satarupa22/MacromolecularLigandDB huggingface dataset:
INPP5D PanDDA analysis group deposition -- Crystal Structure of the phosphatase and C2 domains of SHIP1 in complex with Z2856434812 (PDB entry 5RWA)
Macromolecule: Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.86
Sequence length: 463 residues
Sequence: SMEQPEPDMITIFIGTWNMGNAPPPKKITSWFLSKGQGKTRDDSADYIPHDIYVIGTQEDPLSEKEWLEILKHSLQEITSVTFKTVAIHTLWNIRIVVLAKPEHENRISHICTDNVKTGIANTLGNKGAVGVSFMFNGTSLGFVNSHLTSGSEKKLRRNQNYMNILRFLALGDKKLSPFNITHRFTHLFWFGDLNYRVDLPTWEAETIIQKIKQQQYADLLSHDQLLTERREQKVFLHFEEEEITFAPTYRFERLTRDKYAYTKQKATGMKYNLPSWCDRVLWKSYPLVHVVCQSYGSTSDIMTSDHSPVFATFEAGVTSQFVSKNGPGTVDSQGQIEFLRCYATLKTKSQTKFYLEFHSSCLESFVKSQEGENEEGSEGELVVKFGETLPKLKPIISDPEYLLDQHILISIKSSDSDESYGEGCIALRLEATETQLPIYTPLTHHGELTGHFQGEIKLQTSQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.29
R work: 0.167
R free: 0.1887
Average B factor: 18.239
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 30 mM sodium nitrate, 30 mM dibasic sodium phosphate, 30 mM ammonium sulfate, 100 mM MES/imidazole, pH 6.5, 20% PEG500 MME, 10% PEG20000
Matthews coefficient: 2.11
Solvent content (%): 41.62
Ligand: 4-[(3,4-dihydroisoquinolin-2(1H)-yl)methyl]phenol (O3M)
Ligand formula: C16 H17 N O
Ligand molecular weight: 239.312
Ligand SMILES: c1ccc2c(c1)CCN(C2)Cc3ccc(cc3)O
Ligand InChI: InChI=1S/C16H17NO/c18-16-7-5-13(6-8-16)11-17-10-9-14-3-1-2-4-15(14)12-17/h1-8,18H,9-12H2
Release date: 2020-11-11
PRMT5/MEP50 with compound 29 bound (PDB entry 7SES)
Macromolecule: Protein arginine N-methyltransferase 5
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1.320
Sequence length: 645 residues
Sequence: MDYKDDDDKAAMAVGGAGGSRVSSGRDLNCVPEIADTLGAVAKQGFDFLCMPVFHPRFKREFIQEPAKNRPGPQTRSDLLLSGRDWNTLIVGKLSPWIRPDSKVEKIRRNSEAAMLQELNFGAYLGLPAFLLPLNQEDNTNLARVLTNHIHTGHHSSMFWMRVPLVAPEDLRDDIIENAPTTHTEEYSGEEKTWMWWHNFRTLCDYSKRIAVALEIGADLPSNHVIDRWLGEPIKAAILPTSIFLTNKKGFPVLSKMHQRLIFRLLKLEVQFIITGTNHHSEKEFCSYLQYLEYLSQNRPPPNAYELFAKGYEDYLQSPLQPLMDNLESQTYEVFEKDPIKYSQYQQAIYKCLLDRVPEEEKDTNVQVLMVLGAGRGPLVNASLRAAKQADRRIKLYAVEKNPNAVVTLENWQFEEWGSQVTVVSSDMREWVAPEKADIIVSELLGSFADNELSPECLDGAQHFLKDDGVSIPGEYTSFLAPISSSKLYNEVRACREKDRDPEAQFEMPYVVRLHNFHQLSAPQPCFTFSHPNRDPMIDNNRYCTLEFPVEVNTVLHGFAGYFETVLYQDITLSIRPETHSPGMFSWFPILFPIKQPITVREGQTICVRFWRCSNSKKVWYEWAVTAPVCSAIHNPTGRSYTIGL
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.5
R work: 0.2098
R free: 0.2449
Average B factor: 63.48
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 291
Crystal growth procedure: 100 mM Sodium Citrate pH 5, 10% PEG 4K, 50 mM Sodium Acetate (pH 7)
Matthews coefficient: 2.9
Solvent content (%): 57.59
Ligand: (2P)-2-{4-[4-(aminomethyl)-1-oxo-1,2-dihydrophthalazin-6-yl]-1-methyl-1H-pyrazol-5-yl}naphthalene-1-carbonitrile (97X)
Ligand formula: C24 H18 N6 O
Ligand molecular weight: 406.439
Ligand SMILES: Cn1c(c(cn1)c2ccc3c(c2)C(=NNC3=O)CN)c4ccc5ccccc5c4C#N
