satarupa22/MacromolecularLigandDB huggingface dataset:
Co-complex CYP46A1 with compound 3f (PDB entry 7N6F)
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): 1.4
R work: 0.1597
R free: 0.1847
Average B factor: 19.303
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 290
Crystal growth procedure: 0.4M CaCl2, 10-20% PEG3350
Matthews coefficient: 2.28
Solvent content (%): 41.2
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: 2022-07-27
Crystal Structure of a FVIIa-Trypsin Chimera (ST) in Complex with Soluble Tissue Factor (PDB entry 4ZMA)
Macromolecule: Coagulation factor VII
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.21
Sequence length: 152 residues
Sequence: ANAFLEELRPGSLERECKEEQCSFEEAREIFKDAERTKLFWISYSDGDQCASSPCQNGGSCKDQLQSYICFCLPAFEGRNCETHKDDQLICVNENGGCEQYCSDHTGTKRSCRCHEGYSLLADGVSCTPTVEYPCGKIPILEKRNASKPQGR
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.3
R work: 0.2401
R free: 0.2947
Average B factor: 41.399
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.1
Crystallization temperature (K): 295
Crystal growth procedure: 0.1M Cacodylate,11% PEG 8000 , with seeding
Matthews coefficient: 2.51
Solvent content (%): 51.08
Ligand: CALCIUM ION (CA)
Ligand formula: Ca
Ligand molecular weight: 40.078
Ligand SMILES: [Ca+2]
Ligand InChI: InChI=1S/Ca/q+2
Release date: 2015-12-30
Crystal structure of human PTPN2 in complex with active site inhibitor (PDB entry 9C55)
Macromolecule: Tyrosine-protein phosphatase non-receptor type 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 315 residues
Sequence: GMPTTIEREFEELDTQRRWQPLYLEIRNESHDYPHRVAKFPENRNRNRYRDVSPYDHSRVKLQNAENDYINASLVDIEEAQRSYILTQGPLPNTCCHFWLMVWQQKTKAVVMLNRIVEKESVKCAQYWPTDDQEMLFKETGFSVKLLSEDVKSYYTVHLLQLENINSGETRTISHFHYTTWPDFGVPESPASFLNFLFKVRESGSLNPDHGPAVIHCSAGIGRSGTFSLVDTCLVLMEKGDDINIKQVLLNMRKYRMGLIQTPDQLRFSYMAIIEGAKCIKGDSSIQKRWKELSKEDLSPAFDHSPNKIMTEKYN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.36
R work: 0.1988
R free: 0.2339
Average B factor: 53.45
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 100mM MES/imidazole pH6.5, 7% w/v Peg 8000, 14% v/v ethylene glycol, 30mM sodium l-glutamate, 30mM dl-alanine, 30mM glycine, 30mM dl-lysine HCl, 30mM dl-serine
Matthews coefficient: 2.32
Solvent content (%): 46.91
Ligand: 5-(3-{[1-(BENZYLSULFONYL)PIPERIDIN-4-YL]AMINO}PHENYL)-4-BROMO-3-(CARBOXYMETHOXY)THIOPHENE-2-CARBOXYLIC ACID (527)
Ligand formula: C25 H25 Br N2 O7 S2
Ligand molecular weight: 609.509
Ligand SMILES: c1ccc(cc1)CS(=O)(=O)N2CCC(CC2)Nc3cccc(c3)c4c(c(c(s4)C(=O)O)OCC(=O)O)Br
Ligand InChI: InChI=1S/C25H25BrN2O7S2/c26-21-22(35-14-20(29)30)24(25(31)32)36-23(21)17-7-4-8-19(13-17)27-18-9-11-28(12-10-18)37(33,34)15-16-5-2-1-3-6-16/h1-8,13,18,27H,9-12,14-15H2,(H,29,30)(H,31,32)
Release date: 2024-09-04
