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- PDB-6ne5: Discovery of Potent Myeloid Cell Leukemia-1 (Mcl-1) Inhibitors th... -

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Basic information

Entry
Database: PDB / ID: 6ne5
TitleDiscovery of Potent Myeloid Cell Leukemia-1 (Mcl-1) Inhibitors that Demonstrate in vivo Activity in Mouse Xenograft Models of Human Cancer
ComponentsInduced myeloid leukemia cell differentiation protein Mcl-1
KeywordsAPOPTOSIS / structure based drug discovery / cancer / Mcl-1 / drug discovery
Function / homology
Function and homology information


positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / cellular homeostasis / cell fate determination / mitochondrial fusion / channel activity / Bcl-2 family protein complex / BH3 domain binding / negative regulation of anoikis / protein transmembrane transporter activity / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand ...positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / cellular homeostasis / cell fate determination / mitochondrial fusion / channel activity / Bcl-2 family protein complex / BH3 domain binding / negative regulation of anoikis / protein transmembrane transporter activity / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / extrinsic apoptotic signaling pathway in absence of ligand / negative regulation of autophagy / release of cytochrome c from mitochondria / response to cytokine / Signaling by ALK fusions and activated point mutants / intrinsic apoptotic signaling pathway in response to DNA damage / regulation of apoptotic process / Interleukin-4 and Interleukin-13 signaling / mitochondrial outer membrane / positive regulation of apoptotic process / protein heterodimerization activity / DNA damage response / negative regulation of apoptotic process / protein homodimerization activity / mitochondrion / nucleoplasm / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
Apoptosis regulator, Mcl-1 / Blc2-like / Apoptosis Regulator Bcl-x / Apoptosis regulator, Bcl-2, BH3 motif, conserved site / Apoptosis regulator, Bcl-2 family BH3 motif signature. / Apoptosis regulator, Bcl-2, BH1 motif, conserved site / Apoptosis regulator, Bcl-2 family BH1 motif signature. / Apoptosis regulator, Bcl-2, BH2 motif, conserved site / Apoptosis regulator, Bcl-2 family BH2 motif signature. / BCL (B-Cell lymphoma); contains BH1, BH2 regions ...Apoptosis regulator, Mcl-1 / Blc2-like / Apoptosis Regulator Bcl-x / Apoptosis regulator, Bcl-2, BH3 motif, conserved site / Apoptosis regulator, Bcl-2 family BH3 motif signature. / Apoptosis regulator, Bcl-2, BH1 motif, conserved site / Apoptosis regulator, Bcl-2 family BH1 motif signature. / Apoptosis regulator, Bcl-2, BH2 motif, conserved site / Apoptosis regulator, Bcl-2 family BH2 motif signature. / BCL (B-Cell lymphoma); contains BH1, BH2 regions / Bcl-2 family / Bcl-2, Bcl-2 homology region 1-3 / Bcl2-like / Apoptosis regulator proteins, Bcl-2 family / BCL2-like apoptosis inhibitors family profile. / Bcl-2-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-KJP / Induced myeloid leukemia cell differentiation protein Mcl-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsZhao, B.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)HHSN261200800001E United States
National Institutes of Health/National Cancer Institute (NIH/NCI)P50CA098131 United States
CitationJournal: J.Med.Chem. / Year: 2019
Title: Discovery of Potent Myeloid Cell Leukemia-1 (Mcl-1) Inhibitors That Demonstrate in Vivo Activity in Mouse Xenograft Models of Human Cancer.
Authors: Lee, T. / Christov, P.P. / Shaw, S. / Tarr, J.C. / Zhao, B. / Veerasamy, N. / Jeon, K.O. / Mills, J.J. / Bian, Z. / Sensintaffar, J.L. / Arnold, A.L. / Fogarty, S.A. / Perry, E. / Ramsey, H. ...Authors: Lee, T. / Christov, P.P. / Shaw, S. / Tarr, J.C. / Zhao, B. / Veerasamy, N. / Jeon, K.O. / Mills, J.J. / Bian, Z. / Sensintaffar, J.L. / Arnold, A.L. / Fogarty, S.A. / Perry, E. / Ramsey, H.E. / Cook, R.S. / Hollingshead, M. / Davis Millin, M. / Lee, K.M. / Koss, B. / Budhraja, A. / Opferman, J.T. / Kim, K. / Arteaga, C.L. / Moore, W.J. / Olejniczak, E.T. / Savona, M.R. / Fesik, S.W.
History
DepositionDec 17, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2019Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Induced myeloid leukemia cell differentiation protein Mcl-1
B: Induced myeloid leukemia cell differentiation protein Mcl-1
C: Induced myeloid leukemia cell differentiation protein Mcl-1
D: Induced myeloid leukemia cell differentiation protein Mcl-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,9898
Polymers72,1384
Non-polymers2,8514
Water7,620423
1
A: Induced myeloid leukemia cell differentiation protein Mcl-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7472
Polymers18,0351
Non-polymers7131
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Induced myeloid leukemia cell differentiation protein Mcl-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7472
Polymers18,0351
Non-polymers7131
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Induced myeloid leukemia cell differentiation protein Mcl-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7472
Polymers18,0351
Non-polymers7131
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Induced myeloid leukemia cell differentiation protein Mcl-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7472
Polymers18,0351
Non-polymers7131
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.332, 135.942, 60.051
Angle α, β, γ (deg.)90.00, 95.95, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Induced myeloid leukemia cell differentiation protein Mcl-1 / Bcl-2-like protein 3 / Bcl2-L-3 / Bcl-2-related protein EAT/mcl1 / mcl1/EAT


