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- PDB-3uxh: Design, Synthesis and Biological Evaluation of Potetent Quinoline... -

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Basic information

Entry
Database: PDB / ID: 3uxh
TitleDesign, Synthesis and Biological Evaluation of Potetent Quinoline and Pyrroloquinoline Ammosamide Analogues as Inhibitors of Quinone Reductase 2
ComponentsRibosyldihydronicotinamide dehydrogenase [quinone]
KeywordsOXIDOREDUCTASE/INHIBITOR / Quinone reductase / Cytosol / OXIDOREDUCTASE-INHIBITOR complex
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 / electron transfer activity / oxidoreductase 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
FLAVIN-ADENINE DINUCLEOTIDE / Chem-UXH / Ribosyldihydronicotinamide dehydrogenase [quinone]
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å
AuthorsCushman, M. / Mesecar, A.D. / Fanwick, P.E. / Narasimha, R. / Jensen, K.C.
CitationJournal: J.Med.Chem. / Year: 2012
Title: Design, synthesis, and biological evaluation of potent quinoline and pyrroloquinoline ammosamide analogues as inhibitors of quinone reductase 2.
Authors: Reddy, P.V. / Jensen, K.C. / Mesecar, A.D. / Fanwick, P.E. / Cushman, M.
History
DepositionDec 5, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2012Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Dec 21, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.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_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)53,9848
Polymers51,6992
Non-polymers2,2856
Water6,828379
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7330 Å2
ΔGint-33 kcal/mol
Surface area18090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.455, 84.064, 106.663
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 25849.338 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, EC: 1.10.99.2
#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-UXH / 6,8-diamino-7-chloro-1-methyl-2-oxo-1,2-dihydropyrrolo[4,3,2-de]quinoline-4-carboxamide


Mass: 291.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H10ClN5O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 379 / 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: 2.45 Å3/Da / Density % sol: 49.75 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.7
Details: 1.7M Ammonium Sulfate, 0.1M BisTris, 0.1M NaCl, 5mM DTT, 12uM FAD, pH 6.7, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 26, 2011
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.53→66.08 Å / Num. all: 75026 / Num. obs: 74964 / Observed criterion σ(F): 2 / Observed criterion σ(I): 2

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMAC5.5.0110refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.53→39.11 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.965 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 2.514 / SU ML: 0.044 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.071 / ESU R Free: 0.07 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1839 3780 5 %RANDOM
Rwork0.1624 ---
obs0.1635 74964 97.03 %-
all-75026 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 64.19 Å2 / Biso mean: 22.209 Å2 / Biso min: 4.18 Å2
Baniso -1Baniso -2Baniso -3
1-0.77 Å20 Å20 Å2
2--0.46 Å20 Å2
3----1.24 Å2
Refinement stepCycle: LAST / Resolution: 1.53→39.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3648 0 148 379 4175
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0223926
X-RAY DIFFRACTIONr_angle_refined_deg2.4291.995364
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.715464
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.62124.22173
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.04915619
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9991516
X-RAY DIFFRACTIONr_chiral_restr0.1650.2563
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0212996
X-RAY DIFFRACTIONr_mcbond_it1.3321.52295
X-RAY DIFFRACTIONr_mcangle_it2.12223700
X-RAY DIFFRACTIONr_scbond_it3.02131631
X-RAY DIFFRACTIONr_scangle_it4.6444.51661
LS refinement shellResolution: 1.53→1.57 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 228 -
Rwork0.255 4311 -
all-4539 -
obs--80.88 %
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)
10.86530.00060.0450.93660.13672.6060.0361-0.0261-0.07970.08080.0088-0.01520.2982-0.0205-0.04490.0577-0.0004-0.02570.0024-0.00110.026112.6463-8.3865-4.307
20.8043-0.0229-0.08021.08940.14831.94010.00810.0656-0.0433-0.06650.03530.01290.129-0.0171-0.04330.0207-0.0084-0.01230.01160.00380.01259.3939-7.5497-26.9089
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 230
2X-RAY DIFFRACTION1A301
3X-RAY DIFFRACTION2B1 - 230
4X-RAY DIFFRACTION2B301

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