satarupa22/MacromolecularLigandDB huggingface dataset:
Crystal structure of the bromodomain of human CREBBP bound to pyrazolopiperidine scaffold (PDB entry 5KTU)
Macromolecule: CREB-binding protein
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1.48
Sequence length: 118 residues
Sequence: GSKKIFKPEELRQALMPTLEALYRQDPESLPFRQPVDPQLLGIPDYFDIVKNPMDLSTIKRKLDTGQYQEPWQYVDDVWLMFNNAWLYNRKTSRVYKFCSKLAEVFEQEIDPVMQSLG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.38
R work: 0.1915
R free: 0.2122
Average B factor: 26.338
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 0.2 M magnesium chloride, 0.1 M Bis-Tris pH 6.5, and 25% polyethylene glycol (PEG) 3350
Matthews coefficient: 2.22
Solvent content (%): 44.55
Ligand: 1-(3-phenylazanyl-1,4,6,7-tetrahydropyrazolo[4,3-c]pyridin-5-yl)ethanone (6XB)
Ligand formula: C14 H16 N4 O
Ligand molecular weight: 256.303
Ligand SMILES: CC(=O)N1CCc2c(c(n[nH]2)Nc3ccccc3)C1
Ligand InChI: InChI=1S/C14H16N4O/c1-10(19)18-8-7-13-12(9-18)14(17-16-13)15-11-5-3-2-4-6-11/h2-6H,7-9H2,1H3,(H2,15,16,17)
Release date: 2016-11-02
Human GAR transformylase in complex with GAR substrate and AGF347 inhibitor (PDB entry 8FJW)
Macromolecule: Trifunctional purine biosynthetic protein adenosine-3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 6.3.4.13
Sequence length: 210 residues
Sequence: MARVAVLISGTGSNLQALIDSTREPNSSAQIDIVISNKAAVAGLDKAERAGIPTRVINHKLYKNRVEFDSAIDLVLEEFSIDIVCLAGFMRILSGPFVQKWNGKMLNIHPSLLPSFKGSNAHEQALETGVTVTGCTVHFVAEDVDAGQIILQEAVPVKRGDTVATLSERVKLAEHKIFPAALQLVASGTVQLGENGKICWVKEEHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.08
R work: 0.2075
R free: 0.2361
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.1 M Tris (pH 7.5), 0.333 mM NaCl, 20% polyethylene glycol (PEG) 4000, and 2% PEG 400
Matthews coefficient: 3.51
Solvent content (%): 64.97
Ligand: GLYCINAMIDE RIBONUCLEOTIDE (GAR)
Ligand formula: C7 H13 N2 O8 P
Ligand molecular weight: 284.16
Ligand SMILES: C(C1C(C(C(O1)NC(=O)CN)O)O)OP(=O)([O-])[O-]
Ligand InChI: InChI=1S/C7H15N2O8P/c8-1-4(10)9-7-6(12)5(11)3(17-7)2-16-18(13,14)15/h3,5-7,11-12H,1-2,8H2,(H,9,10)(H2,13,14,15)/p-2/t3-,5-,6-,7-/m1/s1
Release date: 2023-09-06
The co-crystal structure of DYRK2 with YK-2-99B (PDB entry 8HLT)
Macromolecule: Dual specificity tyrosine-phosphorylation-regulated kinase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.12.1
Sequence length: 393 residues
Sequence: GMGKVKATPMTPEQAMKQYMQKLTAFEHHEIFSYPEIYFLGLNAKKRQGMTGGPNNGGYDDDQGSYVQVPHDHVAYRYEVLKVIGKGSFGQVVKAYDHKVHQHVALKMVRNEKRFHRQAAEEIRILEHLRKQDKDNTMNVIHMLENFTFRNHICMTFELLSMNLYELIKKNKFQGFSLPLVRKFAHSILQCLDALHKNRIIHCDLKPENILLKQQGRSGIKVIDFGSSCYEHQRVYTYIQSRFYRAPEVILGARYGMPIDMWSLGCILAELLTGYPLLPGEDEGDQLACMIELLGMPSQKLLDASKRAKNFVSSKGYPRYCTVTTLSDGSVVLNGGRSRRGKLRGPPESREWGNALKGCDDPLFLDFLKQCLEWDPAVRMTPGQALRHPWLRR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.8
