satarupa22/MacromolecularLigandDB huggingface dataset:
Crystal Structure Analysis of PIN1 (PDB entry 6O34)
Macromolecule: Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 5.2.1.8
Sequence length: 163 residues
Sequence: MADEEKLPPGWEKRMSRSSGRVYYFNHITNASQWRRPSGNSSSGGKNGQGEPARVRCSHLLVKHSQSRRPSSWRQEQITRTQEEALELINGYIQKIKSGEEDFESLASQFSDCSSAKARGDLGAFSRGQMQKPFEDASFALRTGEMSGPVFTDSGIHIILRTE
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.57
R work: 0.2033
R free: 0.2513
Average B factor: 38.6968
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 298
Crystal growth procedure: 100 mM HEPES, pH 7.2, 3.0 M ammonium sulfate
Matthews coefficient: 2.25
Solvent content (%): 45.32
Ligand: NONAETHYLENE GLYCOL (2PE)
Ligand formula: C18 H38 O10
Ligand molecular weight: 414.488
Ligand SMILES: C(COCCOCCOCCOCCOCCOCCOCCOCCO)O
Ligand InChI: InChI=1S/C18H38O10/c19-1-3-21-5-7-23-9-11-25-13-15-27-17-18-28-16-14-26-12-10-24-8-6-22-4-2-20/h19-20H,1-18H2
Release date: 2020-02-26
PanDDA analysis group deposition -- Crystal Structure of Kalirin/Rac1 in complex with MolPort-009-565-325 (PDB entry 5QQM)
Macromolecule: Ras-related C3 botulinum toxin substrate 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 178 residues
Sequence: SMQAIKCVVVGDGAVGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPVNLGLWDTAGQEDYDRLRPLSYPQTDVFLICFSLVSPASFENVRAKWYPEVRHHCPNTPIILVGTKLDLRDDKDTIEKLKEKKLTPITYPQGLAMAKEIGAVKYLECSALTQRGLKTVFDEAIRAVL
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.02
R work: 0.2113
R free: 0.2731
Average B factor: 37.948
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 293.15
Crystal growth procedure: 0.1M bis-tris pH 5.5 24% PEG 3350
Matthews coefficient: 2.35
Solvent content (%): 47.64
Ligand: N-(1-benzyl-1H-pyrazol-4-yl)-N'-(5-methyl-1,2-oxazol-3-yl)urea (N74)
Ligand formula: C15 H15 N5 O2
Ligand molecular weight: 297.312
Ligand SMILES: Cc1cc(no1)NC(=O)Nc2cnn(c2)Cc3ccccc3
Ligand InChI: InChI=1S/C15H15N5O2/c1-11-7-14(19-22-11)18-15(21)17-13-8-16-20(10-13)9-12-5-3-2-4-6-12/h2-8,10H,9H2,1H3,(H2,17,18,19,21)
Release date: 2019-12-18
Structure of USP5 zinc-finger ubiquitin binding domain co-crystallized with (2-fluoro-4-((4-phenylpiperidin-1-yl)sulfonyl)benzoyl)glycine (PDB entry 7MS6)
Macromolecule: Ubiquitin carboxyl-terminal hydrolase 5
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.19.12
Sequence length: 121 residues
Sequence: GGEVRQVSKHAFSLKQLDNPARIPPCGWKCSKCDMRENLWLNLTDGSILCGRRYFDGSGGNNHAVEHYRETGYPLAVKLGTITPDGADVYSYDEDDMVLDPSLAEHLSHFGIDMLKMQKTD
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.55
R work: 0.1478
R free: 0.1638
Average B factor: 12.457
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 298
Crystal growth procedure: 2 M ammonium sulfate, 0.2 M sodium acetate, 0.1 M HEPES pH 7.5, 5% MPD
Matthews coefficient: 2.87
Solvent content (%): 57.11