Crystal structure of phosphatidyl inositol 4-kinase II beta in complex with MM1373 (PDB entry 8A5X)
Macromolecule: Phosphatidylinositol 4-kinase type 2-beta,Endolysin
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.1.67
Sequence length: 514 residues
Sequence: VTIGTSEMNAFLDDPEFADIMLRAEQAIEVGIFPERISQGSSGSYFVKDPKRKIIGVFKPKSEEPYGQLNPKWTKYNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDAYKNLGRGCLIPNQGYLSEAGAYLVDNKLHLSIVPKTKVVWLVSETFNYNAIDRAKSRGKKYALEKVPKVGRKFHRIGLPPKIGSFQLFVEGYKEAEYWLRKFEADPLPENIRKQFQSQFERLVILDYIIRNTDRGNDNWLVRYEKQKCEKEIDHKESKWIDDEEFLIKIAAIDNGLAFPFKHPDEWRAYPFHWAWLPQAKVPFSEEIRNLILPYISDMNFVQDLCEDLYELFKTDKGFDKATFESQMSVMRGQILNLTQALRDGKSPFQLVQIPCVIVE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.4
R work: 0.2105
R free: 0.231
Average B factor: 43.98
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 10% w/v PEG 8.000, 20% v/v ethylene glycol, 3% v/v DMSO,
100 mM bicine/Trizma base pH 8.5,
20 mM 1,6-hexanediol, 20 mM 1-butanol, 20 mM 1,2-propanediol, 20 mM 2-propanol, 20 mM 1,4-butanediol, 20 mM 1,3-propanediol
Matthews coefficient: 2.41
Solvent content (%): 48.96
Ligand: 4-azanyl-7-[3-(hydroxymethyl)phenyl]quinazoline-6-carboxamide (L6A)
Ligand formula: C16 H14 N4 O2
Ligand molecular weight: 294.308
Ligand SMILES: c1cc(cc(c1)c2cc3c(cc2C(=O)N)c(ncn3)N)CO
Ligand InChI: InChI=1S/C16H14N4O2/c17-15-13-5-12(16(18)22)11(6-14(13)19-8-20-15)10-3-1-2-9(4-10)7-21/h1-6,8,21H,7H2,(H2,18,22)(H2,17,19,20)
Release date: 2022-10-05
Crystal structure of AKR1B10 in complex with NADP+ and Androst-4-ene-3-beta-6-alpha-diol (PDB entry 5Y7N)
Macromolecule: Aldo-keto reductase family 1 member B10
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.1.1
Sequence length: 316 residues
Sequence: MATFVELSTKAKMPIVGLGTWKSPLGKVKEAVKVAIDAGYRHIDCAYVYQNEHEVGEAIQEKIQEKAVKREDLFIVSKLWPTFFERPLVRKAFEKTLKDLKLSYLDVYLIHWPQGFKSGDDLFPKDDKGNAIGGKATFLDAWEAMEELVDEGLVKALGVSNFSHFQIEKLLNKPGLKYKPVTNQVECHPYLTQEKLIQYCHSKGITVTAYSPLGSPDRPWAKPEDPSLLEDPKIKEIAAKHKKTAAQVLIRFHIQRNVIVIPKSVTPARIVENIQVFDFKLSDEEMATILSFNRNWRACNVLQSSHLEDYPFNAEY
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.5
R work: 0.17789
R free: 0.24471
Average B factor: 31.637
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 9
Crystallization temperature (K): 289
Crystal growth procedure: 100mM Tris, 30-35% PEG 6000, 3-5% 1,6-Hexanediol, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Matthews coefficient: 2.53
Solvent content (%): 51.39
Ligand: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE (NAP)
Ligand formula: C21 H28 N7 O17 P3
Ligand molecular weight: 743.405
Ligand SMILES: c1cc(c[n+](c1)C2C(C(C(O2)COP(=O)([O-])OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)OP(=O)(O)O)O)O)O)C(=O)N