Ligand InChI: InChI=1S/C24H18N6O/c1-30-23(17-8-6-14-4-2-3-5-16(14)20(17)11-25)21(13-27-30)15-7-9-18-19(10-15)22(12-26)28-29-24(18)31/h2-10,13H,12,26H2,1H3,(H,29,31)
Release date: 2022-01-26
Crystal structure of human Rab1b covalently bound to the GEF domain of DrrA/SidM from Legionella pneumophila in the presence of GDP (PDB entry 5O74)
Macromolecule: Multifunctional virulence effector protein DrrA
Type: Protein, polypeptide(L)
Source organism: Legionella pneumophila
EC number: 2.7.7
Sequence length: 197 residues
Sequence: GHMVTRIENLENAKKLWDNANSMLEKGNISGYLKAANELHKFMKEKNLKEDDLRPELSDKTISPKGYAILQSLWGAASDYSRAAATLTESTVEPGLVSAVNKMSAFFMDCKLSPNERATPDPDFKVGKSKILVGIMQFIKDVADPTSKIWMHNTKALMNHKIAAIQKLERSNNVNCETLESVLSSKGENLSEYLSYK
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.5
R work: 0.2286
R free: 0.266
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 293
Crystal growth procedure: 19% PEG 600, 100mM NaCitrate pH 5.5, protein concentration 22mg/ml
Matthews coefficient: 2.27
Solvent content (%): 45.73
Ligand: GUANOSINE-5'-DIPHOSPHATE (GDP)
Ligand formula: C10 H15 N5 O11 P2
Ligand molecular weight: 443.201
Ligand SMILES: c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
Ligand InChI: InChI=1S/C10H15N5O11P2/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(25-9)1-24-28(22,23)26-27(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1
Release date: 2017-10-11
DNA Polymerase Lambda, dCTP:At Mg2+ Product State Ternary Complex, 300 min (PDB entry 7M4F)
Macromolecule: DNA (5'-D(*CP*AP*GP*TP*AP*CP*C)-3')
Type: DNA, polydeoxyribonucleotide
Source organism: Homo sapiens
Sequence length: 7 residues
Sequence: CAGTACC
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.947
R work: 0.2075
R free: 0.2409
Average B factor: 56.0292
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 80-95mM BICINE pH 8.3, 0.3M Na-K Tartrate, 18-22.5% PolyPure PEG
Matthews coefficient: 2.84
Solvent content (%): 56.68
Ligand: SODIUM ION ()
Ligand formula: Na
Ligand molecular weight: 22.99
Ligand SMILES: [Na+]
Ligand InChI: InChI=1S/Na/q+1
Release date: 2022-07-06
Structure of Human MPS1 (TTK) covalently bound to RMS-07 inhibitor (PDB entry 7LQD)
Macromolecule: Dual specificity protein kinase TTK or monopolar spindle 1 kinase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.12.1
Sequence length: 313 residues
Sequence: MHHHHHHSSGVDLGTENLYFQSMSVKGRIYSILKQIGSGGSSKVFQVLNEKKQIYAIKYVNLEEADNQTLDSYRNEIAYLNKLQQHSDKIIRLYDYEITDQYIYMVMECGNIDLNSWLKKKKSIDPWERKSYWKNMLEAVHTIHQHGIVHSDLKPANFLIVDGMLKLIDFGIANQMQPDTTSVVKDSQVGTVNYMPPEAIKDMSSSRENGKSKSKISPKSDVWSLGCILYYMTYGKTPFQQIINQISKLHAIIDPNHEIEFPDIPEKDLQDVLKCCLKRDPKQRISIPELLAHPYVQIQTHPVNQMAKGTTEE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.95
R work: 0.1972
R free: 0.2462
Average B factor: 40.873
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 7.8
