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- PDB-4bgg: Crystal structure of the ACVR1 kinase in complex with LDN-213844 -

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Basic information

Entry
Database: PDB / ID: 4bgg
TitleCrystal structure of the ACVR1 kinase in complex with LDN-213844
ComponentsACTIVIN RECEPTOR TYPE-1
KeywordsTRANSFERASE / INHIBITOR / BMP SIGNALLING
Function / homology
Function and homology information


endocardial cushion cell fate commitment / mitral valve morphogenesis / BMP receptor complex / cardiac muscle cell fate commitment / atrial septum primum morphogenesis / endocardial cushion fusion / positive regulation of cardiac epithelial to mesenchymal transition / acute inflammatory response / positive regulation of determination of dorsal identity / smooth muscle cell differentiation ...endocardial cushion cell fate commitment / mitral valve morphogenesis / BMP receptor complex / cardiac muscle cell fate commitment / atrial septum primum morphogenesis / endocardial cushion fusion / positive regulation of cardiac epithelial to mesenchymal transition / acute inflammatory response / positive regulation of determination of dorsal identity / smooth muscle cell differentiation / activin receptor complex / endocardial cushion formation / transforming growth factor beta receptor activity, type I / activin receptor activity, type I / activin receptor activity, type II / BMP receptor activity / receptor protein serine/threonine kinase / transmembrane receptor protein serine/threonine kinase activity / transforming growth factor beta receptor activity, type II / pharyngeal system development / transforming growth factor beta receptor activity, type III / activin binding / cellular response to BMP stimulus / negative regulation of activin receptor signaling pathway / activin receptor signaling pathway / embryonic heart tube morphogenesis / gastrulation with mouth forming second / dorsal/ventral pattern formation / transforming growth factor beta binding / determination of left/right symmetry / neural crest cell migration / atrioventricular valve morphogenesis / branching involved in blood vessel morphogenesis / ventricular septum morphogenesis / negative regulation of G1/S transition of mitotic cell cycle / SMAD binding / germ cell development / positive regulation of intracellular signal transduction / peptide hormone binding / mesoderm formation / positive regulation of SMAD protein signal transduction / regulation of ossification / BMP signaling pathway / positive regulation of bone mineralization / negative regulation of signal transduction / positive regulation of osteoblast differentiation / transforming growth factor beta receptor signaling pathway / protein tyrosine kinase binding / negative regulation of extrinsic apoptotic signaling pathway / cellular response to growth factor stimulus / osteoblast differentiation / apical part of cell / heart development / in utero embryonic development / cell differentiation / protein kinase activity / positive regulation of cell migration / cadherin binding / protein serine/threonine kinase activity / positive regulation of DNA-templated transcription / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / ATP binding / metal ion binding / plasma membrane
Similarity search - Function
GS domain / Transforming growth factor beta type I GS-motif / GS domain profile. / GS motif / Activin types I and II receptor domain / Activin types I and II receptor domain / Ser/Thr protein kinase, TGFB receptor / Snake toxin-like superfamily / Protein tyrosine and serine/threonine kinase / Phosphorylase Kinase; domain 1 ...GS domain / Transforming growth factor beta type I GS-motif / GS domain profile. / GS motif / Activin types I and II receptor domain / Activin types I and II receptor domain / Ser/Thr protein kinase, TGFB receptor / Snake toxin-like superfamily / Protein tyrosine and serine/threonine kinase / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / 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-844 / CITRATE ANION / Activin receptor type-1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.56 Å
AuthorsSanvitale, C. / Canning, P. / Cooper, C. / Wang, Y. / Mohedas, A.H. / Choi, S. / Yu, P.B. / Cuny, G.D. / Nowak, R. / Coutandin, D. ...Sanvitale, C. / Canning, P. / Cooper, C. / Wang, Y. / Mohedas, A.H. / Choi, S. / Yu, P.B. / Cuny, G.D. / Nowak, R. / Coutandin, D. / Vollmar, M. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Bullock, A. / Structural Genomics Consortium (SGC)
CitationJournal: J.Med.Chem. / Year: 2014
Title: Structure-Activity Relationship of 3,5-Diaryl-2-Aminopyridine Alk2 Inhibitors Reveals Unaltered Binding Affinity for Fibrodysplasia Ossificans Progressiva Causing Mutants.
Authors: Mohedas, A.H. / Wang, Y. / Sanvitale, C.E. / Canning, P. / Choi, S. / Xing, X. / Bullock, A.N. / Cuny, G.D. / Yu, P.B.
History
DepositionMar 26, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 10, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 10, 2014Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ACTIVIN RECEPTOR TYPE-1
B: ACTIVIN RECEPTOR TYPE-1
C: ACTIVIN RECEPTOR TYPE-1
D: ACTIVIN RECEPTOR TYPE-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,15816
Polymers138,1514
Non-polymers3,00812
Water2,882160
1
A: ACTIVIN RECEPTOR TYPE-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5726
Polymers34,5381
Non-polymers1,0355
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ACTIVIN RECEPTOR TYPE-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5105
Polymers34,5381
Non-polymers9734
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: ACTIVIN RECEPTOR TYPE-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1323
Polymers34,5381
Non-polymers5952
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: ACTIVIN RECEPTOR TYPE-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9432
Polymers34,5381
Non-polymers4051
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)85.380, 99.850, 187.438
Angle α, β, γ (deg.)90.00, 92.93, 90.00
Int Tables number5
Space group name H-MI121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.9905, 0.03, 0.1343), (0.0298, -0.9996, 0.0035), (0.1343, 0.0005, -0.9909)-0.9155, -49.1837, 84.8776
2given(0.0738, -0.9971, 0.0183), (-0.9915, -0.0753, -0.1056), (0.1067, -0.0104, -0.9942)12.0373, 16.9018, 39.5642
3given(0.1319, 0.9903, 0.0432), (0.9835, -0.1362, 0.1189), (0.1236, 0.0268, -0.992)102.4266, -120.4142, 40.4223