Ligand InChI: InChI=1S/C21H28N7O17P3/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(44-46(33,34)35)14(30)11(43-21)6-41-48(38,39)45-47(36,37)40-5-10-13(29)15(31)20(42-10)27-3-1-2-9(4-27)18(23)32/h1-4,7-8,10-11,13-16,20-21,29-31H,5-6H2,(H7-,22,23,24,25,32,33,34,35,36,37,38,39)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
Release date: 2018-08-29
Structure of the mitogen activated kinase kinase 7 in complex with pyrazolopyrimidine 1k (PDB entry 6QG7)
Macromolecule: Dual specificity mitogen-activated protein kinase kinase 7
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.12.2
Sequence length: 318 residues
Sequence: MGHHHHHHSAKQTGYLTIGGQRYQAEINDLENLGEMGSGTCGQVWKMRFRKTGHVIAVKQMRRSGNKEENKRILMDLDVVLKSHDCPYIVQCFGTFITNTDVFIAMELMGTCAEKLKKRMQGPIPERILGKMTVAIVKALYYLKEKHGVIHRDVKPSNILLDERGQIKLCDFGISGRLVDSKAKTRSAGCAAYMAPERIDPPDPTKPDYDIRADVWSLGISLVELATGQFPYKNCKTDFEVLTKVLQEEPPLLPGHMGFSGDFQSFVKDCLTKDHRKRPKYNKLLEHSFIKRYETLEVDVASWFKDVMAKTESPRTSG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.1
R work: 0.2337
R free: 0.2679
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 0.2 M Sodiumcitrate
20% PEG3350
Matthews coefficient: 2.32
Solvent content (%): 47.09
Ligand: (R)-1-(3-(4-amino-3-(naphthalen-1-yl)-1H-pyrazolo[3,4-d]pyrimidin-1-yl)piperidin-1-yl)prop-2-en-1-one (6HL)
Ligand formula: C23 H22 N6 O
Ligand molecular weight: 398.46
Ligand SMILES: C=CC(=O)N1CCCC(C1)n2c3c(c(n2)c4cccc5c4cccc5)c(ncn3)N
Ligand InChI: InChI=1S/C23H22N6O/c1-2-19(30)28-12-6-9-16(13-28)29-23-20(22(24)25-14-26-23)21(27-29)18-11-5-8-15-7-3-4-10-17(15)18/h2-5,7-8,10-11,14,16H,1,6,9,12-13H2,(H2,24,25,26)/t16-/m1/s1
Release date: 2019-05-22
Crystal structure of human SIRT5 in complex with diazirine inhibitor 9 (PDB entry 7X3P)
Macromolecule: NAD-dependent protein deacylase sirtuin-5, mitochondrial
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1
Sequence length: 277 residues
Sequence: ARPSSSMADFRKFFAKAKHIVIISGAGVSAESGVPTFRGAGGYWRKWQAQDLATPLAFAHNPSRVWEFYHYRREVMGSKEPNAGHRAIAECETRLGKQGRRVVVITQNIDELHRKAGTKNLLEIHGSLFKTRCTSCGVVAENYKSPICPALSGKGAPEPGTQDASIPVEKLPRCEEAGCGGLLRPHVVWFGENLDPAILEEVDRELAHCDLCLVVGTSSVVYPAAMFAPQVAARGVPVAEFNTETTPATNRFRFHFQGPCGTTLPEALACHENETVS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.56
R work: 0.1388
R free: 0.1634
Average B factor: 15.2122
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 289
Crystal growth procedure: 23%-27% (v/v) PEG 3350, 0.1 M MES, pH 5.5-6.0, 0.1-0.2 M NaCl
Matthews coefficient: 2.47
Solvent content (%): 50.27
Ligand: 5-[[(5~{S})-6-[[(1~{S})-1-(4-hydroxyphenyl)-2-oxidanylidene-2-(prop-2-ynylamino)ethyl]amino]-6-oxidanylidene-5-[[4-[3-(trifluoromethyl)-1,2-diazirin-3-yl]phenyl]carbonylamino]hexyl]amino]-5-sulfanylidene-pentanoic acid (8VG)
Ligand formula: C31 H33 F3 N6 O6 S
Ligand molecular weight: 674.691