R work: 0.2092
R free: 0.2669
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 289.15
Crystal growth procedure: 0.05M HEPES pH7.0, 12%PEG 3350, 1% Trptone, 1mM NaN3
Matthews coefficient: 3.17
Solvent content (%): 61.17
Ligand: (6-{[(4P)-4-(1,3-benzothiazol-5-yl)-5-fluoropyrimidin-2-yl]amino}pyridin-3-yl)(piperazin-1-yl)methanone (XSE)
Ligand formula: C21 H18 F N7 O S
Ligand molecular weight: 435.477
Ligand SMILES: c1cc2c(cc1c3c(cnc(n3)Nc4ccc(cn4)C(=O)N5CCNCC5)F)ncs2
Ligand InChI: InChI=1S/C21H18FN7OS/c22-15-11-25-21(28-19(15)13-1-3-17-16(9-13)26-12-31-17)27-18-4-2-14(10-24-18)20(30)29-7-5-23-6-8-29/h1-4,9-12,23H,5-8H2,(H,24,25,27,28)
Release date: 2023-12-13
human cGAS catalytic domain bound with the inhibitor G108 (PDB entry 6MJU)
Macromolecule: Cyclic GMP-AMP synthase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.86
Sequence length: 372 residues
Sequence: SILVRRDAAPGASKLRAVLEKLKLSRDDISTAAGMVKGVVDHLLLRLKCDSAFRGVGLLNTGSYYEHVKISAPNEFDVMFKLEVPRIQLEEYSNTRAYYFVKFKRNPKENPLSQFLEGEILSASKMLSKFRKIIKEEINDIKDTDVIMKRKRGGSPAVTLLISEKISVDITLALESKSSWPASTQEGLRIQNWLSAKVRKQLRLKPFYLVPKHAKEGNGFQEETWRLSFSHIEKEILNNHGKSKTCCENKEEKCCRKDCLKLMKYLLEQLKERFKDEEHLDKFSSYHVKTAFFHVCTQNPQDSQWDRKDLGLCFDNCVTYFLQCLRTEKLENYFIPEFNLFSSNLIDKRSKEFLTKQIEYERNNEFPVFDEF
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.45
R work: 0.2224
R free: 0.2563
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7
Crystallization temperature (K): 293
Crystal growth procedure: 0.064 M sodium citrate 7.0, 0.1 M HEPES, pH 7.0, 10% PEG5000MME
Matthews coefficient: 2.72
Solvent content (%): 54.84
Ligand: 1-[6,7-dichloro-9-(1H-pyrazol-4-yl)-1,3,4,5-tetrahydro-2H-pyrido[4,3-b]indol-2-yl]-2-hydroxyethan-1-one (JUM)
Ligand formula: C16 H14 Cl2 N4 O2
Ligand molecular weight: 365.214
Ligand SMILES: c1c(c2c3c([nH]c2c(c1Cl)Cl)CCN(C3)C(=O)CO)c4c[nH]nc4
Ligand InChI: InChI=1S/C16H14Cl2N4O2/c17-11-3-9(8-4-19-20-5-8)14-10-6-22(13(24)7-23)2-1-12(10)21-16(14)15(11)18/h3-5,21,23H,1-2,6-7H2,(H,19,20)
Release date: 2019-05-29
Factor XIa in complex with compound 7 (PDB entry 6VLU)
Macromolecule: Coagulation factor XIa light chain
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.27
Sequence length: 238 residues
Sequence: IVGGTASVRGEWPWQVTLHTTSPTQRHLCGGSIIGNQWILTAAHCFYGVESPKILRVYSGILNQSEIKEDTSFFGVQEIIIHDQYKMAESGYDIALLKLETTVNYTDSQRPISLPSKGDRNVIYTDCWVTGWGYRKLRDKIQNTLQKAKIPLVTNEECQKRYRGHKITHKMICAGYREGGKDACKGDSGGPLSCKHNEVWHLVGITSWGEGCAQRERPGVYTNVVEYVDWILEKTQAV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.6
R work: 0.2013
R free: 0.2459
Average B factor: 20.789
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M citrate pH 5, 23% PEG4000, seeded.