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Components

#1: Protein
ACTIVIN RECEPTOR TYPE-1 / ACTIVIN RECEPTOR TYPE I / ACTR-I / ACTIVIN RECEPTOR-LIKE KINASE 2 / ALK-2 / SERINE/THREONINE- ...ACTIVIN RECEPTOR TYPE I / ACTR-I / ACTIVIN RECEPTOR-LIKE KINASE 2 / ALK-2 / SERINE/THREONINE-PROTEIN KINASE RECEPTOR R1 / SKR1 / TGF-B SUPERFAMILY RECEPTOR TYPE I / TSR-I


Mass: 34537.633 Da / Num. of mol.: 4 / Fragment: KINASE DOMAIN, RESIDUES 201-499 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Description: SITE-DIRECTED MUTAGENESIS / Plasmid: PFB-LIC-BSE / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm)
References: UniProt: Q04771, receptor protein serine/threonine kinase
#2: Chemical
ChemComp-844 / 1-{4-[5-(3,4,5-trimethoxyphenyl)pyridin-3-yl]phenyl}piperazine


Mass: 405.489 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C24H27N3O3
#3: Chemical
ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C6H5O7
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsCONSTITUTIVELY ACTIVATING MUTATION INTRODUCED, Q207D

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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: 2.89 Å3/Da / Density % sol: 57.49 % / Description: NONE
Crystal growDetails: 0.2M AMMONIUM CITRATE, 20%(W/V) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 21, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.56→52.91 Å / Num. obs: 49502 / % possible obs: 97 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 10.9
Reflection shellResolution: 2.56→2.64 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 3.2 / % possible all: 98.5

