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- PDB-3rcd: HER2 Kinase Domain Complexed with TAK-285 -

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Basic information

Entry
Database: PDB / ID: 3rcd
TitleHER2 Kinase Domain Complexed with TAK-285
ComponentsReceptor tyrosine-protein kinase erbB-2
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / KINASE DOMAIN / RECEPTOR / TRANSFERASE / TYROSINE-PROTEIN KINASE / TYROSINE KINASE INHIBITOR / TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX / ANTI-ONCOGENE / CELL CYCLE / DISEASE / MUTATION / ATP-BINDING / NUCLEOTIDE-BINDING / GLYCOPROTEIN / PHOSPHOPROTEIN / MEMBRANE / SECRETED
Function / homology
Function and homology information


negative regulation of immature T cell proliferation in thymus / ERBB3:ERBB2 complex / ERBB2-ERBB4 signaling pathway / GRB7 events in ERBB2 signaling / immature T cell proliferation in thymus / RNA polymerase I core binding / regulation of microtubule-based process / ErbB-3 class receptor binding / semaphorin receptor complex / Sema4D induced cell migration and growth-cone collapse ...negative regulation of immature T cell proliferation in thymus / ERBB3:ERBB2 complex / ERBB2-ERBB4 signaling pathway / GRB7 events in ERBB2 signaling / immature T cell proliferation in thymus / RNA polymerase I core binding / regulation of microtubule-based process / ErbB-3 class receptor binding / semaphorin receptor complex / Sema4D induced cell migration and growth-cone collapse / motor neuron axon guidance / neurotransmitter receptor localization to postsynaptic specialization membrane / PLCG1 events in ERBB2 signaling / ERBB2-EGFR signaling pathway / neuromuscular junction development / positive regulation of Rho protein signal transduction / ERBB2 Activates PTK6 Signaling / Drug-mediated inhibition of ERBB2 signaling / Resistance of ERBB2 KD mutants to trastuzumab / Resistance of ERBB2 KD mutants to sapitinib / Resistance of ERBB2 KD mutants to tesevatinib / Resistance of ERBB2 KD mutants to neratinib / Resistance of ERBB2 KD mutants to osimertinib / Resistance of ERBB2 KD mutants to afatinib / Resistance of ERBB2 KD mutants to AEE788 / Resistance of ERBB2 KD mutants to lapatinib / Drug resistance in ERBB2 TMD/JMD mutants / enzyme-linked receptor protein signaling pathway / positive regulation of transcription by RNA polymerase I / ERBB2-ERBB3 signaling pathway / oligodendrocyte differentiation / ERBB2 Regulates Cell Motility / semaphorin-plexin signaling pathway / PI3K events in ERBB2 signaling / positive regulation of cell adhesion / positive regulation of protein targeting to membrane / regulation of angiogenesis / coreceptor activity / Schwann cell development / Signaling by ERBB2 / cellular response to epidermal growth factor stimulus / myelination / Downregulation of ERBB2:ERBB3 signaling / GRB2 events in ERBB2 signaling / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / transmembrane receptor protein tyrosine kinase activity / SHC1 events in ERBB2 signaling / Constitutive Signaling by Overexpressed ERBB2 / neurogenesis / basal plasma membrane / regulation of ERK1 and ERK2 cascade / phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of translation / positive regulation of epithelial cell proliferation / cell surface receptor protein tyrosine kinase signaling pathway / Signaling by ERBB2 TMD/JMD mutants / positive regulation of MAP kinase activity / wound healing / neuromuscular junction / Signaling by ERBB2 ECD mutants / neuron differentiation / Signaling by ERBB2 KD Mutants / receptor protein-tyrosine kinase / receptor tyrosine kinase binding / cellular response to growth factor stimulus / Downregulation of ERBB2 signaling / ruffle membrane / peptidyl-tyrosine phosphorylation / Constitutive Signaling by Aberrant PI3K in Cancer / transmembrane signaling receptor activity / PIP3 activates AKT signaling / myelin sheath / presynaptic membrane / heart development / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / positive regulation of cell growth / basolateral plasma membrane / protein tyrosine kinase activity / positive regulation of MAPK cascade / early endosome / cell surface receptor signaling pathway / receptor complex / endosome membrane / intracellular signal transduction / apical plasma membrane / positive regulation of protein phosphorylation / protein heterodimerization activity / protein phosphorylation / signaling receptor binding / positive regulation of cell population proliferation / negative regulation of apoptotic process / perinuclear region of cytoplasm / signal transduction / nucleoplasm / ATP binding / membrane / identical protein binding / nucleus / plasma membrane
Similarity search - Function
: / Epidermal growth factor receptor transmembrane-juxtamembrane segment / Tyrosine protein kinase, EGF/ERB/XmrK receptor / Growth factor receptor domain 4 / Growth factor receptor domain IV / Receptor L-domain / Furin-like cysteine-rich domain / Receptor L-domain superfamily / Furin-like cysteine rich region / Receptor L domain ...: / Epidermal growth factor receptor transmembrane-juxtamembrane segment / Tyrosine protein kinase, EGF/ERB/XmrK receptor / Growth factor receptor domain 4 / Growth factor receptor domain IV / Receptor L-domain / Furin-like cysteine-rich domain / Receptor L-domain superfamily / Furin-like cysteine rich region / Receptor L domain / Furin-like repeat / Furin-like repeats / Growth factor receptor cysteine-rich domain superfamily / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-03P / Receptor tyrosine-protein kinase erbB-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.21 Å
AuthorsAertgeerts, K. / Skene, R. / Sogabe, S.
CitationJournal: J.Med.Chem. / Year: 2011
Title: Design and Synthesis of Novel Human Epidermal Growth Factor Receptor 2 (HER2)/Epidermal Growth Factor Receptor (EGFR) Dual Inhibitors Bearing a Pyrrolo[3,2-d]pyrimidine Scaffold.
Authors: Ishikawa, T. / Seto, M. / Banno, H. / Kawakita, Y. / Oorui, M. / Taniguchi, T. / Ohta, Y. / Tamura, T. / Nakayama, A. / Miki, H. / Kamiguchi, H. / Tanaka, T. / Habuka, N. / Sogabe, S. / ...Authors: Ishikawa, T. / Seto, M. / Banno, H. / Kawakita, Y. / Oorui, M. / Taniguchi, T. / Ohta, Y. / Tamura, T. / Nakayama, A. / Miki, H. / Kamiguchi, H. / Tanaka, T. / Habuka, N. / Sogabe, S. / Yano, J. / Aertgeerts, K. / Kamiyama, K.
History
DepositionMar 30, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2011Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / 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 / _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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Receptor tyrosine-protein kinase erbB-2
B: Receptor tyrosine-protein kinase erbB-2
C: Receptor tyrosine-protein kinase erbB-2
D: Receptor tyrosine-protein kinase erbB-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,0126
Polymers152,9164
Non-polymers1,0962
Water61334
1
A: Receptor tyrosine-protein kinase erbB-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7772
Polymers38,2291
Non-polymers5481
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Receptor tyrosine-protein kinase erbB-2