Matthews coefficient: 2.24
Solvent content (%): 45.14
Ligand: N-cyclohexyl-D-leucyl-N-[(1-aminoisoquinolin-6-yl)methyl]-4,4-difluoro-L-prolinamide (R2Y)
Ligand formula: C27 H37 F2 N5 O2
Ligand molecular weight: 501.612
Ligand SMILES: CC(C)CC(C(=O)N1CC(CC1C(=O)NCc2ccc3c(c2)ccnc3N)(F)F)NC4CCCCC4
Ligand InChI: InChI=1S/C27H37F2N5O2/c1-17(2)12-22(33-20-6-4-3-5-7-20)26(36)34-16-27(28,29)14-23(34)25(35)32-15-18-8-9-21-19(13-18)10-11-31-24(21)30/h8-11,13,17,20,22-23,33H,3-7,12,14-16H2,1-2H3,(H2,30,31)(H,32,35)/t22-,23+/m1/s1
Release date: 2020-05-06
Parkin (S65DUblR0RBR) (PDB entry 5C23)
Macromolecule: E3 ubiquitin-protein ligase parkin
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 6.3.2
Sequence length: 405 residues
Sequence: MIVFVRFNSSHGFPVEVDSDTSIFQLKEVVAKRQGVPADQLRVIFAGKELRNDWTVQNCDLDQQDIVHIVQRPWRKGQEMNATNSFYVYCKGPCQRVQPGKLRVQCSTCRQATLTLTQGPSCWDDVLIPNRMSGECQSPHCPGTSAEFFFKCGAHPTSDKETSVALHLIATNSRNITCITCTDVRSPVLVFQCNSRHVICLDCFHLYCVTRLNDRQFVHDPQLGYSLPCVAGCPNSLIKELHHFRILGEEQYNRYQQYGAEECVLQMGGVLCPRPGCGAGLLPEPDQRKVTCEGGNGLGCGFAFCRECKEAYHEGECSAVFEASGTTTQAYRVDERAAEQARWEAASKETIKKTTKPCPRCHVPVEKNGGCMHMKCPQPQCRLEWCWNCGCEWNRVCMGDHWFDV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.37
R work: 0.2199
R free: 0.2406
Average B factor: 52.88
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 5.5
Crystallization temperature (K): 277
Crystal growth procedure: PEG3350, LiSO4
Matthews coefficient: 2.47
Solvent content (%): 50.22
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: 2015-07-29
High Resolution Apo Carbonic Anhydrase II (PDB entry 6PEA)
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): 1.36
R work: 0.1485
R free: 0.1643
Average B factor: 18.8117
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.8
Crystallization temperature (K): 298
Crystal growth procedure: 1.6M NaCitrate, 50mM Tris
Matthews coefficient: 2.1
Solvent content (%): 41.38
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: 2020-03-11
Complex structure of JMJD5 and Symmetric Monomethyl-Arginine (MMA) (PDB entry 6AVS)
Macromolecule: Lysine-specific demethylase 8
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11.27
Sequence length: 236 residues
Sequence: GGTVPRLHRPSLQHFREQFLVPGRPVILKGVADHWPCMQKWSLEYIQEIAGCRTVPVEVGSRYTDEEWSQTLMTVNEFISKYIVNEPRDVGYLAQHQLFDQIPELKQDISIPDYCSLGDGEEEEITINAWFGPQGTISPLHQDPQQNFLVQVMGRKYIRLYSPQESGALYPHDTHLLHNTSQVDVENPDLEKFPKFAKAPFLSCILSPGEILFIPVKYWHYVRALDLSFSVSFWWS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.02
R work: 0.241
R free: 0.272
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 0.1M HEPES pH 7.0
8% PEG 3350
Matthews coefficient: 2.3
Solvent content (%): 46.45
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: 2018-02-28
Human Carbonic Anhydrase II in complex with 4-Methoxybenzenesulfonamide (PDB entry 6I0W)
Macromolecule: Carbonic anhydrase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 265 residues
Sequence: GSPEFMSHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHAFNVEFDDSQDKAVLKGGPLDGTYRLIQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDFGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTKGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLLECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.04
R work: 0.1192
R free: 0.1322
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.8
Crystallization temperature (K): 291
Crystal growth procedure: Ammoniumsulfate 2.70 M, pH = 7.8, saturated with para-Chloromercuribenzoic acid.