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3Q4U

3q4u


Resolution: 2.56→52.97 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.922 / SU B: 18.692 / SU ML: 0.208 / Cross valid method: THROUGHOUT / ESU R: 0.558 / ESU R Free: 0.29 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2472 2487 5.1 %RANDOM
Rwork0.21518 ---
obs0.21685 46724 96.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 59.705 Å2
Baniso -1Baniso -2Baniso -3
1-1.21 Å20 Å20.54 Å2
2--1.09 Å20 Å2
3----2.31 Å2
Refinement stepCycle: LAST / Resolution: 2.56→52.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8899 0 215 160 9274
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0199342
X-RAY DIFFRACTIONr_bond_other_d0.0070.028614
X-RAY DIFFRACTIONr_angle_refined_deg1.6151.9712730
X-RAY DIFFRACTIONr_angle_other_deg1.209319709
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.58651154
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.06723.873377
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.728151465
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.5551548
X-RAY DIFFRACTIONr_chiral_restr0.0870.21431
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02110507
X-RAY DIFFRACTIONr_gen_planes_other0.0070.022129
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_it0.6460.8474619
X-RAY DIFFRACTIONr_mcbond_other0.6460.8484618
X-RAY DIFFRACTIONr_mcangle_it1.1521.2685760
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.7111.0844722
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.558→2.624 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.415 151 -
Rwork0.3 3542 -
obs--98.09 %
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)
116.4323-2.14886.210915.05848.080813.0029-0.7376-0.8846-0.91910.31841.08510.34180.26870.7482-0.34750.35420.09750.07810.55680.13810.344847.7856-47.650561.3202
29.2147-2.95952.80321.9452-1.5533.05020.0476-0.4659-0.0339-0.07980.0268-0.14190.11110.2261-0.07430.3403-0.01330.0570.2788-0.07090.286250.0174-44.390851.4838
38.9083-2.8024-0.75223.87920.11393.74810.1453-0.20420.6441-0.0380.0226-0.2763-0.12290.5901-0.16790.2847-0.0510.05150.2665-0.05840.31545.2793-35.60142.3946
434.89616.5404-17.708816.1079-4.98611.0462-0.9709-0.6497-2.0994-0.76870.1742-3.0221-0.01750.99270.79660.7785-0.07520.00911.83490.17941.231462.8603-37.218133.2111
54.9526-0.0933-0.4953.09240.12092.9206-0.01380.5449-0.3978-0.42560.0448-0.10180.40030.2878-0.03090.4581-0.03320.03890.294-0.04590.264537.356-42.879331.1938
617.0682-1.0542-7.347710.0764.502313.3917-0.66880.41230.4285-0.52060.37830.0418-0.2310.6130.29050.4722-0.0383-0.02530.42010.12950.356445.81371.962929.7779
77.6503-0.0984.94433.629-1.703413.7045-0.1268-0.00460.0461-0.0010.0356-0.0766-0.15390.11450.09120.262-0.0730.09360.27330.01260.307549.5829-1.866938.8276
85.57491.3798-1.1522.4321-0.64512.7508-0.02640.0838-0.14950.02730.0016-0.19780.15690.31920.02480.28810.0420.03310.1875-0.04120.27242.8991-7.931945.4296
94.0044-0.66411.52453.0110.01093.6162-0.0682-0.39980.23780.317-0.01640.1073-0.1103-0.05940.08460.28180.02330.05080.2485-0.01120.241131.0615-1.002357.8871
106.38270.29350.8353.01990.16613.5993-0.0681-0.2946-0.33320.30710.03660.38890.4115-0.11530.03150.35290.01470.06830.28280.06970.339628.555-14.987559.776
113.0262-0.8341-0.14425.18931.433713.48520.072-0.2129-0.073-0.2032-0.2248-0.40030.55240.05620.15280.48680.094-0.01150.7138-0.01380.3163.7904-31.1119-6.2361
123.84660.127-0.36043.3657-0.078512.02410.1383-0.2639-0.47360.1286-0.2408-0.08880.7762-0.75530.10250.459-0.07760.02870.7946-0.07020.341461.0507-31.516410.5835
136.4304-1.6290.7465.9263-1.153110.7022-0.0665-0.72060.57980.5076-0.5379-0.7865-2.53550.26990.60440.9797-0.1132-0.0660.8467-0.17520.540168.2356-15.876615.6949
144.57526.84447.955126.20981.895920.1371-0.21070.73330.1181-2.0055-0.3153-0.42250.80962.0810.5261.05120.29920.18291.22650.02540.57550.7123-6.370414.2758
153.98-0.139-2.36937.9066-0.26553.6959-0.2492-0.7340.0097-0.1087-0.38640.4824-0.931-2.15420.63560.98651.0078-0.25413.3095-0.81840.436650.7605-21.966816.6867
163.2956.3044-3.934412.4965-6.415210.4174-0.4140.069-0.4537-1.4725-0.062-0.98970.5628-0.94410.4761.54730.1924-0.28330.98360.06240.849866.312-63.9934-14.3523
172.0246-0.9594-0.398211.4344-2.45515.89870.19490.20640.0989-1.2406-0.2729-0.23140.0576-0.19320.0780.77810.03270.03220.71950.03920.38771.1102-65.2559-3.1362
182.88740.4096-0.00739.3870.1665.94940.06490.0730.0966-0.1721-0.22980.06040.0073-0.12390.16490.4916-0.0679-0.060.53590.09690.329269.5975-68.096510.7791
198.1938-6.16332.970510.6422-2.94593.19350.39180.0505-0.31020.0187-0.29741.74960.5856-0.7579-0.09440.7391-0.32380.08090.91110.04690.844258.3761-79.076517.0754
201.1568-1.01261.496721.4985-0.83842.25290.06340.0979-0.1181.1173-0.3107-1.35020.35820.37080.24730.8844-0.05770.11130.68830.31780.773875.9839-77.657118.6178
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A203 - 232
2X-RAY DIFFRACTION2A233 - 301
3X-RAY DIFFRACTION3A302 - 358
4X-RAY DIFFRACTION4A359 - 369
5X-RAY DIFFRACTION5A370 - 498
6X-RAY DIFFRACTION6B203 - 218
7X-RAY DIFFRACTION7B219 - 258
8X-RAY DIFFRACTION8B259 - 374
9X-RAY DIFFRACTION9B375 - 459
10X-RAY DIFFRACTION10B460 - 498
11X-RAY DIFFRACTION11C204 - 319
12X-RAY DIFFRACTION12C320 - 412
13X-RAY DIFFRACTION13C413 - 457
14X-RAY DIFFRACTION14C458 - 465
15X-RAY DIFFRACTION15C466 - 497
16X-RAY DIFFRACTION16D204 - 229
17X-RAY DIFFRACTION17D230 - 309
18X-RAY DIFFRACTION18D310 - 432
19X-RAY DIFFRACTION19D433 - 462
20X-RAY DIFFRACTION20D463 - 498

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