satarupa22/MacromolecularLigandDB huggingface dataset:
Crystal structure of human PLK4-PB3 in complex with STIL-CC (PDB entry 4YYP)
Macromolecule: Serine/threonine-protein kinase PLK4
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.21
Sequence length: 87 residues
Sequence: SAQLLKSVFVKNVGWATQLTSGAVWVQFNDGSQLVVQAGVSSISYTSPNGQTTRYGENEKLPDYIKQKLQCLSSILLMFSNPTPNFH
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.6
R work: 0.2174
R free: 0.2542
Average B factor: 89.61
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: Thin needles grew in precipitant solution containing 100 mM Hepes, pH 7.0, 20 mM MgCl2 and 22% Poly(acrylic acid sodium salt) 5100. After extensive optimization and seeding plate-like crystals were grown in a drop consisting of 50% PLK4-PB3/STIL-CC complex solution, 33.3% precipitant solution (100 mM phosphate/citrate pH 4.2, 40% (v/v) Ethanol, 5% (w/v) PEG 1000) and 16.7% of seed stock solution.
Matthews coefficient: 3.68
Solvent content (%): 66.64
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: 2015-07-29
Crystal structure of HsRNMT complexed with inhibitor DDD1060606 (PDB entry 8Q69)
Macromolecule: mRNA cap guanine-N7 methyltransferase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1.56
Sequence length: 276 residues
Sequence: SQSRIFYLRNFNNWMKSVLIGEFLEKVRQKKKRDITVLDLGCGKGGDLLKWKKGRINKLVCTDIADVSVKQCQQRYEDMKNRRDSEYIFSAEFITADSSKELLIDKFRDPQMCFDICSCQFVCHYSFESYEQADMMLRNACERLSPGGYFIGTTPNSFELIRRLEASETESFGNEIYTVKFQKKGDYPLFGCKYDFNLEGVVDVPEFLVYFPLLNEMAKKYNMKLVYKKTFLEFYEEKIKNNENKMLLKRMGLGCLSKSEWEATSIYLVFAFEKQQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.96
R work: 0.2423
R free: 0.2892
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 290
Crystal growth procedure: 0.1 M MES pH 6.3-6.9, 50 mM Na2SO4, 18-25 % PEG 6000
Matthews coefficient: 2.12
Solvent content (%): 41.9
Ligand: S-ADENOSYL-L-HOMOCYSTEINE (SAH)
Ligand formula: C14 H20 N6 O5 S
Ligand molecular weight: 384.411
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)CSCCC(C(=O)O)N)O)O)N
Ligand InChI: InChI=1S/C14H20N6O5S/c15-6(14(23)24)1-2-26-3-7-9(21)10(22)13(25-7)20-5-19-8-11(16)17-4-18-12(8)20/h4-7,9-10,13,21-22H,1-3,15H2,(H,23,24)(H2,16,17,18)/t6-,7+,9+,10+,13+/m0/s1
Release date: 2024-08-21
LINKED KDM5A JMJ DOMAIN BOUND TO THE INHIBITOR (S)-N-(1-(3-isopropyl-1H-pyrazole-5-carbonyl)pyrrolidin-3-yl)cyclopropanecarboxamide (Compound N55) (PDB entry 6BH3)
Macromolecule: Lysine-specific demethylase 5A, linked KDM5A JMJ domain
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11
Sequence length: 330 residues
Sequence: HNMAGVGPGGYAAEFVPPPECPVFEPSWEEFTDPLSFIGRIRPLAEKTGICKIRPPKDWQPPFACEVKSFRFTPRVQRLNELEAMTRVRPREAFGFEQAVREYTLQSFGEMADNFKSDYFNMPVHMVPTELVEKEFWRLVSSIEEDVIVEYGADISSKDFGSGFPVKDGRRKILPEEEEYALSGWNLNNMPVLEQSVLAHINVDISGMKVPWLYVGMCFSSFCWHIEDHWSYSINYLHWGEPKTWYGVPSHAAEQLEEVMRELAPELFESQPDLLHQLVTIMNPNVLMEHGVPVYRTNQCAGEFVVTFPRAYHSGFNQGYNFAEAVNFCT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.701