Matthews coefficient: 2.06
Solvent content (%): 40.34
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: 2019-11-20
PanDDA analysis group deposition -- Crystal Structure of DCP2 (NUDT20) in complex with Z450133538 (PDB entry 5QP4)
Macromolecule: DCP2 (NUDT20)
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.1.62
Sequence length: 167 residues
Sequence: SMGVPTYGAIILDETLENVLLVQGYLAKSGWGFPKGKVNKEEAPHDCAAREVFEETGFDIKDYICKDDYIELRINDQLARLYIIPGIPKDTKFNPKTRREIRNIEWFSIEKLPCHRNDMTPKSKLGLAPNKFFMAIPFIRPLRDWLSRRFGDSSDSDNGFSSTGSTP
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.71
R work: 0.2038
R free: 0.2593
Average B factor: 39.997
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 4.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.1 M acetate, pH 4.5, 5-25% PEG3350
Matthews coefficient: 2.49
Solvent content (%): 50.56
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: 2019-05-08
Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor NPD-1361 (PDB entry 7ABJ)
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): 2.11
R work: 0.1809
R free: 0.2178
Average B factor: 47.934
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: 2.64
Solvent content (%): 53.47
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: 2021-10-06
Human DNA polymerase eta-DNA ternary mismatch complex:reaction with 10.0 mM Mn2+ for 30s (PDB entry 7U7D)
Macromolecule: DNA polymerase eta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 435 residues
Sequence: GPHMATGQDRVVALVDMDCFFVQVEQRQNPHLRNKPCAVVQYKSWKGGGIIAVSYEARAFGVTRSMWADDAKKLCPDLLLAQVRESRGKANLTKYREASVEVMEIMSRFAVIERASIDEAYVDLTSAVQERLQKLQGQPISADLLPSTYIEGLPQGPTTAEETVQKEGMRKQGLFQWLDSLQIDNLTSPDLQLTVGAVIVEEMRAAIERETGFQCSAGISHNKVLAKLACGLNKPNRQTLVSHGSVPQLFSQMPIRKIRSLGGKLGASVIEILGIEYMGELTQFTESQLQSHFGEKNGSWLYAMCRGIEHDPVKPRQLPKTIGCSKNFPGKTALATREQVQWWLLQLAQELEERLTKDRNDNDRVATQLVVSIRVQGDKRLSSLRRCCALTRYDAHKMSHDAFTVIKNCNTSGIQTEWSPPLTMLFLCATKFSAS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.57
R work: 0.1817
R free: 0.2179
Average B factor: 31.3039
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6
Crystallization temperature (K): 298
Crystal growth procedure: 10% PEG 2000MME, 0.1 M MES
Matthews coefficient: 2.09
Solvent content (%): 41.18
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: 2022-05-04
Co-complex CYP46A1 with 0420 (compound 6) (PDB entry 7N3L)
Macromolecule: Cholesterol 24-hydroxylase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.14.25
Sequence length: 474 residues
Sequence: MHHHHHHSRYEHIPGPPRPSFLLGHLPCFWKKDEVGGRVLQDVFLDWAKKYGPVVRVNVFHKTSVIVTSPESVKKFLMSTKYNKDSKMYRALQTVFGERLFGQGLVSECNYERWHKQRRVIDLAFSRSSLVSLMETFNEKAEQLVEILEAKADGQTPVSMQDMLTYTAMDILAKAAFGMETSMLLGAQKPLSQAVKLMLEGITASRNTLAKFLPGKRKQLREVRESIRFLRQVGRDWVQRRREALKRGEEVPADILTQILKAEEGAQDDEGLLDNFVTFFIAGHETSANHLAFTVMELSRQPEIVARLQAEVDEVIGSKRYLDFEDLGRLQYLSQVLKESLRLYPPAWGTFRLLEEETLIDGVRVPGNTPLLFSTYVMGRMDTYFEDPLTFNPDRFGPGAPKPRFTYFPFSLGHRSCIGQQFAQMEVKVVMAKLLQRLEFRLVPGQRFGLQEQATLKPLDPVLCTLRPRGWQPA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.631
R work: 0.1669
R free: 0.2004
Average B factor: 20.756
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 290
Crystal growth procedure: 17.5% PEG 3350, 0.4M Calcium chloride
Matthews coefficient: 2.13
Solvent content (%): 42.31
Ligand: PROTOPORPHYRIN IX CONTAINING FE (HEM)
