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- PDB-5lby: Structure of the human quinone reductase 2 (NQO2) in complex with... -

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Basic information

Entry
Database: PDB / ID: 5lby
TitleStructure of the human quinone reductase 2 (NQO2) in complex with crenolanib
ComponentsRibosyldihydronicotinamide dehydrogenase [quinone]
KeywordsOXIDOREDUCTASE / quinone reductase 2 / kinase inhibitor / crenolanib / Ribosyldihydronicotinamide dehydrogenase
Function / homology
Function and homology information


ribosyldihydronicotinamide dehydrogenase (quinone) / dihydronicotinamide riboside quinone reductase activity / quinone catabolic process / resveratrol binding / oxidoreductase activity, acting on other nitrogenous compounds as donors / melatonin binding / NAD(P)H dehydrogenase (quinone) activity / Phase I - Functionalization of compounds / chloride ion binding / FAD binding ...ribosyldihydronicotinamide dehydrogenase (quinone) / dihydronicotinamide riboside quinone reductase activity / quinone catabolic process / resveratrol binding / oxidoreductase activity, acting on other nitrogenous compounds as donors / melatonin binding / NAD(P)H dehydrogenase (quinone) activity / Phase I - Functionalization of compounds / chloride ion binding / FAD binding / oxidoreductase activity / electron transfer activity / protein homodimerization activity / extracellular exosome / zinc ion binding / nucleoplasm / cytosol
Similarity search - Function
: / Flavodoxin-like fold / Flavodoxin-like fold / Flavodoxin domain / Flavoprotein-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-6T2 / FLAVIN-ADENINE DINUCLEOTIDE / Ribosyldihydronicotinamide dehydrogenase [quinone]
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.4 Å
AuthorsSchneider, S. / Medard, G. / Kuester, B.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation Germany
CitationJournal: Science / Year: 2017
Title: The target landscape of clinical kinase drugs.
Authors: Klaeger, S. / Heinzlmeir, S. / Wilhelm, M. / Polzer, H. / Vick, B. / Koenig, P.A. / Reinecke, M. / Ruprecht, B. / Petzoldt, S. / Meng, C. / Zecha, J. / Reiter, K. / Qiao, H. / Helm, D. / ...Authors: Klaeger, S. / Heinzlmeir, S. / Wilhelm, M. / Polzer, H. / Vick, B. / Koenig, P.A. / Reinecke, M. / Ruprecht, B. / Petzoldt, S. / Meng, C. / Zecha, J. / Reiter, K. / Qiao, H. / Helm, D. / Koch, H. / Schoof, M. / Canevari, G. / Casale, E. / Depaolini, S.R. / Feuchtinger, A. / Wu, Z. / Schmidt, T. / Rueckert, L. / Becker, W. / Huenges, J. / Garz, A.K. / Gohlke, B.O. / Zolg, D.P. / Kayser, G. / Vooder, T. / Preissner, R. / Hahne, H. / Tonisson, N. / Kramer, K. / Gotze, K. / Bassermann, F. / Schlegl, J. / Ehrlich, H.C. / Aiche, S. / Walch, A. / Greif, P.A. / Schneider, S. / Felder, E.R. / Ruland, J. / Medard, G. / Jeremias, I. / Spiekermann, K. / Kuster, B.
History
DepositionJun 17, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 29, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Dec 13, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribosyldihydronicotinamide dehydrogenase [quinone]
B: Ribosyldihydronicotinamide dehydrogenase [quinone]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,1408
Polymers53,5512
Non-polymers2,5896
Water7,855436
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7250 Å2
ΔGint-33 kcal/mol
Surface area18030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.586, 79.401, 106.571
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: _ / Auth seq-ID: 2 - 229 / Label seq-ID: 3 - 230

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

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Components

#1: Protein Ribosyldihydronicotinamide dehydrogenase [quinone] / NRH dehydrogenase [quinone] 2 / NRH:quinone oxidoreductase 2 / Quinone reductase 2 / QR2


Mass: 26775.398 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NQO2, NMOR2 / Production host: Escherichia coli (E. coli)
References: UniProt: P16083, ribosyldihydronicotinamide dehydrogenase (quinone)
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical ChemComp-6T2 / 1-(2-{5-[(3-Methyloxetan-3-yl)methoxy]-1H-benzimidazol-1-yl}quinolin-8-yl)piperidin-4-amine / Crenolanib


Mass: 443.541 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H29N5O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 436 / 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: 2.43 Å3/Da / Density % sol: 49.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 180 mM tri-ammonium citrate, 2.2 M ammonium sulphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.4→44.3 Å / Num. obs: 96394 / % possible obs: 93 % / Redundancy: 4.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.038 / Net I/σ(I): 22.6
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.276 / Mean I/σ(I) obs: 5.12 / % possible all: 94.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0151refinement
XDSdata reduction
XDSdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5LBU

5lbu


Resolution: 1.4→44.3 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.978 / SU B: 1.13 / SU ML: 0.021 / Cross valid method: THROUGHOUT / ESU R: 0.044 / ESU R Free: 0.04 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.12544 4827 5 %RANDOM
Rwork0.10512 ---
obs0.10615 91705 93.02 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 15.571 Å2
Baniso -1Baniso -2Baniso -3
1-0.43 Å20 Å20 Å2
2--0.18 Å2-0 Å2
3----0.61 Å2
Refinement stepCycle: 1 / Resolution: 1.4→44.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3612 0 174 436 4222
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.024015
X-RAY DIFFRACTIONr_bond_other_d0.0060.023694
X-RAY DIFFRACTIONr_angle_refined_deg1.8721.9985498
X-RAY DIFFRACTIONr_angle_other_deg1.5023.0088529
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0095482
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.53824.186172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.60215637
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6161517
X-RAY DIFFRACTIONr_chiral_restr0.1240.2583
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0214485
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02946
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
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_it1.8641.1871880
X-RAY DIFFRACTIONr_mcbond_other1.8451.1851879
X-RAY DIFFRACTIONr_mcangle_it2.0821.7872366
X-RAY DIFFRACTIONr_mcangle_other2.0811.7872367
X-RAY DIFFRACTIONr_scbond_it4.171.5372135
X-RAY DIFFRACTIONr_scbond_other4.1711.5372136
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.5942.1533125
X-RAY DIFFRACTIONr_long_range_B_refined4.4216.2365361
X-RAY DIFFRACTIONr_long_range_B_other4.14315.1015124
X-RAY DIFFRACTIONr_rigid_bond_restr9.95237709
X-RAY DIFFRACTIONr_sphericity_free29.0155108
X-RAY DIFFRACTIONr_sphericity_bonded13.89457907
Refine LS restraints NCS

Ens-ID: 1 / Number: 15346 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.398→1.435 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.168 329 -
Rwork0.119 6255 -
obs--86.72 %

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