Mass: 18034.518 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MCL1, BCL2L3 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: Q07820
#2: Chemical
ChemComp-KJP / 3-[(4R)-7-chloro-10-[3-(4-chloro-3,5-dimethylphenoxy)propyl]-4-methyl-1-oxo-6-(1,3,5-trimethyl-1H-pyrazol-4-yl)-3,4-dihydropyrazino[1,2-a]indol-2(1H)-yl]-1-methyl-1H-indole-5-carboxylic acid


Mass: 712.664 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C39H39Cl2N5O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 423 / 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: 2.27 Å3/Da / Density % sol: 45.85 %
Crystal growTemperature: 291 K / Method: evaporation / pH: 7 / Details: PEG 3350, MgCl2, Bis-Tris6.5 / PH range: 6.5-8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.85→30 Å / Num. obs: 42920 / % possible obs: 80 % / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.027 / Rrim(I) all: 0.059 / Rsym value: 0.044 / Χ2: 1.3 / Net I/σ(I): 24.5
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1918 / CC1/2: 0.708 / Rpim(I) all: 0.19 / Rrim(I) all: 0.36 / Rsym value: 0.34 / Χ2: 0.608 / % possible all: 70.3

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IEZ

5iez


Resolution: 1.85→29.612 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.58 / Phase error: 21.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2068 1990 4.66 %
Rwork0.1716 --
obs0.1733 42686 79.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.85→29.612 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4763 0 200 423 5386
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065075
X-RAY DIFFRACTIONf_angle_d0.796879
X-RAY DIFFRACTIONf_dihedral_angle_d7.4192943
X-RAY DIFFRACTIONf_chiral_restr0.041740
X-RAY DIFFRACTIONf_plane_restr0.005861
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.89630.29641280.24712620X-RAY DIFFRACTION72
1.8963-1.94750.28291270.22762615X-RAY DIFFRACTION72
1.9475-2.00480.2771260.21322567X-RAY DIFFRACTION71
2.0048-2.06950.25981280.20212632X-RAY DIFFRACTION72
2.0695-2.14350.23871300.18682645X-RAY DIFFRACTION74
2.1435-2.22930.22971290.17652648X-RAY DIFFRACTION73
2.2293-2.33070.18041300.16692650X-RAY DIFFRACTION73
2.3307-2.45350.19361320.17352696X-RAY DIFFRACTION74
2.4535-2.60710.22821340.18522741X-RAY DIFFRACTION75
2.6071-2.80830.2141420.19192922X-RAY DIFFRACTION81
2.8083-3.09060.20871570.19233186X-RAY DIFFRACTION88
3.0906-3.53720.21651730.16893539X-RAY DIFFRACTION97
3.5372-4.45410.17621750.14323587X-RAY DIFFRACTION99
4.4541-29.61560.17351790.14673648X-RAY DIFFRACTION99
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)
15.466-0.9338-0.00385.0036-0.93394.22370.11180.42510.2356-0.50770.0403-0.3777-0.31660.0325-0.05770.23340.00250.02690.1127-0.05450.155-0.1628-1.465384.2386
24.0417-3.2371-1.07948.2967-1.05354.67310.19110.38780.4503-0.3982-0.4919-1.1612-0.6680.2698-0.01670.2553-0.0266-0.00770.19720.00450.40435.65865.458482.8307