Ligand SMILES: C#CCNC(=O)C(c1ccc(cc1)O)NC(=O)C(CCCCNC(=S)CCCC(=O)O)NC(=O)c2ccc(cc2)C3(N=N3)C(F)(F)F
Ligand InChI: InChI=1S/C31H33F3N6O6S/c1-2-17-36-29(46)26(19-11-15-22(41)16-12-19)38-28(45)23(6-3-4-18-35-24(47)7-5-8-25(42)43)37-27(44)20-9-13-21(14-10-20)30(39-40-30)31(32,33)34/h1,9-16,23,26,41H,3-8,17-18H2,(H,35,47)(H,36,46)(H,37,44)(H,38,45)(H,42,43)/t23-,26-/m0/s1
Release date: 2023-09-06
Crystal structure of a human cytochrome P450 2B6 (Y226H/K262R) in complex with a monoterpene - sabinene (PDB entry 4RQL)
Macromolecule: Cytochrome P450 2B6
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.13
Sequence length: 476 residues
Sequence: MAKKTSSKGKLPPGPRPLPLLGNLLQMDRRGLLKSFLRFREKYGDVFTVHLGPRPVVMLCGVEAIREALVDKAEAFSGRGKIAMVDPFFRGYGVIFANGNRWKVLRRFSVTTMRDFGMGKRSVEERIQEEAQCLIEELRKSKGALMDPTFLFQSITANIICSIVFGKRFHYQDQEFLKMLNLFYQTFSLISSVFGQLFELFSGFLKHFPGAHRQVYKNLQEINAYIGHSVEKHRETLDPSAPRDLIDTYLLHMEKEKSNAHSEFSHQNLNLNTLSLFFAGTETTSTTLRYGFLLMLKYPHVAERVYREIEQVIGPHRPPELHDRAKMPYTEAVIYEIQRFSDLLPMGVPHIVTQHTSFRGYIIPKDTEVFLILSTALHDPHYFEKPDAFNPDHFLDANGALKKTEAFIPFSLGKRICLGEGIARAELFLFFTTILQNFSMASPVAPEDIDLTPQECGVGKIPPTYQIRFLPRHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.105
R work: 0.21101
R free: 0.25771
Average B factor: 26.923
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 291
Crystal growth procedure: 0.1 M HEPES, 25% w/v PEG3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Matthews coefficient: 3.29
Solvent content (%): 62.61
Ligand: 5-CYCLOHEXYL-1-PENTYL-BETA-D-MALTOSIDE (CM5)
Ligand formula: C23 H42 O11
Ligand molecular weight: 494.573
Ligand SMILES: C1CCC(CC1)CCCCCOC2C(C(C(C(O2)CO)OC3C(C(C(C(O3)CO)O)O)O)O)O
Ligand InChI: InChI=1S/C23H42O11/c24-11-14-16(26)17(27)19(29)23(32-14)34-21-15(12-25)33-22(20(30)18(21)28)31-10-6-2-5-9-13-7-3-1-4-8-13/h13-30H,1-12H2/t14-,15-,16-,17+,18-,19-,20-,21-,22-,23-/m1/s1
Release date: 2015-01-28
Crystal structure of the human CHIP TPR domain in complex with a 5mer acetylated optimized peptide (PDB entry 6NSV)
Macromolecule: E3 ubiquitin-protein ligase CHIP
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2.27
Sequence length: 130 residues
Sequence: SPSAQELKEQGNRLFVGRKYPEAAACYGRAITRNPLVAVYYTNRALCYLKMQQHEQALADCRRALELDGQSVKAHFFLGQCQLEMESYDEAIANLQRAYSLAKEQRLNFGDDIPSALRIAKKKRWNSIEE
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.305
R work: 0.2141
R free: 0.2427
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 298
Crystal growth procedure: 0.05 M CaCl2, 0.1 M HEPES pH 7, 28% PEG 4K, 0.01 M CoCl2
Matthews coefficient: 2.08
Solvent content (%): 40.94
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: 2019-07-31
Crystal structure of FRB-FKBP fusion protein in complex with rapamycin (PDB entry 8XI9)
Macromolecule: FRB-FKBP fusion protein
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 202 residues