Crystallization temperature (K): 293
Crystal growth procedure: 0.05 M magnesium chloride hexahydrate, 0.05 M sodium citrate tribasic, 0.1 M Bis-Tris propane, pH 7.8, 22.5% PEG Smear High
Matthews coefficient: 2.84
Solvent content (%): 56.73
Ligand: ~{N}-(2,6-diethylphenyl)-2-[[4-(4-methylpiperazin-1-yl)-2-(propanoylamino)phenyl]amino]-5,6-dihydropyrimido[4,5-e]indolizine-7-carboxamide (YB4)
Ligand formula: C35 H42 N8 O2
Ligand molecular weight: 606.76
Ligand SMILES: CCc1cccc(c1NC(=O)c2ccn-3c2CCc4c3nc(nc4)Nc5ccc(cc5NC(=O)CC)N6CCN(CC6)C)CC
Ligand InChI: InChI=1S/C35H42N8O2/c1-5-23-9-8-10-24(6-2)32(23)39-34(45)27-15-16-43-30(27)14-11-25-22-36-35(40-33(25)43)38-28-13-12-26(21-29(28)37-31(44)7-3)42-19-17-41(4)18-20-42/h8-10,12-13,15-16,21-22H,5-7,11,14,17-20H2,1-4H3,(H,37,44)(H,39,45)(H,36,38,40)
Release date: 2022-02-16
XChem group deposition -- Crystal Structure of human ACVR1 in complex with FM010916a (PDB entry 5S76)
Macromolecule: Activin receptor type-1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.30
Sequence length: 301 residues
Sequence: SMQRTVARDITLLECVGKGRYGEVWRGSWQGENVAVKIFSSRDEKSWFRETELYNTVMLRHENILGFIASDMTSRHSSTQLWLITHYHEMGSLYDYLQLTTLDTVSCLRIVLSIASGLAHLHIEIFGTQGKPAIAHRDLKSKNILVKKNGQCCIADLGLAVMHSQSTNQLDVGNNPRVGTKRYMAPEVLDETIQVDCFDSYKRVDIWAFGLVLWEVARRMVSNGIVEDYKPPFYDVVPNDPSFEDMRKVVCVDQQRPNIPNRWFSDPTLTSLAKLMKECWYQNPSARLTALRIKKTLTKID
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.31
R work: 0.1548
R free: 0.1734
Average B factor: 16.749
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6
Crystallization temperature (K): 277
Crystal growth procedure: 0.1M citrate pH 6.0, 1.4M ammonium sulfate, 0.2M sodium/potassium tartrate
Matthews coefficient: 2.59
Solvent content (%): 52.55
Ligand: 4-methyl-3-[4-(1-methylpiperidin-4-yl)phenyl]-5-(3,4,5-trimethoxyphenyl)pyridine (LU8)
Ligand formula: C27 H32 N2 O3
Ligand molecular weight: 432.555
Ligand SMILES: Cc1c(cncc1c2cc(c(c(c2)OC)OC)OC)c3ccc(cc3)C4CCN(CC4)C
Ligand InChI: InChI=1S/C27H32N2O3/c1-18-23(21-8-6-19(7-9-21)20-10-12-29(2)13-11-20)16-28-17-24(18)22-14-25(30-3)27(32-5)26(15-22)31-4/h6-9,14-17,20H,10-13H2,1-5H3
Release date: 2021-06-23
Crystal structure of EGFR kinase domain in complex with a sulfonyl fluoride probe XO44 (PDB entry 5U8L)
Macromolecule: Epidermal growth factor receptor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 329 residues
Sequence: GSGEAPNQALLRILKETEFKKIKVLGSGAFGTVYKGLWIPEGEKVKIPVAIKELREATSPKANKEILDEAYVMASVDNPHVCRLLGICLTSTVQLIMQLMPFGCLLDYVREHKDNIGSQYLLNWCVQIAKGMNYLEDRRLVHRDLAARNVLVKTPQHVKITDFGRAKLLGAEEKEYHAEGGKVPIKWMALESILHRIYTHQSDVWSYGVTVWELMTFGSKPYDGIPASEISSILEKGERLPQPPICTIDVYMIMRKCWMIDADSRPKFRELIIEFSKMARDPQRYLVIQGDERMHLPSPTDSNFYRALMDEEDMDDVVDADEYLIPQQG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.6
R work: 0.189
R free: 0.202
Average B factor: 22.5