R work: 0.1947
R free: 0.2157
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 289
Crystal growth procedure: 1.2-1.35 M (NH4)2SO4, 0.1 M Tris-HCl (pH 8.6-9.2), 0-20% glycerol, 25 mM (Na/K) dibasic/monobasic phosphate
Matthews coefficient: 2.24
Solvent content (%): 45.17
Ligand: N-{(3S)-1-[5-(propan-2-yl)-1H-pyrazole-3-carbonyl]pyrrolidin-3-yl}cyclopropanecarboxamide (DQJ)
Ligand formula: C15 H22 N4 O2
Ligand molecular weight: 290.361
Ligand SMILES: CC(C)c1cc(n[nH]1)C(=O)N2CCC(C2)NC(=O)C3CC3
Ligand InChI: InChI=1S/C15H22N4O2/c1-9(2)12-7-13(18-17-12)15(21)19-6-5-11(8-19)16-14(20)10-3-4-10/h7,9-11H,3-6,8H2,1-2H3,(H,16,20)(H,17,18)/t11-/m0/s1
Release date: 2018-03-28
Crystal structure of Aurora-A kinase in complex with an allosterically binding fragment (PDB entry 5OS0)
Macromolecule: Aurora kinase A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 265 residues
Sequence: QWALEDFEIGRPLGKGKFGNVYLAREKQSKFILALKVLFKAQLEKAGVEHQLRREVEIQSHLRHPNILRLYGYFHDATRVYLILEYAPLGTVYRELQKLSKFDEQRTATYITELANALSYCHSKRVIHRDIKPENLLLGSAGELKIADFGWSVHAPSSRRTTLAGTLDYLPPEMIEGRMHDEKVDLWSLGVLCYEFLVGKPPFEANTYQETYKRISRVEFTFPDFVTEGARDLISRLLKHNPSQRPMLREVLEHPWITANSSKPS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.74
R work: 0.2173
R free: 0.2635
Average B factor: 43.1512
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 298
Crystal growth procedure: 0.1 M Tris, pH 8.5: 0.5 M NaCl: 0.2 M MgCl2: 32.5 % v/v PEG 3350
Matthews coefficient: 2.79
Solvent content (%): 55.84
Ligand: MAGNESIUM ION (MG)
Ligand formula: Mg
Ligand molecular weight: 24.305
Ligand SMILES: [Mg+2]
Ligand InChI: InChI=1S/Mg/q+2
Release date: 2017-11-01
ULK3 regulates cytokinetic abscission by phosphorylating ESCRT-III proteins (PDB entry 4WZX)
Macromolecule: Serine/threonine-protein kinase ULK3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 95 residues
Sequence: GPHMGTSARDLLREMARDKPRLLAALEVASAAMAKEEAAGGEQDALDLYQHSLGELLLLLAAEPPGRRRELLHTEVQNLMARAEYLKEQVKMRES
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.3859
R work: 0.1513
R free: 0.18
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 295
Crystal growth procedure: 50mM MES pH 6.5, 5mM Cobalt chloride, 800mM ammonium sulfate
Matthews coefficient: 2.19
Solvent content (%): 43.83
Ligand: COBALT (II) ION (CO)
Ligand formula: Co
Ligand molecular weight: 58.933
Ligand SMILES: [Co+2]
Ligand InChI: InChI=1S/Co/q+2
Release date: 2015-06-03
INPP5D PanDDA analysis group deposition -- Crystal Structure of the phosphatase and C2 domains of SHIP1 in complex with Z18197050 (PDB entry 5RYC)
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): 1.56
R work: 0.174
R free: 0.2051
Average B factor: 18.459