Ligand: N-[2-fluoro-4-(4-phenylpiperidine-1-sulfonyl)benzoyl]glycine (ZPV)
Ligand formula: C20 H21 F N2 O5 S
Ligand molecular weight: 420.455
Ligand SMILES: c1ccc(cc1)C2CCN(CC2)S(=O)(=O)c3ccc(c(c3)F)C(=O)NCC(=O)O
Ligand InChI: InChI=1S/C20H21FN2O5S/c21-18-12-16(6-7-17(18)20(26)22-13-19(24)25)29(27,28)23-10-8-15(9-11-23)14-4-2-1-3-5-14/h1-7,12,15H,8-11,13H2,(H,22,26)(H,24,25)
Release date: 2021-06-09
PanDDA analysis group deposition -- Crystal structure of PTP1B in complex with compound_FMOOA000487a (PDB entry 5QFU)
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): 1.613
R work: 0.1936
R free: 0.2146
Average B factor: 40.1037
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 (%): 63.08
Ligand: (1R,4R,5R,6R)-4-methoxy-2-(methylsulfonyl)-2-azabicyclo[3.3.1]nonan-6-ol (JO7)
Ligand formula: C10 H19 N O4 S
Ligand molecular weight: 249.327
Ligand SMILES: COC1CN(C2CCC(C1C2)O)S(=O)(=O)C
Ligand InChI: InChI=1S/C10H19NO4S/c1-15-10-6-11(16(2,13)14)7-3-4-9(12)8(10)5-7/h7-10,12H,3-6H2,1-2H3/t7-,8-,9-,10+/m1/s1
Release date: 2018-10-10
Structure of the stapled peptide YS-01 bound to MDM2 (PDB entry 4UE1)
Macromolecule: E3 UBIQUITIN-PROTEIN LIGASE MDM2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 6.3.2
Sequence length: 114 residues
Sequence: GPLGSSQIPASEQETLVRPKPLLLKLLKSVGAQKDTYTMKEVLFYLGQYIMTKRLYDAAQQHIVYCSNDLLGDLFGVPSFSVKEHRKIYTMIYRNLVVVNQQESSDSGTSVSEN
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.45
R work: 0.14048
R free: 0.18367
Average B factor: 21.362
Crystallization pH: 4.2
Crystal growth procedure: 0.1 M SODIUM CITRATE PH 4.2, 0.2 M SODIUM CHLORIDE AND 20 % PEG8000
Matthews coefficient: 2.8
Solvent content (%): 56
Release date: 2016-01-13
Crystal structure of PRMT5:MEP50 in complex with MTA and oxamide compound 1 (PDB entry 8VET)
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): 2.63
R work: 0.22426
R free: 0.27691
Average B factor: 82.204
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 6.5
Crystallization temperature (K): 291
Crystal growth procedure: 10% PEG 4000, 0.2M magnesium chloride, 0.1M MES (pH 6.5)
Matthews coefficient: 2.83
Solvent content (%): 56.57
Ligand: 5'-DEOXY-5'-METHYLTHIOADENOSINE (MTA)
Ligand formula: C11 H15 N5 O3 S
Ligand molecular weight: 297.334
Ligand SMILES: CSCC1C(C(C(O1)n2cnc3c2ncnc3N)O)O
Ligand InChI: InChI=1S/C11H15N5O3S/c1-20-2-5-7(17)8(18)11(19-5)16-4-15-6-9(12)13-3-14-10(6)16/h3-5,7-8,11,17-18H,2H2,1H3,(H2,12,13,14)/t5-,7-,8-,11-/m1/s1
Release date: 2024-04-24
Rio2 structure (PDB entry 6FDO)
Macromolecule: Serine/threonine-protein kinase RIO2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 353 residues