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277
Crystal growth procedure: Salt: 0.2 M Ammonium sulfate
Buffer: 0.1 M HEPES (pH 7.50)
Precipitant: 20.0 %w/v PEG 8000
Precipitant: 5.7 %v/v  iso-propanol
Matthews coefficient: 2.07
Solvent content (%): 40.71
Ligand: SULFATE ION (SO4)
Ligand formula: O4 S
Ligand molecular weight: 96.063
Ligand SMILES: [O-]S(=O)(=O)[O-]
Ligand InChI: InChI=1S/H2O4S/c1-5(2,3)4/h(H2,1,2,3,4)/p-2
Release date: 2017-01-25
Structure of the M4 muscarinic acetylcholine receptor (M4-mT4L) bound to tiotropium (PDB entry 5DSG)
Macromolecule: Muscarinic acetylcholine receptor M4,Endolysin,Endolysin,Muscarinic acetylcholine receptor M4
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.2.1.17
Sequence length: 422 residues
Sequence: GPSSHNRYETVEMVFIATVTGSLSLVTVVGNILVMLSIKVNRQLQTVNNYFLFSLACADLIIGAFSMNLYTVYIIKGYWPLGAVVCDLWLALDYVVSNASVMNLLIISFDRYFCVTKPLTYPARRTTKMAGLMIAAAWVLSFVLWAPAILFWQFVVGKRTVPDNQCFIQFLSNPAVTFGTAIAAFYLPVVIMTVLYIHISLASRSRVNIFEMLRIDEGGGSGGDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDAYQMAARERKVTRTIFAILLAFILTWTPYNVMVLVNTFCQSCIPDTVWSIGYWLCYVNSTINPACYALCNATFKKTFRHLLLCQYRNIGTARHHHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.6
R work: 0.2265
R free: 0.2403
Average B factor: 72.2251
Crystallization method: LIPIDIC CUBIC PHASE
Crystallization temperature (K): 293
Crystal growth procedure: Reconstituted in 10:1 monoolein:cholesterol mix. Precipitant solution: 20 - 40% PEG300, 100 mM MES, pH 5.5 - 7.5,  and 10 - 150 mM EDTA, pH 8.0
Matthews coefficient: 2.62
Solvent content (%): 53.02
Ligand: (1R,2R,4S,5S,7S)-7-{[hydroxy(dithiophen-2-yl)acetyl]oxy}-9,9-dimethyl-3-oxa-9-azoniatricyclo[3.3.1.0~2,4~]nonane (0HK)
Ligand formula: C19 H22 N O4 S2
Ligand molecular weight: 392.512
Ligand SMILES: C[N+]1(C2CC(CC1C3C2O3)OC(=O)C(c4cccs4)(c5cccs5)O)C
Ligand InChI: InChI=1S/C19H22NO4S2/c1-20(2)12-9-11(10-13(20)17-16(12)24-17)23-18(21)19(22,14-5-3-7-25-14)15-6-4-8-26-15/h3-8,11-13,16-17,22H,9-10H2,1-2H3/q+1/t11-,12-,13+,16-,17+
Release date: 2016-03-16
Native state mass spectrometry, surface plasmon resonance and X-ray crystallography correlate strongly as a fragment screening combination (PDB entry 5FNL)
Macromolecule: CARBONIC ANHYDRASE 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 260 residues
Sequence: MSHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHAFNVEFDDSQDKAVLKGGPLDGTYRLIQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDFGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTKGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLLECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.59
R work: 0.14805
R free: 0.19711
Average B factor: 14.423
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystal growth procedure: 15 MG/ML PROTEIN WITH 2.7 M AMMONIUM SULFATE, 100 MM TRIS PH 8.5 AT 8 C IN SITTING DROPS.
