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- PDB-9pq7: MBP-Mcl1 in complex with ligand 21b -

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Basic information

Entry
Database: PDB / ID: 9pq7
TitleMBP-Mcl1 in complex with ligand 21b
ComponentsMaltose/maltodextrin-binding periplasmic protein,Induced myeloid leukemia cell differentiation protein Mcl-1
KeywordsSIGNALING PROTEIN / Myeloid cell leukemia 1 / Mcl-1 / B-cell lymphoma 2 / Bcl-2 / BH3 mimetic / Protein-protein interaction / Modulator / Apoptosis / Cancer / Leukemia / Myeloma / Lymphoma
Function / homology
Function and homology information


positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / cell fate determination / cellular homeostasis / mitochondrial fusion / Bcl-2 family protein complex / detection of maltose stimulus / maltose transport complex / carbohydrate transport / BH3 domain binding / negative regulation of anoikis ...positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / cell fate determination / cellular homeostasis / mitochondrial fusion / Bcl-2 family protein complex / detection of maltose stimulus / maltose transport complex / carbohydrate transport / BH3 domain binding / negative regulation of anoikis / carbohydrate transmembrane transporter activity / protein transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / response to cytokine / extrinsic apoptotic signaling pathway in absence of ligand / ATP-binding cassette (ABC) transporter complex / negative regulation of autophagy / release of cytochrome c from mitochondria / cell chemotaxis / intrinsic apoptotic signaling pathway in response to DNA damage / Signaling by ALK fusions and activated point mutants / positive regulation of neuron apoptotic process / outer membrane-bounded periplasmic space / channel activity / Interleukin-4 and Interleukin-13 signaling / regulation of apoptotic process / mitochondrial outer membrane / periplasmic space / positive regulation of apoptotic process / protein heterodimerization activity / DNA damage response / negative regulation of apoptotic process / mitochondrion / nucleoplasm / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
Apoptosis regulator, Mcl-1 / 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-2 family / BCL (B-Cell lymphoma); contains BH1, BH2 regions / Bcl2-like ...Apoptosis regulator, Mcl-1 / 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-2 family / BCL (B-Cell lymphoma); contains BH1, BH2 regions / Bcl2-like / Bcl-2, Bcl-2 homology region 1-3 / Apoptosis regulator proteins, Bcl-2 family / BCL2-like apoptosis inhibitors family profile. / Bcl-2-like superfamily / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein
Similarity search - Domain/homology
: / FORMIC ACID / Maltose/maltodextrin-binding periplasmic protein / Induced myeloid leukemia cell differentiation protein Mcl-1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.24 Å
AuthorsMiller, B.R. / Shaffer, P.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: J.Med.Chem. / Year: 2025
Title: In Pursuit of Best-in-Class MCL-1 Inhibitors: Discovery of Highly Potent 1,4-Indoyl Macrocycles with Favorable Physicochemical Properties.
Authors: Velter, I.A. / Lento, W. / Peschiulli, A. / Reuillon, T.D. / Ferrer, S. / Orgaz-Gordillo, S. / Buijnsters, P. / De Boeck, B.C.A.G. / Demin, S. / Van Roosbroeck, Y. / Jouffroy, M. / Vos, A. / ...Authors: Velter, I.A. / Lento, W. / Peschiulli, A. / Reuillon, T.D. / Ferrer, S. / Orgaz-Gordillo, S. / Buijnsters, P. / De Boeck, B.C.A.G. / Demin, S. / Van Roosbroeck, Y. / Jouffroy, M. / Vos, A. / Miller, B. / Shaffer, P. / Koo, S.J. / Dominguez Blanco, M. / McQueen, L. / Altrocchi, C. / Bueters, R. / Vinken, P. / Bekkers, M. / Steyvers, H. / Guttke, C. / Walker, D. / Bauser, M. / Wilson, D.M. / Philippar, U. / Rombouts, F.J.R.
History
DepositionJul 22, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 8, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Maltose/maltodextrin-binding periplasmic protein,Induced myeloid leukemia cell differentiation protein Mcl-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,5686
Polymers57,3111
Non-polymers1,2575
Water13,655758
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)99.433, 136.936, 38.653
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-1145-