Theoretical massNumber of molelcules
Total (without water)38,2291
Polymers38,2291
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Receptor tyrosine-protein kinase erbB-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7772
Polymers38,2291
Non-polymers5481
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Receptor tyrosine-protein kinase erbB-2


Theoretical massNumber of molelcules
Total (without water)38,2291
Polymers38,2291
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Receptor tyrosine-protein kinase erbB-2
B: Receptor tyrosine-protein kinase erbB-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,0063
Polymers76,4582
Non-polymers5481
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1680 Å2
ΔGint-16 kcal/mol
Surface area28000 Å2
MethodPISA
6
C: Receptor tyrosine-protein kinase erbB-2
D: Receptor tyrosine-protein kinase erbB-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,0063
Polymers76,4582
Non-polymers5481
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1680 Å2
ΔGint-17 kcal/mol
Surface area28040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.542, 64.936, 92.360
Angle α, β, γ (deg.)90.420, 89.720, 90.350
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D

NCS domain segments:

Component-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: 2

Dom-IDEns-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA710 - 10229 - 321
21CC710 - 10229 - 321
12BB710 - 10109 - 309
22DD710 - 10109 - 309

NCS ensembles :
ID
1
2

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Components

#1: Protein
Receptor tyrosine-protein kinase erbB-2 / Metastatic lymph node gene 19 protein / MLN 19 / Proto-oncogene Neu / Proto-oncogene c-ErbB-2 / ...Metastatic lymph node gene 19 protein / MLN 19 / Proto-oncogene Neu / Proto-oncogene c-ErbB-2 / Tyrosine kinase-type cell surface receptor HER2 / p185erbB2