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: 2.1
Solvent content (%): 41.44
Ligand: methyl 4-sulfanylbenzoate (WL1)
Ligand formula: C8 H8 O2 S
Ligand molecular weight: 168.213
Ligand SMILES: COC(=O)c1ccc(cc1)S
Ligand InChI: InChI=1S/C8H8O2S/c1-10-8(9)6-2-4-7(11)5-3-6/h2-5,11H,1H3
Release date: 2020-11-11
Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor NPD-1335 (PDB entry 6HWO)
Macromolecule: cAMP-specific 3',5'-cyclic phosphodiesterase 4D
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.4.53
Sequence length: 364 residues
Sequence: GSHMIPRFGVKTEQEDVLAKELEDVNKWGLHVFRIAELSGNRPLTVIMHTIFQERDLLKTFKIPVDTLITYLMTLEDHYHADVAYHNNIHAADVVQSTHVLLSTPALEAVFTDLEILAAIFASAIHDVDHPGVSNQFLINTNSELALMYNDSSVLENHHLAVGFKLLQEENCDIFQNLTKKQRQSLRKMVIDIVLATDMSKHMNLLADLKTMVETKKVTSSGVLLLDNYSDRIQVLQNMVHCADLSNPTKPLQLYRQWTDRIMEEFFRQGDRERERGMEISPMCDKHNASVEKSQVGFIDYIVHPLWETWADLVHPDAQDILDTLEDNREWYQSTIPQSPSPAPDDPEEGRQGQTEKFQFELTL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.99
R work: 0.19819
R free: 0.25539
Average B factor: 43.247
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: 24% PEG 3350, 30% Ethylene Glycol, 0.1 M HEPES pH 7.5
Matthews coefficient: 2.62
Solvent content (%): 53.1
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: 2019-07-24
The Crystal Structure of TGF beta R2 kinase domain from Biortus. (PDB entry 8YGZ)
Macromolecule: TGF-beta receptor type-2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.30
Sequence length: 314 residues
Sequence: GHNTELLPIELDTLVGKGRFAEVYKAKLKQNTSEQFETVAVKIFPYEEYASWKTEKDIFSDINLKHENILQFLTAEERKTELGKQYWLITAFHAKGNLQEYLTRHVISWEDLRKLGSSLARGIAHLHSDHTPCGRPKMPIVHRDLKSSNILVKNDLTCCLCDFGLSLRLDPTLSVDDLANSGQVGTARYMAPEVLASAMNLENVESFKQTDVYSMALVLWEMTSRCNAVGEVKDYEPPFGSKVREHPCVASMADNVLADAGRPEIPSFWLNHQGIQMVCETLTECWDHDPEARLTAQCVAERFSELEHLDRLSG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.1
R work: 0.1949
R free: 0.254
Average B factor: 44.21
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.2M Li2SO4, 0.1M Tris-HCl pH8.5, 30% PEG4,000
Matthews coefficient: 2.5
Solvent content (%): 50.83
Ligand: 1,2-ETHANEDIOL (EDO)
Ligand formula: C2 H6 O2
Ligand molecular weight: 62.068
Ligand SMILES: C(CO)O
Ligand InChI: InChI=1S/C2H6O2/c3-1-2-4/h3-4H,1-2H2
Release date: 2024-03-13
Human DNA polymerase lambda- MgdATP binary complex and complex with 6 paired DNA (PDB entry 4XQ8)
Macromolecule: DNA polymerase lambda
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 334 residues
Sequence: AQPSSQKATNHNLHITEKLEVLAKAYSVQGDKWRALGYAKAINALKSFHKPVTSYQEACSIPGIGKRMAEKIIEILESGHLRKLDHISESVPVLELFSNIWGAGTKTAQMWYQQGFRSLEDIRSQASLTTQQAIGLKHYSDFLERMPREEATEIEQTVQKAAQAFNSGLLCVACGSYRRGKATCGDVDVLITHPDGRSHRGIFSRLLDSLRQEGFLTDDLVSQEENGQQQKYLGVCRLPGPGRRHRRLDIIVVPYSEFACALLYFTGSAHFNRSMRALAKTKGMSLSEHALSTAVVRNTHGCKVGPGRVLPTPTEKDVFRLLGLPYREPAERDW