Ligand formula: C34 H32 Fe N4 O4
Ligand molecular weight: 616.487
Ligand SMILES: Cc1c2n3c(c1CCC(=O)O)C=C4C(=C(C5=[N]4[Fe]36[N]7=C(C=C8N6C(=C5)C(=C8C)C=C)C(=C(C7=C2)C)C=C)C)CCC(=O)O
Ligand InChI: InChI=1S/C34H34N4O4.Fe/c1-7-21-17(3)25-13-26-19(5)23(9-11-33(39)40)31(37-26)16-32-24(10-12-34(41)42)20(6)28(38-32)15-30-22(8-2)18(4)27(36-30)14-29(21)35-25;/h7-8,13-16H,1-2,9-12H2,3-6H3,(H4,35,36,37,38,39,40,41,42);/q;+2/p-2/b25-13-,26-13-,27-14-,28-15-,29-14-,30-15-,31-16-,32-16-;
Release date: 2022-02-23
Crystal structure of CK2 with compound 7b (PDB entry 5H8G)
Macromolecule: Casein kinase II subunit alpha
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 333 residues
Sequence: MSGPVPSRARVYTDVNTHRPREYWDYESHVVEWGNQDDYQLVRKLGRGKYSEVFEAINITNNEKVVVKILKPVKKKKIKREIKILENLRGGPNIITLADIVKDPVSRTPALVFEHVNNTDFKQLYQTLTDYDIRFYMYEILKALDYCHSMGIMHRDVKPHNVMIDHEHRKLRLIDWGLAEFYHPGQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRKEPFFHGHDNYDQLVRIAKVLGTEDLYDYIDKYNIELDPRFNDILGRHSRKRWERFVHSENQHLVSPEALDFLDKLLRYDHQSRLTAREAMEHPYFYTVVKDQAR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.0
R work: 0.1589
R free: 0.1982
Average B factor: 19.1
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 22-26% PEG 6K, 200 mM ammonium sulfate, 100 mM MES, pH 6.5
Matthews coefficient: 1.93
Solvent content (%): 36.4
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: 2016-02-10
Crystal structure of human exonuclease 1 Exo1 (WT) in complex with 5' recessed-end DNA (rIV) (PDB entry 5V06)
Macromolecule: Exonuclease 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1
Sequence length: 358 residues
Sequence: MGIQGLLQFIKEASEPIHVRKYKGQVVAVDTYCWLHKGAIACAEKLAKGEPTDRYVGFCMKFVNMLLSHGIKPILVFDGCTLPSKKEVERSRRERRQANLLKGKQLLREGKVSEARECFTRSINITHAMAHKVIKAARSQGVDCLVAPYEADAQLAYLNKAGIVQAIITEDSDLLAFGCKKVILKMDQFGNGLEIDQARLGMCRQLGDVFTEEKFRYMCILSGCDYLSSLRGIGLAKACKVLRLANNPDIVKVIKKIGHYLKMNITVPEDYINGFIRANNTFLYQLVFDPIKRKLIPLNAYEDDVDPETLSYAGQYVDDSIALQIALGNKDINTFEQIDDYNPDTAMPAHSRENLYFQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.75
R work: 0.2185
R free: 0.2655
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 290
Crystal growth procedure: 100 mM sodium acetate, pH 7.0, 10 mM potassium chloride, 2-4% PEG4000
Matthews coefficient: 2.62
Solvent content (%): 53.06
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: 2017-05-24
Vascular endothelial protein tyrosine phosphatase in complex with Cpd-2 (PDB entry 8JBY)
Macromolecule: Receptor-type tyrosine-protein phosphatase beta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 295 residues
Sequence: GPLGSPGIPNQFEGHFMKLQADSNYLLSKEYEELKDVGRNQSCDIALLPENRGKNRYNNILPYDATRVKLSNVDDDPCSDYINASYIPGNNFRREYIVTQGPLPGTKDDFWKMVWEQNVHNIVMVTQCVEKGRVKCDHYWPADQDSLYYGDLILQMLSESVLPEWTIREFKICGEEQLDAHRLIRHFHYTVWPDHGVPETTQSLIQFVRTVRDYINRSPGAGPTVVHCSAGVGRTGTFIALDRILQQLDSKDSVDIYGAVHDLRLHRVHMVQTECQYVYLHQCVRDVLRARKLRS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.99
R work: 0.1834
R free: 0.2074
Average B factor: 56.36
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.8
Crystallization temperature (K): 277
Crystal growth procedure: 100mM HEPES, 9.5%(v/v) PEG 6000, 8.8%(v/v) ethylene glycol, soaking the crystal with 6.25 mM Cpd-2
Matthews coefficient: 2.95
Solvent content (%): 58.25
Ligand: 4-(hydroxymethyl)-5-(1-methylindol-3-yl)-1,2-oxazole-3-carboxylic acid (U7L)