Sequence: MGKVNVAKLRYMSRDDFRVLTAVEMGMKNHEIVPGSLIASIASLKHGGCNKVLRELVKHKLIAWERTKTVQGYRLTNAGYDYLALKTLSSRQVVESVGNQMGVGKESDIYIVANEEGQQFALKLHRLGRTSFRNLKNKRDYHKHRHNVSWLYLSRLSAMKEFAYMKALYERKFPVPKPIDYNRHAVVMELINGYPLCQIHHVEDPASVYDEAMELIVKLANHGLIHGDFNEFNLILDESDHITMIDFPQMVSTSHPNAEWYFDRDVKCIKDFFMKRFSYESELFPTFKDIRREDTLDVEVSASGYTKEMQADDELLHPLGPDDKNIETKEGSEFSFSDGEVAEKAEVYGSENE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.6
R work: 0.195
R free: 0.25
Average B factor: 81.33
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 298
Crystal growth procedure: Morpheus D2
Matthews coefficient: 2.52
Solvent content (%): 51.27
Release date: 2019-01-30
Human dihydroorotate dehydrogenase bound to 4-quinoline carboxylic acid inhibitor 43 (PDB entry 6CJF)
Macromolecule: Dihydroorotate dehydrogenase (quinone), mitochondrial
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.3.5.2
Sequence length: 374 residues
Sequence: GDERFYAEHLMPTLQGLLDPESAHRLAVRFTSLGLLPRARFQDSDMLEVRVLGHKFRNPVGIAAGFDKHGEAVDGLYKMGFGFVEIGSVTPKPQEGNPRPRVFRLPEDQAVINRYGFNSHGLSVVEHRLRARQQKQAKLTEDGLPLGVNLGKNKTSVDAAEDYAEGVRVLGPLADYLVVNVSSPNTAGLRSLQGKAELRRLLTKVLQERDGLRRVHRPAVLVKIAPDLTSQDKEDIASVVKELGIDGLIVTNTTVSRPAGLQGALRSETGGLSGKPLRDLSTQTIREMYALTQGRVPIIGVGGVSSGQDALEKIRAGASLVQLYTALTFWGPPVVGKVKRELEALLKEQGFGGVTDAIGADHRRLEAGHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.63
R work: 0.1632
R free: 0.1888
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 1.72 M ammonium sulfate, 1.4 M sodium chloride, 0.1 M sodium acetate pH 5.3, 10 mM DTT
Matthews coefficient: 2.01
Solvent content (%): 38.75
Ligand: FLAVIN MONONUCLEOTIDE (FMN)
Ligand formula: C17 H21 N4 O9 P
Ligand molecular weight: 456.344
Ligand SMILES: Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)CC(C(C(COP(=O)(O)O)O)O)O
Ligand InChI: InChI=1S/C17H21N4O9P/c1-7-3-9-10(4-8(7)2)21(15-13(18-9)16(25)20-17(26)19-15)5-11(22)14(24)12(23)6-30-31(27,28)29/h3-4,11-12,14,22-24H,5-6H2,1-2H3,(H,20,25,26)(H2,27,28,29)/t11-,12+,14-/m0/s1
Release date: 2018-05-23
Crystal structure of human DCAF1 WD40 repeats (Q1250L) in complex with compound 4 (PDB entry 8OG9)
Macromolecule: DDB1- and CUL4-associated factor 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 367 residues
Sequence: GGGREPKQRRQAPINFTSRLNRRASFPKYGGVDGGCFDRHLIFSRFRPISVFREANEDESGFTCCAFSARERFLMLGTCTGQLKLYNVFSGQEEASYNCHNSAITHLEPSRDGSLLLTSATWSQPLSALWGMKSVFDMKHSFTEDHYVEFSKHSQDRVIGTKGDIAHIYDIQTGNKLLTLFNPDLANNYKRNCATFNPTDDLVLNDGVLWDVRSALAIHKFDKFNMNISGVFHPNGLEVIINTEIWDLRTFHLLHTVPALDQCRVVFNHTGTVMYGAMLQADDEDDLMEERMKSPFGSSFRTFNATDYKPIATIDVKRNIFDLCTDTKDCYLAVIENQGSMDALNMDTVCRLYEVGRQRLAEDEDEE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.945
R work: 0.1905
R free: 0.2404
Average B factor: 57.668
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M MES pH6.5, 2.13M Lithium acetate
Matthews coefficient: 2.83
Solvent content (%): 56.49
Ligand: 5-[1-(4-chlorophenyl)cyclopropyl]imidazo[2,1-a]isoquinoline (VM3)
Ligand formula: C20 H15 Cl N2
Ligand molecular weight: 318.8
Ligand SMILES: c1ccc2c(c1)cc(n3c2ncc3)C4(CC4)c5ccc(cc5)Cl
