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- PDB-5ujb: Structure of a Mcl-1 Inhibitor Binding to Site 3 of Human Serum A... -

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Basic information

Entry
Database: PDB / ID: 5ujb
TitleStructure of a Mcl-1 Inhibitor Binding to Site 3 of Human Serum Albumin
ComponentsSerum albumin
KeywordsTRANSPORT PROTEIN / Human Serum Albumin / Free fraction / Apoptosis / cancer / Mcl-1 / drug discovery
Function / homology
Function and homology information


exogenous protein binding / Ciprofloxacin ADME / enterobactin binding / cellular response to calcium ion starvation / Heme biosynthesis / HDL remodeling / negative regulation of mitochondrial depolarization / Prednisone ADME / Heme degradation / Aspirin ADME ...exogenous protein binding / Ciprofloxacin ADME / enterobactin binding / cellular response to calcium ion starvation / Heme biosynthesis / HDL remodeling / negative regulation of mitochondrial depolarization / Prednisone ADME / Heme degradation / Aspirin ADME / antioxidant activity / toxic substance binding / Scavenging of heme from plasma / Recycling of bile acids and salts / cellular response to starvation / platelet alpha granule lumen / fatty acid binding / Post-translational protein phosphorylation / Cytoprotection by HMOX1 / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / pyridoxal phosphate binding / Platelet degranulation / protein-folding chaperone binding / blood microparticle / copper ion binding / endoplasmic reticulum lumen / Golgi apparatus / endoplasmic reticulum / protein-containing complex / DNA binding / extracellular space / extracellular exosome / extracellular region / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Serum Albumin; Chain A, Domain 1 - #10 / Serum albumin/Alpha-fetoprotein/Afamin / ALB/AFP/VDB / Serum albumin, N-terminal / Serum albumin, conserved site / Serum albumin-like / Serum albumin family / Albumin domain signature. / Albumin domain profile. / serum albumin ...Serum Albumin; Chain A, Domain 1 - #10 / Serum albumin/Alpha-fetoprotein/Afamin / ALB/AFP/VDB / Serum albumin, N-terminal / Serum albumin, conserved site / Serum albumin-like / Serum albumin family / Albumin domain signature. / Albumin domain profile. / serum albumin / Serum Albumin; Chain A, Domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-6AK / PHOSPHATE ION / Albumin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsZhao, B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)BOA 29XS129 United States
Citation
Journal: Bioorg. Med. Chem. / Year: 2017
Title: Structure of a Myeloid cell leukemia-1 (Mcl-1) inhibitor bound to drug site 3 of Human Serum Albumin.
Authors: Zhao, B. / Sensintaffar, J. / Bian, Z. / Belmar, J. / Lee, T. / Olejniczak, E.T. / Fesik, S.W.
#1: Journal: FEBS Lett. / Year: 2016
Title: Discovery and biological characterization of potent myeloid cell leukemia-1 inhibitors.
Authors: Lee, T. / Bian, Z. / Zhao, B. / Hogdal, L.J. / Sensintaffar, J.L. / Goodwin, C.M. / Belmar, J. / Shaw, S. / Tarr, J.C. / Veerasamy, N. / Matulis, S.M. / Koss, B. / Fischer, M.A. / Arnold, A. ...Authors: Lee, T. / Bian, Z. / Zhao, B. / Hogdal, L.J. / Sensintaffar, J.L. / Goodwin, C.M. / Belmar, J. / Shaw, S. / Tarr, J.C. / Veerasamy, N. / Matulis, S.M. / Koss, B. / Fischer, M.A. / Arnold, A.L. / Camper, D.V. / Browning, C.F. / Rossanese, O.W. / Budhraja, A. / Opferman, J. / Boise, L.H. / Savona, M.R. / Letai, A. / Olejniczak, E.T. / Fesik, S.W.
History
DepositionJan 17, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 3, 2017Provider: repository / Type: Initial release
Revision 1.1May 31, 2017Group: Database references
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serum albumin
B: Serum albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,5556
Polymers138,9392
Non-polymers1,6154
Water00
1
A: Serum albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,2773
Polymers69,4701
Non-polymers8082
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Serum albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,2773
Polymers69,4701
Non-polymers8082
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.844, 182.338, 58.925
Angle α, β, γ (deg.)90.00, 105.15, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Serum albumin


Mass: 69469.695 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: ALB, GIG20, GIG42, PRO0903, PRO1708, PRO2044, PRO2619, PRO2675, UNQ696/PRO1341
Production host: Homo sapiens (human) / References: UniProt: P02768
#2: Chemical ChemComp-6AK / 4-{8-chloro-11-[3-(4-chloro-3,5-dimethylphenoxy)propyl]-1-oxo-7-(1,3,5-trimethyl-1H-pyrazol-4-yl)-4,5-dihydro-1H-[1,4]diazepino[1,2-a]indol-2(3H)-yl}-1-methyl-1H-indole-6-carboxylic acid


Mass: 712.664 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C39H39Cl2N5O4
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
Has protein modificationY

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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: 2.2 Å3/Da / Density % sol: 43.99 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 7 / Details: 25-30% PEG3350, 50 mM K2PO4

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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: Mar 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→28.439 Å / Num. obs: 30593 / % possible obs: 92.8 % / Redundancy: 3 % / CC1/2: 0.96 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.05 / Rsym value: 0.073 / Net I/σ(I): 17.87
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.385 / Mean I/σ(I) obs: 1.82 / Num. unique obs: 1351 / CC1/2: 0.389 / Rpim(I) all: 0.276 / Rsym value: 0.739 / % possible all: 81.4