HOH

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Maltose/maltodextrin-binding periplasmic protein,Induced myeloid leukemia cell differentiation protein Mcl-1 / MMBP / Maltodextrin-binding protein / Maltose-binding protein / MBP / Bcl-2-like protein 3 / Bcl2-L- ...MMBP / Maltodextrin-binding protein / Maltose-binding protein / MBP / Bcl-2-like protein 3 / Bcl2-L-3 / Bcl-2-related protein EAT/mcl1 / mcl1/EAT


Mass: 57310.883 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Homo sapiens (human)
Gene: malE, b4034, JW3994, MCL1, BCL2L3 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AEX9, UniProt: Q07820
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE

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Non-polymers , 4 types, 762 molecules

#3: Chemical ChemComp-A1CMG / 17-chloranyl-33-fluoranyl-12-[2-(2-methoxyethoxy)ethyl]-5,14,22-trimethyl-28-oxa-9-thia-5,6,12,13,24-pentazaheptacyclo[27.7.1.1^{4,7}.0^{11,15}.0^{16,21}.0^{20,24}.0^{30,35}]octatriaconta-1(36),4(38),6,11(15),13,16,18,20,22,29(37),30(35),31,33-tridecaene-23-carboxylic acid


Mass: 760.316 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H43ClFN5O5S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 758 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.26 Å3/Da / Density % sol: 45.56 %
Crystal growTemperature: 285 K / Method: vapor diffusion / pH: 7.5 / Details: 19% (w/v) PEG3350, 0.17M Magnesium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9998 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 2, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9998 Å / Relative weight: 1
ReflectionResolution: 1.24→80.46 Å / Num. obs: 119188 / % possible obs: 80 % / Redundancy: 8.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.039 / Rrim(I) all: 0.037 / Rsym value: 0.039 / Net I/σ(I): 20.6
Reflection shellResolution: 1.244→1.34 Å / Redundancy: 7.3 % / Rmerge(I) obs: 1.164 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 5959 / Rsym value: 1.164 / % possible all: 20.3

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Processing

Software
NameVersionClassification
autoPROCdata reduction
XDS(VERSION Mar 15)data reduction
autoPROCdata reduction
autoPROC(Version 1.1.7)data scaling
Aimlessdata scaling
REFMAC5.8.0155refinement
XDSdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.24→80.46 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.974 / SU B: 1.956 / SU ML: 0.035 / Cross valid method: THROUGHOUT / ESU R: 0.049 / ESU R Free: 0.049 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1709 6203 5.2 %RANDOM
Rwork0.13315 ---
obs0.13513 112985 80.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.48 Å2
Baniso -1Baniso -2Baniso -3
1--0.44 Å20 Å20 Å2
2--1.1 Å2-0 Å2
3----0.66 Å2
Refinement stepCycle: LAST / Resolution: 1.24→80.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4042 0 86 758 4886
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.024373
X-RAY DIFFRACTIONr_bond_other_d0.0020.024167
X-RAY DIFFRACTIONr_angle_refined_deg1.5031.9775973
X-RAY DIFFRACTIONr_angle_other_deg2.04839628
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1275568
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.37124.947190
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.97215.073749
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2981518
X-RAY DIFFRACTIONr_chiral_restr0.0930.2658
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215018
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02970
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_it3.1632.4412146
X-RAY DIFFRACTIONr_mcbond_other3.1632.4422147
X-RAY DIFFRACTIONr_mcangle_it3.6424.1392703
X-RAY DIFFRACTIONr_mcangle_other3.6674.1422704
X-RAY DIFFRACTIONr_scbond_it5.8742.992227
X-RAY DIFFRACTIONr_scbond_other5.8642.9862221
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.9554.7743251
X-RAY DIFFRACTIONr_long_range_B_refined6.08625.095346
X-RAY DIFFRACTIONr_long_range_B_other5.50723.6745135
X-RAY DIFFRACTIONr_rigid_bond_restr11.83338540
X-RAY DIFFRACTIONr_sphericity_free32.3785524
X-RAY DIFFRACTIONr_sphericity_bonded12.99958664
LS refinement shellResolution: 1.244→1.276 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 27 -
Rwork0.324 494 -
obs--4.81 %

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