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.798
R work: 0.1817
R free: 0.2399
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 277
Crystal growth procedure: 0.1 M Lithium Sulfate monohydrate, 0.1 M HEPES-Sodium, 0.1 M Potassium Sodium Tartrate
Matthews coefficient: 2.58
Solvent content (%): 52.27
Ligand: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE (DTP)
Ligand formula: C10 H16 N5 O12 P3
Ligand molecular weight: 491.182
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3CC(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)N
Ligand InChI: InChI=1S/C10H16N5O12P3/c11-9-8-10(13-3-12-9)15(4-14-8)7-1-5(16)6(25-7)2-24-29(20,21)27-30(22,23)26-28(17,18)19/h3-7,16H,1-2H2,(H,20,21)(H,22,23)(H2,11,12,13)(H2,17,18,19)/t5-,6+,7+/m0/s1
Release date: 2016-02-24
The PH domain of Bruton's tyrosine kinase mutant R28C (PDB entry 6TUH)
Macromolecule: Tyrosine-protein kinase BTK
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 169 residues
Sequence: AAVILESIFLKRSQQKKKTSPLNFKKRLFLLTVHKLSYYEYDFERGRRGSKKGSIDVEKITCVETVVPEKNPPPERQIPRRGEESSEMEQISIIERFPYPFQVVYDEGPLYVFSPTEELRKRWIHQLKNVIRYNSDLVQKYHPSFWIDGQYLCCSQTAKNAMGCQILEN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.25
R work: 0.236
R free: 0.276
Average B factor: 71.72
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 298
Crystal growth procedure: 0.1 M TRIS 8.5 pH, 32.5% w/v PEG 3350, 200mM MgCl2
Matthews coefficient: 2.23
Solvent content (%): 44.92
Ligand: 4,5,6,7-tetrahydro-1-benzofuran-3-carboxylic acid (NXT)
Ligand formula: C9 H10 O3
Ligand molecular weight: 166.174
Ligand SMILES: c1c(c2c(o1)CCCC2)C(=O)O
Ligand InChI: InChI=1S/C9H10O3/c10-9(11)7-5-12-8-4-2-1-3-6(7)8/h5H,1-4H2,(H,10,11)
Release date: 2020-11-25
Crystal structure of mouse Xyloside xylosyltransferase 1 complexed with manganese,acceptor ligand and UDP-Glucose (PDB entry 4WMA)
Macromolecule: Xyloside xylosyltransferase 1
Type: Protein, polypeptide(L)
Source organism: Mus musculus
EC number: 2.4.2
Sequence length: 306 residues
Sequence: SLEGGVVVPVDYHLLMMFTKAEHNAPLQAKARVALSSLLRLAKFEAHEVLNLHFVSEEASREVAKALLRELLPPAAGFKCKVIFHDVAVLTDKLFPVVEAMQKYFSAGSGTYYSDSIFFLSVAMHQIMPKEIPRIIQLDLDLKYKTNIRELFEEFDNFLPGAVIGIAREMQPVYRHTFWQFRHENPKTRVGDPPPEGLPGFNSGVMLLNLEAMRQSPLYSHLLEPSWVQQLADKYHFRGHLGDQDFFTMIGMEHPELFHVLDCTWNRQLCTWWRDHGYSDVFQAYFRCEGHVKIYHGNCNTPIPED
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.62
R work: 0.21914
R free: 0.24252
Average B factor: 31.982
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.2 M Li2SO4, 0.1 M Bis-Tris, and 21% PEG3350
Matthews coefficient: 2.46
Solvent content (%): 50.03
Ligand: MANGANESE (II) ION (MN)
Ligand formula: Mn
Ligand molecular weight: 54.938
Ligand SMILES: [Mn+2]
Ligand InChI: InChI=1S/Mn/q+2
Release date: 2015-09-30
X-Ray Characterization of Striatal-Enriched Protein Tyrosine Phosphatase Inhibitors (PDB entry 5OVX)