33.0642-2.1958-0.74374.31840.84123.3191-0.3233-0.1671-0.07180.53950.3049-0.60780.60280.2232-0.06420.29510.01520.01610.2321-0.05610.17244.1363-10.739192.2673
40.9230.72250.82252.56320.88660.7096-0.4330.3859-0.7474-0.44330.12620.41420.5365-0.66050.32660.5039-0.290.13690.1524-0.2890.3613-9.0472-16.104987.9646
53.7717-2.5182-1.8963.92541.53474.34640.15840.2429-0.1395-0.2517-0.19810.24460.0002-0.19520.00510.11750.0059-0.02310.0832-0.01160.186-2.8195-9.397786.9921
67.90950.94993.70930.92180.79083.7383-0.068-0.91521.46150.1493-0.00190.1676-1.2495-0.16720.0050.3479-0.0410.11220.24-0.07340.172-3.2764.378798.7411
75.3227-0.35341.7885.0227-0.36874.7112-0.00230.2490.1063-0.3224-0.02020.27540.03030.007-0.09440.1167-0.0214-0.01650.09010.0080.1057-17.5454-42.547180.5165
83.841-0.76682.11155.576-0.51153.948-0.0436-0.00240.0669-0.19550.21210.22790.2737-0.0976-0.21320.2161-0.0321-0.04890.20570.02090.2228-21.9735-49.250976.9805
92.4311-1.70580.06387.14651.58322.7523-0.1993-0.3996-0.41430.58880.18231.35420.2679-0.19340.1180.1689-0.01340.05670.18120.04410.2335-24.7297-43.095389.9317
103.2678-0.9507-0.59445.2316-0.35176.032-0.26710.15420.3044-0.33010.04310.2463-0.432-0.21940.1070.2650.0622-0.09940.1819-0.03780.2399-21.7665-22.239686.904
112.2148-0.35820.70333.4360.05022.9221-0.04870.36440.1295-0.14250.0648-0.4594-0.58690.79950.14430.2874-0.1063-0.00510.1921-0.030.2603-10.2837-26.687283.5317
121.2719-0.67360.70233.916-0.76893.7732-0.1609-0.02310.02710.21860.00890.1434-0.5583-0.07850.03340.1056-0.0130.00490.0854-0.0150.1037-19.2819-32.143487.126
133.0398-1.40262.07965.2342-2.18646.45150.15360.14140.1054-0.1463-0.101-0.3570.01590.62310.01750.1525-0.00560.02430.1226-0.03040.1816-10.3999-37.653383.8385
148.3663.1817-2.753.2961-0.41354.7327-0.1108-0.6003-0.37030.4819-0.04110.2520.4540.25370.14260.28620.0354-0.00090.14020.01630.1946-16.8442-48.839294.7775
158.05551.34861.44095.2430.28584.41340.1862-0.4673-0.45630.4708-0.13770.00220.62280.0091-0.08830.22070.03330.02110.12990.01090.1499-3.4511-0.942164.6667
163.75591.40250.13036.0278-0.13732.8516-0.0918-0.5548-0.18120.6123-0.1471-0.22251.03860.0745-0.07470.54540.0242-0.07780.51280.18460.44471.7539-7.7367.4426
175.74124.0894-0.8997.7391-0.83753.10630.11510.1088-0.41360.12990.0488-0.52670.3360.3063-0.15450.25180.0940.02790.2217-0.02390.16253.2082-1.413755.6377
187.3499-1.8282-3.9944.69173.40563.7035-0.32-0.50390.084-0.04090.1574-0.072-0.07690.64610.07540.2607-0.0316-0.01480.16920.05120.13862.869719.325857.8549
193.46180.70833.38045.86841.5233.47150.2449-0.4280.32970.4595-0.37970.62980.0318-0.24310.23960.2707-0.0240.02340.2464-0.03820.2333-4.433117.239971.4411
204.8616-1.15120.96145.4711.9858.0947-0.0271-0.12760.087-0.3839-0.2110.5543-0.4729-0.78570.31430.11740.0224-0.04410.2073-0.01780.2558-11.905614.806858.7317
211.22150.72670.07962.75611.37923.78920.0309-0.07790.01820.0214-0.12970.3101-0.0538-0.25070.01470.05750.01930.03140.12960.00240.1716-5.44957.322260.5714