Matthews coefficient: 2.1
Solvent content (%): 41.4
Ligand: ZINC ION (ZN)
Ligand formula: Zn
Ligand molecular weight: 65.409
Ligand SMILES: [Zn+2]
Ligand InChI: InChI=1S/Zn/q+2
Release date: 2016-09-28
Structure of human DNA polymerase iota bound to template 1-methyl-deoxyadenosine crystallized in the presence of dCTP (PDB entry 5ULX)
Macromolecule: DNA (5'-D(*AP*GP*GP*AP*CP*CP*(DOC))-3')
Type: DNA, polydeoxyribonucleotide
Source organism: unidentified
Sequence length: 7 residues
Sequence: AGGACCC
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.96
R work: 0.216
R free: 0.239
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6
Crystallization temperature (K): 277
Crystal growth procedure: 100 mM MES, pH 6.0, 14 % PEG 5KMME, 0.4 M Ammonium Sulfate
Matthews coefficient: 2.67
Solvent content (%): 53.88
Ligand: CHLORIDE ION (CL)
Ligand formula: Cl
Ligand molecular weight: 35.453
Ligand SMILES: [Cl-]
Ligand InChI: InChI=1S/ClH/h1H/p-1
Release date: 2017-04-19
Crystal structure of BRAF kinase domain with PF-07284890 (PDB entry 9BFB)
Macromolecule: Serine/threonine-protein kinase B-raf
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 294 residues
Sequence: MGHHHHHHGLVPRGSDSSDDWEIPDGQITVGQRIGSGSFGTVYKGKWHGDVAVKMLNVTAPTPQQLQAFKNEVGVLRKTRHVNILLFMGYSTKPQLAIVTQWCEGSSLYHHLHIIETKFEMIKLIDIARQTAQGMDYLHAKSIIHRDLKSNNIFLHEDLTVKIGDFGLATVKSRWSGSHQFEQLSGSILWMAPEVIRMQDKNPYSFQSDVYAFGIVLYELMTGQLPYSNINNRDQIIAMVGAGALSPDLSKVRSNCPKAMKRLMAECLKKKRDERPLFPQILASIELLARSLPK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.92
R work: 0.1639
R free: 0.1888
Average B factor: 29.06
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 7
Crystallization temperature (K): 293
Crystal growth procedure: 100mM Hepes pH 7.0, 15 % PEG 8K, 10% Tacsimate
Matthews coefficient: 2.87
Solvent content (%): 57.16
Ligand: DI(HYDROXYETHYL)ETHER (PEG)
Ligand formula: C4 H10 O3
Ligand molecular weight: 106.12
Ligand SMILES: C(COCCO)O
Ligand InChI: InChI=1S/C4H10O3/c5-1-3-7-4-2-6/h5-6H,1-4H2
Release date: 2024-08-14
PanDDA analysis group deposition -- Crystal structure of PTP1B in complex with compound_FMOOA000505a (PDB entry 5QFD)
Macromolecule: Tyrosine-protein phosphatase non-receptor type 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 321 residues
Sequence: MEMEKEFEQIDKSGSWAAIYQDIRHEASDFPSRVAKLPKNKNRNRYRDVSPFDHSRIKLHQEDNDYINASLIKMEEAQRSYILTQGPLPNTVGHFWEMVWEQKSRGVVMLNRVMEKGSLKCAQYWPQKEEKEMIFEDTNLKLTLISEDIKSYYTVRQLELENLTTQETREILHFHYTTWPDFGVPESPASFLNFLFKVRESGSLSPEHGPVVVHCSAGIGRSGTFCLADTCLLLMDKRKDPSSVDIKKVLLEMRKFRMGLIQTADQLRFSYLAVIEGAKFIMGDSSVQDQWKELSHEDLEPPPEHIPPPPRPPKRILEPHN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.693