Macromolecule: Tyrosine-protein phosphatase non-receptor type 5
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 305 residues
Sequence: MHHHHHHSSGVDLGTENLYFQSMSRVLQAEELHEKALDPFLLQAEFFEIPMNFVDPKEYDIPGLVRKNRYKTILPNPHSRVCLTSPDPDDPLSSYINANYIRGYGGEEKVYIATQGPIVSTVADFWRMVWQEHTPIIVMITNIEEMNEKCTEYWPEEQVAYDGVEITVQKVIHTEDYRLRLISLKSGTEERGLKHYWFTSWPDQKTPDRAPPLLHLVREVEEAAQQEGPHCAPIIVHCSAGIGRTGCFIATSICCQQLRQEGVVDILKTTCQLRQDRGGMIQTCEQYQFVHHVMSLYEKQLSHQS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.1
R work: 0.1954
R free: 0.228
Average B factor: 27.5
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 26-28% PEG3350, 0.1M Bis-Tris pH5.5, 0.2M Lithium sulfate
Matthews coefficient: 2.53
Solvent content (%): 51.29
Ligand: [(~{S})-[4-[3-[(~{S})-(3,4-dichlorophenyl)-oxidanyl-methyl]phenyl]phenyl]-oxidanyl-methyl]phosphonic acid (AY5)
Ligand formula: C20 H17 Cl2 O5 P
Ligand molecular weight: 439.226
Ligand SMILES: c1cc(cc(c1)C(c2ccc(c(c2)Cl)Cl)O)c3ccc(cc3)C(O)P(=O)(O)O
Ligand InChI: InChI=1S/C20H17Cl2O5P/c21-17-9-8-16(11-18(17)22)19(23)15-3-1-2-14(10-15)12-4-6-13(7-5-12)20(24)28(25,26)27/h1-11,19-20,23-24H,(H2,25,26,27)/t19-,20-/m0/s1
Release date: 2017-11-22
Human butyrylcholinesterase in complex with the S enantiomer of a chlorotacrine-tryptophan multi-target inhibitor. (PDB entry 6I0B)
Macromolecule: Cholinesterase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.1.8
Sequence length: 529 residues
Sequence: EDDIIIATKNGKVRGMQLTVFGGTVTAFLGIPYAQPPLGRLRFKKPQSLTKWSDIWNATKYANSCCQNIDQSFPGFHGSEMWNPNTDLSEDCLYLNVWIPAPKPKNATVLIWIYGGGFQTGTSSLHVYDGKFLARVERVIVVSMNYRVGALGFLALPGNPEAPGNMGLFDQQLALQWVQKNIAAFGGNPKSVTLFGESAGAASVSLHLLSPGSHSLFTRAILQSGSFNAPWAVTSLYEARNRTLNLAKLTGCSRENETEIIKCLRNKDPQEILLNEAFVVPYGTPLSVNFGPTVDGDFLTDMPDILLELGQFKKTQILVGVNKDEGTAFLVYGAPGFSKDNNSIITRKEFQEGLKIFFPGVSEFGKESILFHYTDWVDDQRPENYREALGDVVGDYNFICPALEFTKKFSEWGNNAFFYYFEHRSSKLPWPEWMGVMHGYEIEFVFGLPLERRDQYTKAEEILSRSIVKRWANFAKYGNPQETQNQSTSWPVFKSTEQKYLTLNTESTRIMTKLRAQQCRFWTSFFPKV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.384
R work: 0.1892
R free: 0.2439
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: MES pH 6.5
Ammonium Sulphate
Matthews coefficient: 3.1
Solvent content (%): 60.38
Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose (NAG)
Ligand formula: C8 H15 N O6
Ligand molecular weight: 221.208
Ligand SMILES: CC(=O)NC1C(C(C(OC1O)CO)O)O
Ligand InChI: InChI=1S/C8H15NO6/c1-3(11)9-5-7(13)6(12)4(2-10)15-8(5)14/h4-8,10,12-14H,2H2,1H3,(H,9,11)/t4-,5-,6-,7-,8-/m1/s1
Release date: 2019-03-27
Crystal structure of human MTH1(G2K/D120N mutant) in complex with 2-oxo-dATP at pH 9.7 (PDB entry 8I1J)
Macromolecule: 7,8-dihydro-8-oxoguanine triphosphatase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.1.55
Sequence length: 156 residues