Ligand InChI: InChI=1S/C20H15ClN2/c21-16-7-5-15(6-8-16)20(9-10-20)18-13-14-3-1-2-4-17(14)19-22-11-12-23(18)19/h1-8,11-13H,9-10H2
Release date: 2023-06-14
The Crystal Structure of LIMK2a from Biortus (PDB entry 8WSW)
Macromolecule: LIM domain kinase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 303 residues
Sequence: DLIHGEVLGKGFFGQAIKVTHKATGKVMVMKELIRCDEETQKTFLTEVKVMRSLDHPNVLKFIGVLYKDKKLNLLTEYIEGGTLKDFLRSMDPFPWQQKVRFAKGIASGMAYLHSMCIIHRDLNSHNCLIKLDKTVVVADFGLSRLIVEERKRAPMEKATTKKRTLRKNDRKKRYTVVGNPYWMAPEMLNGKSYDETVDIFSFGIVLCEIIGQVYADPDCLPRTLDFGLNVKLFWEKFVPTDCPPAFFPLAAICCRLEPESRPAFSKLEDSFEALSLYLGELGIPLPAELEELDHTVSMQYGL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.5
R work: 0.2093
R free: 0.2563
Average B factor: 59.277
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 0.1M HEPES ,7.3,10% w/vPEG 8000, 8%v/v Ethylene glycol
Matthews coefficient: 2.86
Solvent content (%): 57.03
Ligand: ~{N}-[5-[2-[2,6-bis(chloranyl)phenyl]-5-[bis(fluoranyl)methyl]pyrazol-3-yl]-1,3-thiazol-2-yl]-2-methyl-propanamide (LH0)
Ligand formula: C17 H14 Cl2 F2 N4 O S
Ligand molecular weight: 431.287
Ligand SMILES: CC(C)C(=O)Nc1ncc(s1)c2cc(nn2c3c(cccc3Cl)Cl)C(F)F
Ligand InChI: InChI=1S/C17H14Cl2F2N4OS/c1-8(2)16(26)23-17-22-7-13(27-17)12-6-11(15(20)21)24-25(12)14-9(18)4-3-5-10(14)19/h3-8,15H,1-2H3,(H,22,23,26)
Release date: 2023-11-15
Crystal structure of human DNA polymerase eta incorporating 5F-dUTP across dA (PDB entry 8GKR)
Macromolecule: DNA polymerase eta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 432 residues
Sequence: MATGQDRVVALVDMDCFFVQVEQRQNPHLRNKPCAVVQYKSWKGGGIIAVSYEARAFGVTRSMWADDAKKLCPDLLLAQVRESRGKANLTKYREASVEVMEIMSRFAVIERASIDEAYVDLTSAVQERLQKLQGQPISADLLPSTYIEGLPQGPTTAEETVQKEGMRKQGLFQWLDSLQIDNLTSPDLQLTVGAVIVEEMRAAIERETGFQCSAGISHNKVLAKLACGLNKPNRQTLVSHGSVPQLFSQMPIRKIRSLGGKLGASVIEILGIEYMGELTQFTESQLQSHFGEKNGSWLYAMCRGIEHDPVKPRQLPKTIGCSKNFPGKTALATREQVQWWLLQLAQELEERLTKDRNDNDRVATQLVVSIRVQGDKRLSSLRRCCALTRYDAHKMSHDAFTVIKNCNTSGIQTEWSPPLTMLFLCATKFSAS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.784
R work: 0.1997
R free: 0.2815
Average B factor: 53.97
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 100 mM MES, pH 6.5, 20% PEG2000 MME, 5 mM calcium chloride
Matthews coefficient: 2.06
Solvent content (%): 40.3
Ligand: 2'-deoxy-5-fluorouridine 5'-(tetrahydrogen triphosphate) (B7P)
Ligand formula: C9 H14 F N2 O14 P3
Ligand molecular weight: 486.132
Ligand SMILES: C1C(C(OC1N2C=C(C(=O)NC2=O)F)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O
Ligand InChI: InChI=1S/C9H14FN2O14P3/c10-4-2-12(9(15)11-8(4)14)7-1-5(13)6(24-7)3-23-28(19,20)26-29(21,22)25-27(16,17)18/h2,5-7,13H,1,3H2,(H,19,20)(H,21,22)(H,11,14,15)(H2,16,17,18)/t5-,6+,7+/m0/s1
Release date: 2023-09-20
Human Neutrophil Elastase in-complex with Ecotin Peptide (PDB entry 7WHU)