R work: 0.2029
R free: 0.2325
Average B factor: 34.3339
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: well solution: 0.3 M magnesium acetate, 0.1 M HEPES pH 7.5, 0.1% beta-mercaptoethanol, 13-14% PEG 8000, 2% ethanol
Matthews coefficient: 3.33
Solvent content (%): 63.12
Ligand: (6R)-5,6-dihydro-1H-2,6-methano-1lambda~6~-1lambda~6~,2,5-benzothiadiazocine-1,1,4(3H)-trione (JN1)
Ligand formula: C10 H10 N2 O3 S
Ligand molecular weight: 238.263
Ligand SMILES: c1ccc2c(c1)C3CN(S2(=O)=O)CC(=O)N3
Ligand InChI: InChI=1S/C10H10N2O3S/c13-10-6-12-5-8(11-10)7-3-1-2-4-9(7)16(12,14)15/h1-4,8H,5-6H2,(H,11,13)/t8-/m0/s1
Release date: 2018-10-10
Crystal structure of phosphorylated pT220 Casein Kinase I delta (CK1d), conformation 2 and 3 (PDB entry 7P7G)
Macromolecule: Casein kinase I isoform delta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 296 residues
Sequence: SMMELRVGNRYRLGRKIGSGSFGDIYLGTDIAAGEEVAIKLECVKTKHPQLHIESKIYKMMQGGVGIPTIRWCGAEGDYNVMVMELLGPSLEDLFNFCSRKFSLKTVLLLADQMISRIEYIHSKNFIHRDVKPDNFLMGLGKKGNLVYIIDFGLAKKYRDARTHQHIPYRENKNLTGTARYASINTHLGIEQSRRDDLESLGYVLMYFNLGSLPWQGLKAATKRQKYERISEKKMSTPIEVLCKGYPSEFATYLNFCRSLRFDDKPDYSYLRQLFRNLFHRQGFSYDYVFDWNMLK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.7
R work: 0.1708
R free: 0.2079
Average B factor: 26.34
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277.15
Crystal growth procedure: 12% PEG 3350 and 0.1 M ammonium citrate
Matthews coefficient: 2.04
Solvent content (%): 39.81
Ligand: CITRIC ACID (CIT)
Ligand formula: C6 H8 O7
Ligand molecular weight: 192.124
Ligand SMILES: C(C(=O)O)C(CC(=O)O)(C(=O)O)O
Ligand InChI: InChI=1S/C6H8O7/c7-3(8)1-6(13,5(11)12)2-4(9)10/h13H,1-2H2,(H,7,8)(H,9,10)(H,11,12)
Release date: 2022-04-13
JAK2 in complex with 4-{8-methoxy-2-[(1-methyl-1H-pyrazol-4-yl)amino]quinazolin-6-yl}phenol (PDB entry 7Q7I)
Macromolecule: Tyrosine-protein kinase JAK2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 316 residues
Sequence: MHHHHHHDYKDDDDKENLYFQGRDPTQFEERHLKFLQQLGKGNFGSVEMCRYDPLQDNTGEVVAVKKLQHSTEEHLRDFEREIEILKSLQHDNIVKYKGVCYSAGRRNLKLIMEYLPYGSLRDYLQKHKERIDHIKLLQYTSQICKGMEYLGTKRYIHRDLATRNILVENENRVKIGDFGLTKVLPQDKEYYKVKEPGESPIFWYAPESLTESKFSVASDVWSFGVVLYELFTYIEKSKSPPAEFMRMIGNDKQGQSIVTHLIELLKNNGRLPRPDGCPDEIYMIMTECWNNNVNQRPSFRDLALRVDQIRDNMAG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.78
R work: 0.187
R free: 0.222
Average B factor: 30.96
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 1.46-1.60 M trisodium citrate (untitrated)
Matthews coefficient: 2.17
Solvent content (%): 43.29
Ligand: 4-[8-methoxy-2-[(1-methylpyrazol-4-yl)amino]quinazolin-6-yl]phenol (9I8)