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4K2C

4k2c


Resolution: 2.7→28.757 Å / Cross valid method: THROUGHOUT / σ(F): 1.47 / Phase error: 31.9 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2155 2105 6.9 %
Rwork0.1739 --
obs0.1774 30496 92.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→28.757 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8702 0 110 0 8812
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0149346
X-RAY DIFFRACTIONf_angle_d1.77612659
X-RAY DIFFRACTIONf_dihedral_angle_d19.4015815
X-RAY DIFFRACTIONf_chiral_restr0.0791382
X-RAY DIFFRACTIONf_plane_restr0.0121629
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7014-2.76880.29691320.24381823X-RAY DIFFRACTION77
2.7688-2.84360.32161270.24291832X-RAY DIFFRACTION78
2.8436-2.92710.25741300.23431865X-RAY DIFFRACTION80
2.9271-3.02140.31951340.22531889X-RAY DIFFRACTION82
3.0214-3.12920.31061450.21611964X-RAY DIFFRACTION83
3.1292-3.25420.25481380.21452001X-RAY DIFFRACTION86
3.2542-3.40190.23931390.19922024X-RAY DIFFRACTION89
3.4019-3.58070.23591490.18832115X-RAY DIFFRACTION90
3.5807-3.80430.20911420.18022123X-RAY DIFFRACTION91
3.8043-4.09670.17911500.16892135X-RAY DIFFRACTION92
4.0967-4.50650.19181520.15022162X-RAY DIFFRACTION91
4.5065-5.15310.20061470.15262141X-RAY DIFFRACTION92
5.1531-6.47150.22061530.17682184X-RAY DIFFRACTION93
6.4715-24.10550.15461550.12922189X-RAY DIFFRACTION92
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)
11.9315-0.2053-0.36761.97610.95222.8648-0.35011.1133-0.9018-1.03380.2228-0.4280.518-0.05930.14021.1982-0.18860.21970.7131-0.15480.464116.582-10.9697-1.157
22.52160.5769-0.50111.33531.27481.8967-0.05270.4008-0.5007-0.4276-0.0877-1.38180.58860.19660.06560.77140.07630.30450.45160.0650.72626.158-6.93211.4784
31.73430.0086-0.36674.3185-0.93242.9014-0.22230.52090.1402-0.72650.2738-0.5835-0.5123-0.3215-0.03890.7688-0.04030.11390.49320.0250.358817.82187.43417.0496
42.91752.7094-1.8487.4472-1.67012.7714-0.36440.0401-0.09140.03030.3632-0.4405-0.1367-0.13990.03550.57020.011-0.12310.43580.05810.219113.20955.774717.8302
54.4718-1.0067-0.51123.30860.93943.1886-0.10170.2182-0.1121-0.5075-0.03090.1954-0.1252-0.50060.08910.6027-0.1183-0.12580.6418-0.03560.2607-3.8533-1.469711.8577
63.7068-0.8064-0.53364.8243-0.33655.042-0.5095-0.1635-0.61451.07810.47390.96580.1436-1.04440.170.62670.03010.16960.75390.05060.4688-15.9253-7.102431.8363
73.61081.23470.23491.7393-0.07241.56090.4634-0.29391.07830.6759-0.3082-0.0152-0.2449-0.3434-0.09390.79960.09250.03420.5607-0.10770.33518.0599.895540.6689
83.4711-0.02970.17973.0196-0.37362.1162-0.0827-0.3927-0.13570.36190.3248-0.07220.0545-0.0865-0.14940.67120.0395-0.00260.5416-0.07840.162913.13730.448935.9111
93.1692.5751-2.91146.2349-2.94195.83550.4578-0.25140.34571.1441-0.6071-0.7378-0.1980.9049-0.28180.5873-0.0423-0.09030.6061-0.08210.449330.901411.618934.7619
100.37750.3203-0.20654.6889-2.65114.63190.64-0.63540.47241.8034-0.513-0.9072-1.33460.4888-0.27021.2973-0.1275-0.04090.7712-0.10910.915333.876818.370141.3593
112.59290.0680.33832.1590.21071.5956-0.04490.1060.4583-0.28320.1186-0.7097-0.2849-0.0313-0.00120.45990.0181-0.05270.3402-0.05310.660628.313551.044922.6673
123.2804-0.4897-0.15452.3846-0.33841.7271-0.2046-1.20310.52060.75010.4688-0.0477-0.087-0.2598-0.22240.69130.184-0.1130.8349-0.11120.48027.969151.900645.7949
133.3584-0.2954-0.93543.60230.43383.3968-0.05110.1586-0.1501-0.42780.07620.18390.2349-0.34940.09330.40380.0191-0.09520.32890.05720.51440.284940.83613.6953
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 74 )
2X-RAY DIFFRACTION2chain 'A' and (resid 75 through 130 )
3X-RAY DIFFRACTION3chain 'A' and (resid 131 through 173 )
4X-RAY DIFFRACTION4chain 'A' and (resid 174 through 206 )
5X-RAY DIFFRACTION5chain 'A' and (resid 207 through 292 )
6X-RAY DIFFRACTION6chain 'A' and (resid 293 through 377 )
7X-RAY DIFFRACTION7chain 'A' and (resid 378 through 414 )
8X-RAY DIFFRACTION8chain 'A' and (resid 415 through 503 )
9X-RAY DIFFRACTION9chain 'A' and (resid 504 through 535 )
10X-RAY DIFFRACTION10chain 'A' and (resid 536 through 571 )
11X-RAY DIFFRACTION11chain 'B' and (resid 4 through 222 )
12X-RAY DIFFRACTION12chain 'B' and (resid 223 through 377 )
13X-RAY DIFFRACTION13chain 'B' and (resid 378 through 568 )

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