Macromolecule: Neutrophil elastase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.37
Sequence length: 267 residues
Sequence: MTLGRRLACLFLACVLPALLLGGTALASEIVGGRRARPHAWPFMVSLQLRGGHFCGATLIAPNFVMSAAHCVANVNVRAVRVVLGAHNLSRREPTRQVFAVQRIFENGYDPVNLLNDIVILQLNGSATINANVQVAQLPAQGRRLGNGVQCLAMGWGLLGRNRGIASVLQELNVTVVTSLCRRSNVCTLVRGRQAGVCFGDSGSPLVCNGLIHGIASFVRGGCASGLYPDAFAPVAQFVNWIDSIIQRSEDNPCPHPRDPDPASRTH
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.89
R work: 0.2523
R free: 0.3058
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 297
Crystal growth procedure: 0.2 M Ammonium sulfate, 0.1 M BIS-TRIS pH 5.5 and 25% w/v Polyethylene glycol 3350 (PEG3350)
Matthews coefficient: 2.24
Solvent content (%): 45.12
Ligand: GLYCEROL (GOL)
Ligand formula: C3 H8 O3
Ligand molecular weight: 92.094
Ligand SMILES: C(C(CO)O)O
Ligand InChI: InChI=1S/C3H8O3/c4-1-3(6)2-5/h3-6H,1-2H2
Release date: 2022-07-06
Crystal structure of RhoA protein with covalent inhibitor DC-Rhoin (PDB entry 6KX3)
Macromolecule: Transforming protein RhoA
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.5.2
Sequence length: 181 residues
Sequence: MAAIRKKLVIVGDGAVGKTSLLIVFSKDQFPEVYVPTVFENYVADIEVDGKQVELALWDTAGQEDYDRLRPLSYPDTDVILMVFSIDSPDSLENIPEKWTPEVKHFCPNVPIILVGNKKDLRNDEHTRRELAKMKQEPVKPEEGRDMANRIGAFGYMETSAKTKDGVREVFEMATRAALQA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.981
R work: 0.2207
R free: 0.2677
Average B factor: 41.2361
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 4.5
Crystallization temperature (K): 289
Crystal growth procedure: 10 mg/mL mutant, 0.2M NaCl, 0.1M acetate Na (pH 4.5), 1.26M ammonium sulfate
Matthews coefficient: 2.88
Solvent content (%): 57.22
Ligand: prop-2-enyl (3R)-1,1-bis(oxidanylidene)-2,3-dihydro-1-benzothiophene-3-carboxylate (8ZO)
Ligand formula: C12 H12 O4 S
Ligand molecular weight: 252.286
Ligand SMILES: C=CCOC(=O)C1CS(=O)(=O)c2c1cccc2
Ligand InChI: InChI=1S/C12H12O4S/c1-2-7-16-12(13)10-8-17(14,15)11-6-4-3-5-9(10)11/h2-6,10H,1,7-8H2/t10-/m1/s1
Release date: 2020-08-19
Human PARP-1 bound to NAD+ analog benzamide adenine dinucleotide (BAD) (PDB entry 6BHV)
Macromolecule: Poly [ADP-ribose] polymerase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.4.2.30
Sequence length: 271 residues
Sequence: MGSSHHHHHHSSGLVPRGSHMTKSKLPKPVQDLIKMIFGSGSGSGGDPIDVNYEKLKTDIKVVDRDSEEAEIIRKYVKNTHATTHNAYDLEVIDIFKIEREGECQRYKPFKQLHNRRLLWHGSRTTNFAGILSQGLRIAPPEAPVTGYMFGKGIYFADMVSKSANYCHTSQGDPIGLILLGEVALGNMYELKHASHISKLPKGKHSVKGLGKTTPDPSANISLDGVDVPLGTGISSGVNDTSLLYNEYIVYDIAQVNLKYLLKLKFNFKTS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.3
R work: 0.19771
R free: 0.22233
Average B factor: 74.854
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: PARP-1 CATdeltaHD (30 mg/ml) was crystallized in the presence of 1.6 mM BAD in 24 to 29% PEG 3350, 0.2 M NaCl, 0.1 M Bis-Tris pH 5.5
Matthews coefficient: 2.15