Ligand formula: C19 H17 N5 O2
Ligand molecular weight: 347.371
Ligand SMILES: Cn1cc(cn1)Nc2ncc3cc(cc(c3n2)OC)c4ccc(cc4)O
Ligand InChI: InChI=1S/C19H17N5O2/c1-24-11-15(10-21-24)22-19-20-9-14-7-13(8-17(26-2)18(14)23-19)12-3-5-16(25)6-4-12/h3-11,25H,1-2H3,(H,20,22,23)
Release date: 2022-02-02
Crystal structure of human UBE2A (RAD6A) (PDB entry 6CYO)
Macromolecule: Ubiquitin-conjugating enzyme E2 A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2.23
Sequence length: 155 residues
Sequence: GSHMSTPARRRLMRDFKRLQEDPPAGVSGAPSENNIMVWNAVIFGPEGTPFEDGTFKLTIEFTEEYPNKPPTVRFVSKMFHPNVYADGSICLDILQNRWSPTYDVSSILTSIQSLLDEPNPNSPANSQAAQLYQENKREYEKRVSAIVEQSWRDC
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.85
R work: 0.204
R free: 0.214
Average B factor: 46.4198
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 50 mM di-Sodium succinate pH 7.0 and 12-14% PEG 3350
Matthews coefficient: 2.46
Solvent content (%): 49.95
Release date: 2018-12-12
DDR1, 2-[4-bromo-2-oxo-1'-(1H-pyrazolo[4,3-b]pyridine-5-carbonyl)spiro[indole-3,4'-piperidine]-1-yl]-N-(2,2,2-trifluoroethyl)acetamide, 1.291A, P212121, Rfree=17.4% (PDB entry 6FEX)
Macromolecule: Epithelial discoidin domain-containing receptor 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 321 residues
Sequence: PGAVGDGPPRVDFPRSRLRFKEKLGEGQFGEVHLCEVDSPQDLVSLDFPLNVRKGHPLLVAVKILRPDATKNARNDFLKEVKIMSRLKDPNIIRLLGVCVQDDPLCMITDYMENGDLNQFLSAHQLEDKAAEGAPGDPTISYPMLLHVAAQIASGMRYLATLNFVHRDLATRNCLVGENFTIKIADFGMSRNLYAGDYYRVQGRAVLPIRWMAWECILMGKFTTASDVWAFGVTLWEVLMLCRAQPFGQLTDEQVIENAGEFFRDQGRQVYLSRPPACPQGLYELMLRCWSRESEQRPPFSQLHRFLAEDALNTVHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.291
R work: 0.1374
R free: 0.1737
Average B factor: 20.8042
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 293
Crystal growth procedure: 11.3 mg/mL protein in 20mM HEPES/NaOH pH7.5, 5mM DTT, 5% glycerol, 0.1M NaCl mixed 1.3:1 with 90mM MES/NaOH pH6.5, 0.18M potassium iodide, 0.2M Li2SO4, 22.5% PEG 4K
Matthews coefficient: 2.09
Solvent content (%): 41.11
Ligand: 2-[4-bromanyl-2-oxidanylidene-1'-(1~{H}-pyrazolo[4,3-b]pyridin-5-ylcarbonyl)spiro[indole-3,4'-piperidine]-1-yl]-~{N}-[2,2,2-tris(fluoranyl)ethyl]ethanamide (D6Z)
Ligand formula: C23 H20 Br F3 N6 O3
Ligand molecular weight: 565.343
Ligand SMILES: c1cc2c(c(c1)Br)C3(CCN(CC3)C(=O)c4ccc5c(n4)cn[nH]5)C(=O)N2CC(=O)NCC(F)(F)F
Ligand InChI: InChI=1S/C23H20BrF3N6O3/c24-13-2-1-3-17-19(13)22(21(36)33(17)11-18(34)28-12-23(25,26)27)6-8-32(9-7-22)20(35)15-5-4-14-16(30-15)10-29-31-14/h1-5,10H,6-9,11-12H2,(H,28,34)(H,29,31)
Release date: 2018-11-28
