-0.0594-0.07120.15660.198-0.1322-0.02320.3326-0.0608-0.07870.25370.00390.3964-14.106164.31096.9266
51.6731-0.58270.51361.0158-0.23560.78880.07730.13730.0658-0.0639-0.0712-0.05250.05190.1073-0.00380.1587-0.00580.0040.19010.00440.1756-0.774388.9854-0.4622
63.35540.46380.55282.58640.01211.57210.14350.30280.0828-0.0449-0.2392-0.02920.02240.0270.08240.13760.00290.00340.24230.01630.1407-10.070792.9377-9.5135
71.8053-0.45120.6231.0522-0.76511.34450.1780.2499-0.2361-0.1858-0.08560.01630.31230.0781-0.07750.2350.0307-0.00950.2155-0.03790.1757-2.031977.3067-4.8159
83.0170.66541.11712.5101-0.97532.16850.12090.00810.23870.12330.1210.7365-0.0571-0.5557-0.14020.222-0.0531-0.02820.33790.01180.4529-29.923378.341-2.533
92.2004-1.0274-1.05540.8210.26272.78370.1163-0.0824-0.0646-0.08990.02780.1460.0896-0.3833-0.11110.2698-0.1004-0.06630.30220.02820.3914-28.962572.65174.8828
101.0582-0.48390.00870.2351-0.1281.0486-0.0754-0.258-0.02980.24230.1734-0.24660.03180.3899-0.00980.11020.1225-0.11380.3254-0.04010.1039-55.159459.859314.549
110.3976-0.19790.0720.46170.21090.18320.0223-0.0490.0692-0.00250.1993-0.3053-0.02760.2336-0.0003-0.0772-0.0570.02270.2344-0.1270.2265-48.771968.0038-2.5927
120.3279-0.003-0.09771.36240.48610.49920.04930.0337-0.0151-0.2432-0.01620.0651-0.1010.04950.00140.0848-0.00260.00710.0761-0.00920.0042-74.506463.955-13.4447
131.3485-0.40070.09021.1480.62680.67540.11310.0538-0.191-0.16850.0806-0.1319-0.01370.1805-0.01570.0695-0.03150.060.1127-0.01790.0611-60.081361.9859-11.8557
140.9306-0.33240.18091.0463-0.25381.46010.0399-0.0045-0.21640.03130.1342-0.30270.22330.25950.03540.03390.0653-0.00880.2166-0.11270.2225-48.42150.5029-4.6735
150.74530.1220.57912.7291-0.47962.8513-0.0581-0.28150.49340.76240.18150.0031-0.4112-0.2617-0.12110.47020.01220.09940.2509-0.07110.3244-24.303134.20545.0368
161.23070.9626-0.10271.7176-0.21550.51020.1830.09240.45130.17190.0220.2966-0.1864-0.1015-0.18150.29060.12240.11890.28030.08090.4558-34.132235.9878-12.1814
171.52190.4932-0.40980.8816-0.3630.7305-0.05410.1242-0.0499-0.0960.0912-0.01280.0519-0.0921-0.03210.16370.01420.00880.16460.00110.1465-19.438212.109-19.5253
182.280.1067-0.29733.1578-0.27750.8351-0.23870.1709-0.0491-0.11960.1707-0.10920.0441-0.04590.05840.217-0.00910.02660.1703-0.00230.1391-11.403718.1085-28.5985
191.46610.3871-0.9111.52-0.31041.1973-0.0480.30740.1579-0.14830.17450.208-0.0592-0.2844-0.12260.19680.0284-0.02870.27480.04260.179-28.949319.0045-23.89
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'C' and (resid 345 through 389 )C345 - 389
2X-RAY DIFFRACTION2chain 'C' and (resid 390 through 439 )C390 - 439
3X-RAY DIFFRACTION3chain 'A' and (resid 36 through 61 )A36 - 61
4X-RAY DIFFRACTION4chain 'A' and (resid 62 through 105 )A62 - 105
5X-RAY DIFFRACTION5chain 'A' and (resid 106 through 220 )A106 - 220
6X-RAY DIFFRACTION6chain 'A' and (resid 221 through 263 )A221 - 263
7X-RAY DIFFRACTION7chain 'A' and (resid 264 through 344 )A264 - 344
8X-RAY DIFFRACTION8chain 'A' and (resid 345 through 389 )A345 - 389
9X-RAY DIFFRACTION9chain 'A' and (resid 390 through 439 )A390 - 439
10X-RAY DIFFRACTION10chain 'B' and (resid 36 through 61 )B36 - 61
11X-RAY DIFFRACTION11chain 'B' and (resid 62 through 106 )B62 - 106
12X-RAY DIFFRACTION12chain 'B' and (resid 107 through 295 )B107 - 295
13X-RAY DIFFRACTION13chain 'B' and (resid 296 through 389 )B296 - 389
14X-RAY DIFFRACTION14chain 'B' and (resid 390 through 439 )B390 - 439
15X-RAY DIFFRACTION15chain 'C' and (resid 36 through 61 )C36 - 61
16X-RAY DIFFRACTION16chain 'C' and (resid 62 through 105 )C62 - 105
17X-RAY DIFFRACTION17chain 'C' and (resid 106 through 220 )C106 - 220
18X-RAY DIFFRACTION18chain 'C' and (resid 221 through 263 )C221 - 263
19X-RAY DIFFRACTION19chain 'C' and (resid 264 through 344 )C264 - 344

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