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- PDB-4hbp: Crystal Structure of FAAH in complex with inhibitor -

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Basic information

Entry
Database: PDB / ID: 4hbp
TitleCrystal Structure of FAAH in complex with inhibitor
ComponentsFatty-acid amide hydrolase 1
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Fatty Acid Amide Hydrolase / Amidase activity / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


Arachidonic acid metabolism / fatty acid amide hydrolase / fatty acid amide hydrolase activity / monoacylglycerol catabolic process / acylglycerol lipase activity / amidase activity / fatty acid catabolic process / Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases / hydrolase activity, acting on ester bonds / organelle membrane ...Arachidonic acid metabolism / fatty acid amide hydrolase / fatty acid amide hydrolase activity / monoacylglycerol catabolic process / acylglycerol lipase activity / amidase activity / fatty acid catabolic process / Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases / hydrolase activity, acting on ester bonds / organelle membrane / positive regulation of vasoconstriction / fatty acid metabolic process / phospholipid binding / Golgi membrane / lipid binding / endoplasmic reticulum membrane / identical protein binding
Similarity search - Function
Amidase, conserved site / Amidases signature. / Amidase signature (AS) enzymes / Amidase signature (AS) domain / Amidase signature domain / Amidase signature (AS) superfamily / Amidase / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Chem-17J / Fatty-acid amide hydrolase 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.91 Å
AuthorsBehnke, C. / Skene, R.J.
CitationJournal: Bioorg.Med.Chem. / Year: 2013
Title: Synthesis, SAR study, and biological evaluation of a series of piperazine ureas as fatty acid amide hydrolase (FAAH) inhibitors.
Authors: Kono, M. / Matsumoto, T. / Kawamura, T. / Nishimura, A. / Kiyota, Y. / Oki, H. / Miyazaki, J. / Igaki, S. / Behnke, C.A. / Shimojo, M. / Kori, M.
History
DepositionSep 28, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fatty-acid amide hydrolase 1
B: Fatty-acid amide hydrolase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,7854
Polymers121,0522
Non-polymers7332
Water50428
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3150 Å2
ΔGint-21 kcal/mol
Surface area35850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.920, 103.920, 251.965
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: THR / End label comp-ID: THR / Refine code: 2 / Auth seq-ID: 37 - 573 / Label seq-ID: 8 - 544

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Fatty-acid amide hydrolase 1 / Anandamide amidohydrolase 1 / Oleamide hydrolase 1


Mass: 60525.852 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Faah, Faah1 / Production host: Escherichia coli (E. coli) / References: UniProt: P97612, fatty acid amide hydrolase
#2: Chemical ChemComp-17J / 4-(3-phenyl-1,2,4-thiadiazol-5-yl)-N-(pyridin-3-yl)piperazine-1-carboxamide


Mass: 366.440 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H18N6OS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 3.24 Å3/Da / Density % sol: 62.09 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 4.5
Details: 40% PEG400, 0.1M sodium acetate, pH 4.5, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 4, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 35463 / % possible obs: 99.3 %
Reflection shellResolution: 2.9→3 Å / % possible all: 82.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1MT5

1mt5


Resolution: 2.91→48.06 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.868 / SU B: 33.153 / SU ML: 0.288 / Cross valid method: THROUGHOUT / ESU R: 1.996 / ESU R Free: 0.399 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27338 1762 5 %RANDOM
Rwork0.22332 ---
obs0.2258 33366 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 40.644 Å2
Baniso -1Baniso -2Baniso -3
1-3.39 Å21.7 Å20 Å2
2--3.39 Å20 Å2
3----5.09 Å2
Refinement stepCycle: LAST / Resolution: 2.91→48.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8044 0 38 28 8110
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0228280
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1921.99611265
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.00651062
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.83623.856306
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.268151341
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.731545
X-RAY DIFFRACTIONr_chiral_restr0.0760.21284
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.026223
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1820.23932
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2970.25750
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1070.2199
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2430.237
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.1711.55466
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.29728521
X-RAY DIFFRACTIONr_scbond_it0.45133208
X-RAY DIFFRACTIONr_scangle_it0.7924.52744
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
2112tight positional0.020.05
1851medium positional0.340.5
2112tight thermal0.020.5
1851medium thermal0.142
LS refinement shellResolution: 2.909→2.984 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.382 112 -
Rwork0.314 2194 -
obs--100 %
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)
12.0901-0.29270.11012.29390.16543.19410.0062-0.2617-0.03210.36670.0657-0.34950.1280.5019-0.0719-0.01490.1373-0.0562-0.01050.0060.0402-8.477-47.12-28.077
21.6136-0.10450.0370.56570.45161.3625-0.0254-0.071-0.03590.17940.0238-0.03070.00670.17260.0016-0.10070.07340.0081-0.19360.01140.0148-18.193-43.249-38.826
31.145-0.5342-0.38981.55190.32271.58860.0095-0.0321-0.02730.0564-0.03590.1424-0.1372-0.22060.0264-0.13070.09590.0095-0.1720.00810.0287-30.81-36.684-47.221
42.1352-0.2470.10152.11680.57873.08310.060.68180.4886-0.4192-0.0429-0.1425-0.67280.2141-0.01710.25090.13330.03270.11670.17020.1181-11.059-33.631-89.573
50.7880.61450.53452.47880.67431.61220.04680.25270.1324-0.1597-0.0566-0.0611-0.13550.04140.0099-0.06240.0950.0336-0.06940.04540.0039-10.328-45.236-79.957
61.9005-0.3392-0.18531.39250.02341.25880.00030.3112-0.2232-0.2403-0.0973-0.06130.21260.13480.0969-0.06290.08850.0626-0.08720.00540.0025-6.997-59.793-72.762
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A37 - 177
2X-RAY DIFFRACTION2A178 - 307
3X-RAY DIFFRACTION3A308 - 573
4X-RAY DIFFRACTION4B37 - 177
5X-RAY DIFFRACTION5B178 - 307
6X-RAY DIFFRACTION6B308 - 573

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