FGFR1 kinase domain with a dual-warhead covalent inhibitor CXF-007 (PDB entry 8XLO)
Macromolecule: Fibroblast growth factor receptor 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 310 residues
Sequence: GPAGVSEYELPEDPRWELPRDRLVLGKPLGEGCFGQVVLAEAIGLDKDKPNRVTKVAVKMLKSDATEKDLSDLISEMEMMKMIGKHKNIINLLGACTQDGPLYVIVEYASKGNLREYLQARRPPGLEYSYNPSHNPEEQLSSKDLVSCAYQVARGMEYLASKKCIHRDLAARNVLVTEDNVMKIADFGLARDIHHIDYYKKTTNGRLPVKWMAPEALFDRIYTHQSDVWSFGVLLWEIFTLGGSPYPGVPVEELFKLLKEGHRMDKPSNCTNELYMMMRDCWHAVPSQRPTFKQLVEDLDRIVALTSNQE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.36
R work: 0.2079
R free: 0.2545
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 277.15
Crystal growth procedure: 18% (w/v) PEG 8000, 0.2 M Li2SO4, and 0.1 M MES, pH 6.5
Matthews coefficient: 2.7
Solvent content (%): 54.45
Ligand: CXF007 (A1LVQ)
Ligand formula: C34 H33 N7 O5
Ligand molecular weight: 619.67
Ligand SMILES: COc1cc(cc(c1)OC)N2Cc3cnc(nc3N(C2=O)CCc4ccc(cc4)NC(=O)C=C)Nc5ccccc5NC(=O)C=C
Ligand InChI: InChI=1S/C34H33N7O5/c1-5-30(42)36-24-13-11-22(12-14-24)15-16-40-32-23(21-41(34(40)44)25-17-26(45-3)19-27(18-25)46-4)20-35-33(39-32)38-29-10-8-7-9-28(29)37-31(43)6-2/h5-14,17-20H,1-2,15-16,21H2,3-4H3,(H,36,42)(H,37,43)(H,35,38,39)
Release date: 2024-03-27
Crystal structure of c-Met in complex with AMG 337 (PDB entry 5EYD)
Macromolecule: Hepatocyte growth factor receptor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 309 residues
Sequence: QNTVHIDLSALNPELVQAVQHVVIGPSSLIVHFNEVIGRGHFGCVYHGTLLDNDGKKIHCAVKSLNRITDIGEVSQFLTEGIIMKDFSHPNVLSLLGICLRSEGSPLVVLPYMKHGDLRNFIRNETHNPTVKDLIGFGLQVAKGMKYLASKKFVHRDLAARNCMLDEKFTVKVADFGLARDMYDKEYYSVHNKTGAKLPVKWMALESLQTQKFTTKSDVWSFGVLLWELMTRGAPPYPDVNTFDITVYLLQGRRLLQPEYCPDPLYEVMLKCWHPKAEMRPSFSELVSRISAIFSTFIGEHYVHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.85
R work: 0.1933
R free: 0.2489
Average B factor: 29.2
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.8
Crystallization temperature (K): 293
Crystal growth procedure: 12% PEG 4000, 3% (v/v) ethanol, 6% (v/v) isopropanol, 40 mM beta-mercaptoethanol, 100 mM HEPES (pH 7.8)
Matthews coefficient: 2.04
Solvent content (%): 39.68
Ligand: 6-[(1~{R})-1-[8-fluoranyl-6-(1-methylpyrazol-4-yl)-[1,2,4]triazolo[4,3-a]pyridin-3-yl]ethyl]-3-(2-methoxyethoxy)-1,6-naphthyridin-5-one (5T1)
Ligand formula: C23 H22 F N7 O3
Ligand molecular weight: 463.464
Ligand SMILES: CC(c1nnc2n1cc(cc2F)c3cnn(c3)C)N4C=Cc5c(cc(cn5)OCCOC)C4=O
Ligand InChI: InChI=1S/C23H22FN7O3/c1-14(30-5-4-20-18(23(30)32)9-17(11-25-20)34-7-6-33-3)21-27-28-22-19(24)8-15(13-31(21)22)16-10-26-29(2)12-16/h4-5,8-14H,6-7H2,1-3H3/t14-/m1/s1
Release date: 2016-02-10