Mass: 38229.012 Da / Num. of mol.: 4 / Fragment: UNP residues 713-1028
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ERBB2, HER2, MLN19, NEU, NGL / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P04626, receptor protein-tyrosine kinase
#2: Chemical ChemComp-03P / N-{2-[4-({3-chloro-4-[3-(trifluoromethyl)phenoxy]phenyl}amino)-5H-pyrrolo[3,2-d]pyrimidin-5-yl]ethyl}-3-hydroxy-3-methylbutanamide / TAK-285


Mass: 547.957 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H25ClF3N5O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 1.98 Å3/Da / Density % sol: 37.95 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 20% PEG 3550, 200MM DI-AMMONIUM TARTRATE, 100 MM PIPES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Aug 17, 2007
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 14548 / % possible obs: 76.3 % / Redundancy: 1.7 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 8.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
3.2-3.311.50.211142.6
3.31-3.451.50.194154
3.45-3.61.60.151164.3
3.6-3.791.70.142169.7
3.79-4.031.70.122178.2
4.03-4.341.70.096186.7
4.34-4.781.80.087189.6
4.78-5.471.80.087191
5.47-6.891.80.082190.6
6.89-501.90.036195.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PP0

3pp0


Resolution: 3.21→40 Å / Cor.coef. Fo:Fc: 0.896 / Cor.coef. Fo:Fc free: 0.78 / Occupancy max: 1 / Occupancy min: 0.65 / SU B: 74.49 / SU ML: 0.578 / SU R Cruickshank DPI: 0.6524 / Cross valid method: THROUGHOUT / ESU R Free: 0.848 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29352 749 5.2 %RANDOM
Rwork0.22375 ---
obs0.22729 13792 75.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.502 Å2
Baniso -1Baniso -2Baniso -3
1--1.03 Å20.23 Å2-0.03 Å2
2--3.57 Å20.05 Å2
3----2.54 Å2
Refinement stepCycle: LAST / Resolution: 3.21→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8860 0 76 34 8970
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0229116
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2351.98712328
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.84351086
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.03922.68388
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.263151658
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1191588
X-RAY DIFFRACTIONr_chiral_restr0.080.21386
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0216794
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.4361.55502
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.80128932
X-RAY DIFFRACTIONr_scbond_it0.49323614
X-RAY DIFFRACTIONr_scangle_it0.90133396
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1124TIGHT POSITIONAL0.020.05
1A1130MEDIUM POSITIONAL0.040.5
1A1124TIGHT THERMAL0.030.5
1A1130MEDIUM THERMAL0.042
2B1084TIGHT POSITIONAL0.020.05
2B1092MEDIUM POSITIONAL0.020.5
2B1084TIGHT THERMAL0.030.5
2B1092MEDIUM THERMAL0.032
LS refinement shellResolution: 3.213→3.296 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 33 -
Rwork0.239 536 -
obs--39.73 %
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)
11.048-0.0921.68931.7178-0.02023.1289-0.0345-0.021-0.14430.0140.11030.0699-0.0294-0.0457-0.07580.046-0.04250.04080.0504-0.02560.09317.5758-1.781321.4752
23.61440.6751-2.99851.0736-0.16225.38480.18350.1156-0.00870.1244-0.02090.00410.0972-0.2753-0.16260.0376-0.0213-0.00180.0496-0.02830.0531-4.17841.9303-24.9254
31.7327-0.73181.6041.308-0.70334.8041-0.00160.0699-0.1138-0.00920.02630.0056-0.06950.1364-0.02460.0409-0.04680.02910.0657-0.05380.0618-32.5423-33.556-67.9797
43.17360.3193-2.78350.5821-0.49345.30410.07040.1414-0.06310.0309-0.1111-0.02740.18120.11210.04070.05390.0076-0.04210.0520.00170.0771-20.8661-30.7055-21.622
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A710 - 799
2X-RAY DIFFRACTION1A800 - 1022
3X-RAY DIFFRACTION1A9001
4X-RAY DIFFRACTION2B710 - 799
5X-RAY DIFFRACTION2B800 - 1010
6X-RAY DIFFRACTION3C710 - 799
7X-RAY DIFFRACTION3C800 - 1022
8X-RAY DIFFRACTION3C9001
9X-RAY DIFFRACTION4D710 - 799
10X-RAY DIFFRACTION4D800 - 1010

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