Sequence: MKASRLYTLVLVLQPQRVLLGMKKRGFGAGRWNGFGGKVQEGETIEDGARRELQEESGLTVDALHKVGQIVFEFVGEPELMDVHVFCTDSIQGTPVESDEMRPCWFQLDQIPFKDMWPDNSYWFPLLLQKKKFHGYFKFQGQDTILDYTLREVDTV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.08
R work: 0.1418
R free: 0.1742
Average B factor: 20.24
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: sodium citrate, caps, NaCl
Matthews coefficient: 1.83
Solvent content (%): 32.82
Ligand: [[(2R,3S,5R)-5-(6-azanyl-2-oxidanylidene-1H-purin-9-yl)-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate (6U4)
Ligand formula: C10 H16 N5 O13 P3
Ligand molecular weight: 507.181
Ligand SMILES: C1C(C(OC1N2C=NC3=C(NC(=O)N=C32)N)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O
Ligand InChI: InChI=1S/C10H16N5O13P3/c11-8-7-9(14-10(17)13-8)15(3-12-7)6-1-4(16)5(26-6)2-25-30(21,22)28-31(23,24)27-29(18,19)20/h3-6,16H,1-2H2,(H,21,22)(H,23,24)(H2,18,19,20)(H3,11,13,14,17)/t4-,5+,6+/m0/s1
Release date: 2023-03-22
Carbonic Anhydrase IX-mimic Complexed with 2-((3-Aminopropyl)(phenethyl)amino)-N-(4-fluorobenzyl)-N-(4-sulfamoylphenethyl)acetamide (PDB entry 7SUY)
Macromolecule: Carbonic anhydrase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 257 residues
Sequence: HWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHSFQVTFDDSQDKAVLKGGPLDGTYRLLQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDVGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTEGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLAECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.405
R work: 0.1653
R free: 0.1873
Average B factor: 19.3444
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.8
Crystallization temperature (K): 293
Crystal growth procedure: 1.6 M sodium citrate, 50 mM tris base
Matthews coefficient: 2.1
Solvent content (%): 41.52
Ligand: N-[(furan-2-yl)methyl]-N-[2-(4-sulfamoylphenyl)ethyl]glycinamide (C97)
Ligand formula: C15 H19 N3 O4 S
Ligand molecular weight: 337.394
Ligand SMILES: c1cc(oc1)CN(CCc2ccc(cc2)S(=O)(=O)N)C(=O)CN
Ligand InChI: InChI=1S/C15H19N3O4S/c16-10-15(19)18(11-13-2-1-9-22-13)8-7-12-3-5-14(6-4-12)23(17,20)21/h1-6,9H,7-8,10-11,16H2,(H2,17,20,21)
Release date: 2022-04-06
PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with FMSOA000686b (PDB entry 7GSZ)
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): 1.91
R work: 0.1996
R free: 0.2409
Average B factor: 44.292
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.3 M magnesium acetate, 0.1 M HEPES pH 7.5, 0.1% beta-mercaptoethanol, 13-14% PEG 8000, 2% ethanol
Matthews coefficient: 3.39
Solvent content (%): 63.77
Ligand: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL (TRS)
Ligand formula: C4 H12 N O3
Ligand molecular weight: 122.143
Ligand SMILES: C(C(CO)(CO)[NH3+])O
Ligand InChI: InChI=1S/C4H11NO3/c5-4(1-6,2-7)3-8/h6-8H,1-3,5H2/p+1
Release date: 2024-01-24