Solvent content (%): 42.72
Ligand: [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl [(2R,3S,4R,5S)-5-(3-carbamoylphenyl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate (non-preferred name) (DQV)
Ligand formula: C22 H28 N6 O14 P2
Ligand molecular weight: 662.437
Ligand SMILES: c1cc(cc(c1)C(=O)N)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)O)O)O)O
Ligand InChI: InChI=1S/C22H28N6O14P2/c23-19-13-21(26-7-25-19)28(8-27-13)22-17(32)15(30)12(41-22)6-39-44(36,37)42-43(34,35)38-5-11-14(29)16(31)18(40-11)9-2-1-3-10(4-9)20(24)33/h1-4,7-8,11-12,14-18,22,29-32H,5-6H2,(H2,24,33)(H,34,35)(H,36,37)(H2,23,25,26)/t11-,12-,14-,15-,16-,17-,18+,22-/m1/s1
Release date: 2018-02-28
X-ray structure of the complex between human alpha thrombin and a thrombin binding aptamer variant (TBA-3Leu), which contains leucyl amide in the side chain of Thy3 at N3. (PDB entry 6Z8X)
Macromolecule: Prothrombin
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.5
Sequence length: 36 residues
Sequence: TFGSGEADCGLRPLFEKKSLEDKTERELLESYIDGR
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.53
R work: 0.2448
R free: 0.2915
Average B factor: 69.54
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.6
Crystallization temperature (K): 293
Crystal growth procedure: 18% v/v 2-propanol, 18% w/v PEG 4000, 100 mM tri-sodium citrate, pH 5.6
Matthews coefficient: 3.88
Solvent content (%): 68.3
Ligand: D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide (0G6)
Ligand formula: C21 H34 Cl N6 O3
Ligand molecular weight: 453.986
Ligand SMILES: c1ccc(cc1)CC(C(=O)N2CCCC2C(=O)NC(CCCNC(=[NH2+])N)C(CCl)O)N
Ligand InChI: InChI=1S/C21H33ClN6O3/c22-13-18(29)16(8-4-10-26-21(24)25)27-19(30)17-9-5-11-28(17)20(31)15(23)12-14-6-2-1-3-7-14/h1-3,6-7,15-18,29H,4-5,8-13,23H2,(H,27,30)(H4,24,25,26)/p+1/t15-,16+,17+,18-/m1/s1
Release date: 2021-01-27
Crystal structure of TrkA in complex with PF-05206283 (PDB entry 5JFV)
Macromolecule: High affinity nerve growth factor receptor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 308 residues
Sequence: MHHHHHHLVPRGSVHHIKRRDIVLKWELGEGAFGKVFLAECHNLLPEQDKMLVAVKALKEASESARQDFQREAELLTMLQHQHIVRFFGVCTEGRPLLMVFEYMRHGDLNRFLRSHGPDAKLLAGGEDVAPGPLGLGQLLAVASQVAAGMVYLAGLHFVHRDLATRNCLVGQGLVVKIGDFGMSRDIYSTDYYRVGGRTMLPIRWMPPESILYRKFTTESDVWSFGVVLWEIFTYGKQPWYQLSNTEAIDCITQGRELERPRACPPEVYAIMRGCWQREPQQRHSIKDVHARLQALAQAPPVYLDVLG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.59
R work: 0.1717
R free: 0.1915
Average B factor: 31.07
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 277
Crystal growth procedure: protein was concentrated to 10mg/ml. Crystals of complexes were grown using the hanging drop vapour diffusion method from 0.1M HEPES pH7.5, 0.1M MgCl2 and 10% EtOH at 4C
Matthews coefficient: 2.96
Solvent content (%): 62.47