Ligand formula: C14 H12 N2 O4
Ligand molecular weight: 272.256
Ligand SMILES: Cn1cc(c2c1cccc2)c3c(c(no3)C(=O)O)CO
Ligand InChI: InChI=1S/C14H12N2O4/c1-16-6-9(8-4-2-3-5-11(8)16)13-10(7-17)12(14(18)19)15-20-13/h2-6,17H,7H2,1H3,(H,18,19)
Release date: 2024-02-28
Native state mass spectrometry, surface plasmon resonance and X-ray crystallography correlate strongly as a fragment screening combination (PDB entry 5FLO)
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): 1.66
R work: 0.15831
R free: 0.21513
Average B factor: 14.928
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 (%): 42.1
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: 2016-03-02
Cyclophilin A complexed with the tri-vector ligand 8. (PDB entry 6GJI)
Macromolecule: Peptidyl-prolyl cis-trans isomerase A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 5.2.1.8
Sequence length: 165 residues
Sequence: MVNPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGFGYKGSCFHRIIPGFMCQGGDFTRHNGTGGKSIYGEKFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKTEWLDGKHVVFGKVKEGMNIVEAMERFGSRNGKTSKKITIADCGQLE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.6
R work: 0.15254
R free: 0.19071
Average B factor: 29.126
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8
Crystallization temperature (K): 279.15
Crystal growth procedure: PEG 8000, Tris-HCl
Matthews coefficient: 2.82
Solvent content (%): 56.36
Ligand: ethyl 2-[[(4-aminophenyl)methyl-[(1-methyl-1,2,3-triazol-4-yl)methyl]carbamoyl]amino]ethanoate (F1E)
Ligand formula: C16 H22 N6 O3
Ligand molecular weight: 346.384
Ligand SMILES: CCOC(=O)CNC(=O)N(Cc1ccc(cc1)N)Cc2cn(nn2)C
Ligand InChI: InChI=1S/C16H22N6O3/c1-3-25-15(23)8-18-16(24)22(11-14-10-21(2)20-19-14)9-12-4-6-13(17)7-5-12/h4-7,10H,3,8-9,11,17H2,1-2H3,(H,18,24)
Release date: 2018-11-07
The Fk1 domain of FKBP51 in complex with (2'R,5'S,12'R)-12'-cyclohexyl-2'-[2-(3,4-dimethoxyphenyl)ethyl]-3',19'-dioxa-10',13',16'-triazaspiro[cyclopropane-1,15'- tricyclo[18.3.1.0-5,10]tetracosane]-1'(24'),20',22'-triene-4',11',14',17'-tetrone (PDB entry 7AOU)
Macromolecule: Peptidyl-prolyl cis-trans isomerase FKBP5
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 5.2.1.8
Sequence length: 128 residues
Sequence: GAPATVTEQGEDITSKKDRGVLKIVKRVGNGEETPMIGDKVYVHYKGKLSNGKKFDSSHDRNEPFVFSLGKGQVIKAWDIGVATMKKGEICHLLCKPEYAYGSAGSLPKIPSNATLFFEIELLDFKGE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.16
R work: 0.1428
R free: 0.1753
Average B factor: 17.696
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: 32% PEG-3350, 0.2 M NH4-acetate and HEPES-NaOH pH 7.5
Matthews coefficient: 2.28
Solvent content (%): 46.06
Ligand: (2'R,5'S,12'R)-12'-cyclohexyl-2'-[2-(3,4-dimethoxyphenyl)ethyl]-3',19'-dioxa-10',13',16'-triazaspiro[cyclopropane-1,15'- tricyclo[18.3.1.0-5,10]tetracosane]-1'(24'),20',22'-triene-4',11',14',17'-tetrone (RTT)
Ligand formula: C37 H47 N3 O8
Ligand molecular weight: 661.784
Ligand SMILES: COc1ccc(cc1OC)CCC2c3cccc(c3)OCC(=O)NC4(CC4)C(=O)NC(C(=O)N5CCCCC5C(=O)O2)C6CCCCC6
Ligand InChI: InChI=1S/C37H47N3O8/c1-45-30-17-15-24(21-31(30)46-2)14-16-29-26-11-8-12-27(22-26)47-23-32(41)39-37(18-19-37)36(44)38-33(25-9-4-3-5-10-25)34(42)40-20-7-6-13-28(40)35(43)48-29/h8,11-12,15,17,21-22,25,28-29,33H,3-7,9-10,13-14,16,18-20,23H2,1-2H3,(H,38,44)(H,39,41)/t28-,29+,33+/m0/s1
Release date: 2021-04-21