Structural Details of Ufd1 binding to p97 (PDB entry 5B6C)
Macromolecule: Transitional endoplasmic reticulum ATPase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.4.6
Sequence length: 174 residues
Sequence: GSNRPNRLIVDEAINEDNSVVSLSQPKMDELQLFRGDTVLLKGKKRREAVCIVLSDDTCSDEKIRMNRVVRNNLRVRLGDVISIQPCPDVKYGKRIHVLPIDDTVEGITGNLFEVYLKPYFLEAYRPIRKGDIFLVRGGMRAVEFKVVETDPSPYCIVAPDTVIHCEGEPIKRA
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.55
R work: 0.15797
R free: 0.1995
Average B factor: 17.623
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293.15
Crystal growth procedure: 21%(w/v) PEG 8000, 2.9mM n-nonyl-beta-thiomaltoside, 0.1M HEPES, pH 7.5
Matthews coefficient: 2.33
Solvent content (%): 47.18
Release date: 2017-01-04
Thioesterase Domain of Human Fatty Acid Synthase (FASN-TE) binding a competitive inhibitor SBP-7635 (PDB entry 7MHD)
Macromolecule: Fatty acid synthase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.2.14
Sequence length: 298 residues
Sequence: GSGGGGGSTQLNLRSLLVNPEGPTLMRLNSVQSSERPLFLVHPIEGSTTVFHSLASRLSIPTYGLQCTRAAPLDSIHSLAAYYIDCIRQVQPEGPYRVAGYSYGACVAFEMCSQLQAQQSPAPTHNSLFLFDGSPTYVLAYTQSYRAKLTPGCEAEAETEAICFFVQQFTDMEHNRVLEALLPLKGLEERVAAAVDLIIKSHQGLDRQELSFAARSFYYKLRAAEQYTPKAKYHGNVMLLRAKTGGAYGEDLGADYNLSQVCDGKVSVHVIEGDHRTLLEGSGLESIISIIHSSLAEH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.03
R work: 0.1928
R free: 0.2457
Average B factor: 42.494
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.3 ul of 8 mg/ml FASN-TE in 100 mM NaCl, 50 mM BisTris pH 6.0, 10 mM DTT, 0.5 mM of the inhibitor and 1% DMSO were mixed with 0.2 ul of well solution 10% PEG400, 50 mM TRIS-Cl pH 8.5, 1 mM DTT, 1 mM Ethylenediaminetetraacetic acid disodium salt (EDTA), 300 mM NaCl.
Matthews coefficient: 1.97
Solvent content (%): 37.64
Ligand: N,N-diethyl-4-{2-[(2-fluorophenyl)methyl]-1,3-thiazol-4-yl}benzene-1-sulfonamide (ZEP)
Ligand formula: C20 H21 F N2 O2 S2
Ligand molecular weight: 404.521
Ligand SMILES: CCN(CC)S(=O)(=O)c1ccc(cc1)c2csc(n2)Cc3ccccc3F
Ligand InChI: InChI=1S/C20H21FN2O2S2/c1-3-23(4-2)27(24,25)17-11-9-15(10-12-17)19-14-26-20(22-19)13-16-7-5-6-8-18(16)21/h5-12,14H,3-4,13H2,1-2H3
Release date: 2022-04-20
Structure of Human Polycomb Repressive Complex 2 (PRC2) with oncogenic histone H3K27M peptide (PDB entry 5HYN)
Macromolecule: H3K27M
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 13 residues
Sequence: ATKAARMSAPATG
Oligomeric state: Hetero 5-mer
Stoichiometry: A1, B1, C1, D1, E1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.95
R work: 0.2191
R free: 0.2733
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 291
Crystal growth procedure: 25% PEG3350, 400mM Ammonian Citrate pH6.5
Matthews coefficient: 2.82
Solvent content (%): 56.33
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: 2016-05-11