224.9182-1.6432-3.23781.15072.05853.705-0.16860.0415-0.4839-0.2782-0.11670.25710.6896-0.05550.32460.2440.02650.01690.1651-0.01510.2398-4.0499-6.105749.5016
235.2149-3.31630.5936.3804-1.55594.79440.04080.38160.5197-0.3008-0.1948-0.1805-0.48180.22730.17250.31-0.0227-0.04720.13850.03050.18298.1328-28.366650.8786
242.7086-1.18650.93992.4701-1.90695.111-0.07980.64750.5150.2564-0.4558-0.6312-0.99670.96470.49230.4151-0.121-0.10310.40050.09160.359214.2524-25.845657.0848
251.61741.93742.27823.00823.31283.75180.25640.0075-0.37520.37070.0531-0.38550.3230.0689-0.17180.15780.0256-0.03630.16540.00240.246210.9626-46.629863.7182
266.0194-2.3714-1.21585.022.224.26940.22260.3146-0.2779-0.5459-0.17850.44130.00990.24590.08080.19990.017-0.06440.17860.00780.20242.5776-45.36653.1024
272.5496-1.8856-0.27174.71860.4594.63150.05780.072-0.03820.0094-0.13930.1442-0.2222-0.2230.04120.12890.0092-0.03260.13240.01360.14174.361-35.419256.2383
281.81241.1573-1.01191.09290.03591.89690.2262-0.25760.48430.7549-0.15460.3586-1.4194-0.01750.13650.83020.0664-0.09180.16750.00990.32864.0535-20.131863.5106
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 172:191 )A172 - 191
2X-RAY DIFFRACTION2( CHAIN A AND RESID 192:202 )A192 - 202
3X-RAY DIFFRACTION3( CHAIN A AND RESID 203:239 )A203 - 239
4X-RAY DIFFRACTION4( CHAIN A AND RESID 240:260 )A240 - 260
5X-RAY DIFFRACTION5( CHAIN A AND RESID 261:308 )A261 - 308
6X-RAY DIFFRACTION6( CHAIN A AND RESID 309:322 )A309 - 322
7X-RAY DIFFRACTION7( CHAIN B AND RESID 172:191 )B172 - 191
8X-RAY DIFFRACTION8( CHAIN B AND RESID 192:202 )B192 - 202
9X-RAY DIFFRACTION9( CHAIN B AND RESID 203:223 )B203 - 223
10X-RAY DIFFRACTION10( CHAIN B AND RESID 224:239 )B224 - 239
11X-RAY DIFFRACTION11( CHAIN B AND RESID 240:255 )B240 - 255
12X-RAY DIFFRACTION12( CHAIN B AND RESID 256:283 )B256 - 283
13X-RAY DIFFRACTION13( CHAIN B AND RESID 284:308 )B284 - 308
14X-RAY DIFFRACTION14( CHAIN B AND RESID 309:322 )B309 - 322
15X-RAY DIFFRACTION15( CHAIN C AND RESID 172:191 )C172 - 191
16X-RAY DIFFRACTION16( CHAIN C AND RESID 192:202 )C192 - 202
17X-RAY DIFFRACTION17( CHAIN C AND RESID 203:223 )C203 - 223
18X-RAY DIFFRACTION18( CHAIN C AND RESID 224:235 )C224 - 235
19X-RAY DIFFRACTION19( CHAIN C AND RESID 236:246 )C236 - 246
20X-RAY DIFFRACTION20( CHAIN C AND RESID 247:255 )C247 - 255
21X-RAY DIFFRACTION21( CHAIN C AND RESID 256:308 )C256 - 308
22X-RAY DIFFRACTION22( CHAIN C AND RESID 309:321 )C309 - 321
23X-RAY DIFFRACTION23( CHAIN D AND RESID 172:191 )D172 - 191
24X-RAY DIFFRACTION24( CHAIN D AND RESID 192:223 )D192 - 223
25X-RAY DIFFRACTION25( CHAIN D AND RESID 224:235 )D224 - 235
26X-RAY DIFFRACTION26( CHAIN D AND RESID 236:254 )D236 - 254
27X-RAY DIFFRACTION27( CHAIN D AND RESID 255:308 )D255 - 308
28X-RAY DIFFRACTION28( CHAIN D AND RESID 309:321 )D309 - 321

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