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- PDB-6t8q: HKATII IN COMPLEX WITH LIGAND (2R)-N-benzyl-1-[6-methyl-5-(oxan-4... -

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Basic information

Entry
Database: PDB / ID: 6t8q
TitleHKATII IN COMPLEX WITH LIGAND (2R)-N-benzyl-1-[6-methyl-5-(oxan-4-yl)-7-oxo-6H,7H-[1,3]thiazolo[5,4-d]pyrimidin-2-yl]pyrrolidine-2-carboxamide
ComponentsKynurenine/alpha-aminoadipate aminotransferase, mitochondrial
KeywordsTRANSFERASE / ALPHA & BETA PROTEIN / PLP-DEPENDENT TRANSFERASE / KAT II / KYNURENINE AM / PROTEROS BIOSTRUCTURES GMBH
Function / homology
Function and homology information


glycine transaminase / methionine-glyoxylate transaminase / glycine:2-oxoglutarate aminotransferase activity / methionine-glyoxylate transaminase activity / 2-aminoadipate transaminase / 2-aminoadipate transaminase activity / kynurenine-glyoxylate transaminase activity / alpha-amino acid metabolic process / kynurenine-glyoxylate transaminase / L-lysine catabolic process to acetyl-CoA via saccharopine ...glycine transaminase / methionine-glyoxylate transaminase / glycine:2-oxoglutarate aminotransferase activity / methionine-glyoxylate transaminase activity / 2-aminoadipate transaminase / 2-aminoadipate transaminase activity / kynurenine-glyoxylate transaminase activity / alpha-amino acid metabolic process / kynurenine-glyoxylate transaminase / L-lysine catabolic process to acetyl-CoA via saccharopine / kynurenine-oxoglutarate transaminase / kynurenine-oxoglutarate transaminase activity / kynurenine metabolic process / Lysine catabolism / glutamate metabolic process / 2-oxoglutarate metabolic process / Tryptophan catabolism / biosynthetic process / pyridoxal phosphate binding / mitochondrial matrix / protein homodimerization activity
Similarity search - Function
Aminotransferase, class I/classII / Aminotransferase class I and II / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / : / Chem-MVQ / Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.51 Å
AuthorsBlaesse, M. / Venalainen, J.
Funding support Finland, 1items
OrganizationGrant numberCountry
Other government Finland
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2020
Title: Discovery of sulfonamides and 9-oxo-2,8-diazaspiro[5,5]undecane-2-carboxamides as human kynurenine aminotransferase 2 (KAT2) inhibitors.
Authors: Kalliokoski, T. / Rummakko, P. / Rantanen, M. / Blaesse, M. / Augustin, M. / Ummenthala, G.R. / Choudhary, S. / Venalainen, J.
History
DepositionOct 24, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 4, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 11, 2020Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Mar 18, 2020Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Jan 24, 2024Group: 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_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_conn_type
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_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_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 / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,43812
Polymers50,9911
Non-polymers1,44711
Water2,828157
1
A: Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial
hetero molecules

A: Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,87724
Polymers101,9822
Non-polymers2,89522
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_654-x+y+1,y,-z-1/21
Buried area11370 Å2
ΔGint-153 kcal/mol
Surface area30420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.829, 144.829, 139.653
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-510-

CL

21A-601-

HOH

31A-652-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial / KAT/AadAT / 2-aminoadipate aminotransferase / 2-aminoadipate transaminase / Alpha-aminoadipate ...KAT/AadAT / 2-aminoadipate aminotransferase / 2-aminoadipate transaminase / Alpha-aminoadipate aminotransferase / AadAT / Kynurenine aminotransferase II / Kynurenine--oxoglutarate aminotransferase II / Kynurenine--oxoglutarate transaminase 2 / Kynurenine--oxoglutarate transaminase II


Mass: 50991.148 Da / Num. of mol.: 1 / Fragment: NONE
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AADAT, KAT2 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q8N5Z0, 2-aminoadipate transaminase, kynurenine-oxoglutarate transaminase

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Non-polymers , 5 types, 168 molecules

#2: Chemical ChemComp-MVQ / (2~{R})-1-[6-methyl-5-(oxan-4-yl)-7-oxidanylidene-[1,3]thiazolo[5,4-d]pyrimidin-2-yl]-~{N}-(phenylmethyl)pyrrolidine-2-carboxamide


Mass: 453.557 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H27N5O3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cd
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / 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: 4.39 Å3/Da / Density % sol: 72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG 400, cadmium chloride, sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.51→125.43 Å / Num. obs: 28843 / % possible obs: 95.9 % / Redundancy: 4.3 % / Biso Wilson estimate: 30.166 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.05 / Rrim(I) all: 0.107 / Χ2: 0.972 / Net I/σ(I): 10.63 / Num. measured all: 151149 / Scaling rejects: 40
Reflection shellResolution: 2.51→2.76 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.431 / Mean I/σ(I) obs: 46.86 / Num. measured obs: 527 / Num. possible: 274 / Num. unique obs: 202 / CC1/2: 0.999 / Rrim(I) all: 0.023 / % possible all: 97.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0155refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TF5

5tf5


Resolution: 2.51→125.43 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.936 / SU B: 12.996 / SU ML: 0.146 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.233 / ESU R Free: 0.198
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2162 928 3.2 %RANDOM
Rwork0.1783 ---
obs0.1795 27915 95.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 151.04 Å2 / Biso mean: 56.36 Å2 / Biso min: 17.37 Å2
Baniso -1Baniso -2Baniso -3
1-0.6 Å20.3 Å20 Å2
2--0.6 Å20 Å2
3----1.94 Å2
Refinement stepCycle: final / Resolution: 2.51→125.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3369 0 45 158 3572
Biso mean--55.27 48.51 -
Num. residues----429
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0193482
X-RAY DIFFRACTIONr_bond_other_d0.0050.023303
X-RAY DIFFRACTIONr_angle_refined_deg1.6731.9864717
X-RAY DIFFRACTIONr_angle_other_deg1.29637607
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0875433
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.20224.71138
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.59915567
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4211514
X-RAY DIFFRACTIONr_chiral_restr0.0930.2523
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213919
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02754
LS refinement shellResolution: 2.51→2.575 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 73 -
Rwork0.3 2044 -
all-2117 -
obs--97.38 %
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)
10.6062-0.02460.22641.48780.4782.2235-0.038-0.10080.02540.1421-0.09720.19810.0853-0.38610.13520.2835-0.01840.00540.1202-0.02330.030663.305-9.86-20.554
23.88054.01784.21074.68494.5386.3774-0.1097-0.74950.88960.2964-0.611.0598-0.0792-1.0390.71980.55150.03950.07430.3157-0.06610.292552.998-17.621-50.723
31.8091-1.47023.20364.0021-3.26716.34430.3083-0.273-0.3904-0.15980.20450.2671.02-0.7165-0.51280.7003-0.18230.03320.2026-0.05170.162667.018-34.251-39.808
42.8117-1.78321.22933.6828-0.1292.9988-0.2029-0.36360.33740.3738-0.0116-0.46090.12670.55310.21450.4670.0354-0.0710.33170.02510.074287.728-15.6-5.177
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 15
2X-RAY DIFFRACTION1A75 - 325
3X-RAY DIFFRACTION2A16 - 40
4X-RAY DIFFRACTION3A41 - 74
5X-RAY DIFFRACTION4A326 - 440

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