Ligand: N-{5-[4-amino-7-(propan-2-yl)-7H-pyrrolo[2,3-d]pyrimidine-5-carbonyl]pyridin-3-yl}-2-(4-chlorophenyl)acetamide (6K1)
Ligand formula: C23 H21 Cl N6 O2
Ligand molecular weight: 448.905
Ligand SMILES: CC(C)n1cc(c2c1ncnc2N)C(=O)c3cc(cnc3)NC(=O)Cc4ccc(cc4)Cl
Ligand InChI: InChI=1S/C23H21ClN6O2/c1-13(2)30-11-18(20-22(25)27-12-28-23(20)30)21(32)15-8-17(10-26-9-15)29-19(31)7-14-3-5-16(24)6-4-14/h3-6,8-13H,7H2,1-2H3,(H,29,31)(H2,25,27,28)
Release date: 2017-03-01
Structure of human JAK2 FERM/SH2 in complex with Leptin Receptor (PDB entry 6E2P)
Macromolecule: Tyrosine-protein kinase JAK2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 484 residues
Sequence: GSDPVLQVYLYHSLGKSEADYLTFPSGEYVAEEICIAASKACGITPVYHNMFALMSETERIWYPPNHVFHIDESTRHNVLYRIRFYFPRWYCSGSNRAYRHGISRGAEAPLLDDFVMSYLFAQWRHDFVHGWIKVPVTHETQEECLGMAVLDMMRIAKENDQTPLAIYNSISYKTFLPKCIRAKIQDYHILTRKRIRYRFRRFIQQFSQCKATARNLKLKYLINLETLQSAFYTEKFEVKEPGSGPSGEEIFATIIITGNGGIQWSRGKHKESETLTEQDLQLYCDFPNIIDVSIKQANQEGSNESRVVTIHKQDGKNLEIELSSLREALSFVSLIDGYYRLTADAHHYLCKEVAPPAVLENIQSNCHGPISMDFAISKLKKAGNQTGLYVLRCSPKDFNKYFLTFAVERENVIEYKHCLITKNENEEYNLSGTKKNFSSLKDLLNCYQMETVRSDNIIFQFTKCCPPKPKDKSNLLVFRTGNS
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.83
R work: 0.2274
R free: 0.2426
Average B factor: 106.19
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 277.15
Crystal growth procedure: 0.1 M MES, pH 6.5, 0.2 M magnesium chloride, 5-10% PEG4000, 10% ethylene glycol
Matthews coefficient: 3.94
Solvent content (%): 68.76
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: 2018-08-08
Crystal Structure of Ephrin A2 (EphA2) Receptor Protein Kinase with Compound 2d (PDB entry 5NK6)
Macromolecule: Ephrin type-A receptor 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 306 residues
Sequence: GDPNQAVLKFTTEIHPSCVTRQKVIGAGEFGEVYKGMLKTSSGKKEVPVAIKTLKAGYTEKQRVDFLGEAGIMGQFSHHNIIRLEGVISKYKPMMIITEYMENGALDKFLREKDGEFSVLQLVGMLRGIAAGMKYLANMNYVHRDLAARNILVNSNLVCKVSDFGLSRVLEDDPEATYTTSGGKIPIRWTAPEAISYRKFTSASDVWSFGIVMWEVMTYGERPYWELSNHEVMKAINDGFRLPTPMDCPSAIYQLMMQCWQQERARRPKFADIVSILDKLIRAPDSLKTLADFDPRVSIRLPSTSG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.267
R work: 0.1714
R free: 0.1858
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 291
Crystal growth procedure: 37.5% MPD/PEG1000/PEG3350 (MD), 0.1 M Amino Acids Mix (MD), 0.1 M Bis-Tris pH5.5
Matthews coefficient: 1.98
Solvent content (%): 37.8
Ligand: ~{N}-(2-chloranyl-6-methyl-phenyl)-2-[[3-[(4-oxidanylcyclohexyl)carbamoyl]phenyl]amino]-1,3-thiazole-5-carboxamide (90W)
Ligand formula: C24 H25 Cl N4 O3 S
Ligand molecular weight: 484.998
Ligand SMILES: Cc1cccc(c1NC(=O)c2cnc(s2)Nc3cccc(c3)C(=O)NC4CCC(CC4)O)Cl
Ligand InChI: InChI=1S/C24H25ClN4O3S/c1-14-4-2-7-19(25)21(14)29-23(32)20-13-26-24(33-20)28-17-6-3-5-15(12-17)22(31)27-16-8-10-18(30)11-9-16/h2-7,12-13,16,18,30H,8-11H2,1H3,(H,26,28)(H,27,31)(H,29,32)/t16-,18-
Release date: 2017-06-07