Sequence: MGWHEMWHEGLEEASRLYFGERNVKGMFEVLEPLHAMMERGPQTLKETSFNQAYGRDLMEAQEWCRKYMKSGNVKDLTQAWDLYYHVFRRISKQMGVQVETISPGDGRTFPKRGQTCVVHYTGMLEDGKKFDSSRDRNKPFKFMLGKQEVIRGWEEGVAQMSVGQRAKLTISPDYAYGATGHPGIIPPHATLVFDVELLKLE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.85
R work: 0.1872
R free: 0.2184
Average B factor: 30.64
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.4
Crystallization temperature (K): 293
Crystal growth procedure: 4.4M Sodium Acetate
Matthews coefficient: 2.45
Solvent content (%): 49.9
Ligand: RAPAMYCIN IMMUNOSUPPRESSANT DRUG (RAP)
Ligand formula: C51 H79 N O13
Ligand molecular weight: 914.172
Ligand SMILES: CC1CCC2CC(C(=CC=CC=CC(CC(C(=O)C(C(C(=CC(C(=O)CC(OC(=O)C3CCCCN3C(=O)C(=O)C1(O2)O)C(C)CC4CCC(C(C4)OC)O)C)C)O)OC)C)C)C)OC
Ligand InChI: InChI=1S/C51H79NO13/c1-30-16-12-11-13-17-31(2)42(61-8)28-38-21-19-36(7)51(60,65-38)48(57)49(58)52-23-15-14-18-39(52)50(59)64-43(33(4)26-37-20-22-40(53)44(27-37)62-9)29-41(54)32(3)25-35(6)46(56)47(63-10)45(55)34(5)24-30/h11-13,16-17,25,30,32-34,36-40,42-44,46-47,53,56,60H,14-15,18-24,26-29H2,1-10H3/b13-11+,16-12+,31-17+,35-25+/t30-,32-,33-,34-,36-,37+,38+,39+,40-,42+,43+,44-,46-,47+,51-/m1/s1
Release date: 2024-08-07
Crystal Structure of Thrombin in complex with compound20a (PDB entry 6ZUN)
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 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.793
R work: 0.2265
R free: 0.2622
Average B factor: 57.292
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 283
Crystal growth procedure: 0.02 M phosphate buffer pH 7.5, 
27% PEG 8000, 100 mM NaCl
Matthews coefficient: 2.48
Solvent content (%): 50.48
Ligand: [2-[(3-chlorophenyl)methylamino]-7-methoxy-1,3-benzoxazol-5-yl]-[(3~{R},4~{R})-3-methyl-4-oxidanyl-piperidin-1-yl]methanone (QQ5)
Ligand formula: C22 H24 Cl N3 O4
Ligand molecular weight: 429.897
Ligand SMILES: CC1CN(CCC1O)C(=O)c2cc3c(c(c2)OC)oc(n3)NCc4cccc(c4)Cl
Ligand InChI: InChI=1S/C22H24ClN3O4/c1-13-12-26(7-6-18(13)27)21(28)15-9-17-20(19(10-15)29-2)30-22(25-17)24-11-14-4-3-5-16(23)8-14/h3-5,8-10,13,18,27H,6-7,11-12H2,1-2H3,(H,24,25)/t13-,18-/m1/s1
Release date: 2020-08-26
Crystal structure of human JARID1B in complex with 2-oxoglutarate. (PDB entry 5FUP)
Macromolecule: LYSINE-SPECIFIC DEMETHYLASE 5B
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11
Sequence length: 479 residues
Sequence: SMFLPPPECPVFEPSWEEFADPFAFIHKIRPIAEQTGICKVRPPPDWQPPFACDVDKLHFTPRIQRLNELEAQTRVKLGGGGARDYTLRTFGEMADAFKSDYFNMPVHMVPTELVEKEFWRLVSTIEEDVTVEYGADIASKEFGSGFPVRDGKIKLSPEEEEYLDSGWNLNNMPVMEQSVLAHITADICGMKLPWLYVGMCFSSFCWHIEDHWSYSINYLHWGEPKTWYGVPGYAAEQLENVMKKLAPELFVSQPDLLHQLVTIMNPNTLMTHEVPVYRTNQCAGEFVITFPRAYHSGFNQGFNFAEAVNFCTVDWLPLGRQCVEHYRLLHRYCVFSHDEMICKMASKADVLDVVVASTVQKDMAIMIEDEKALRETVRKLGVIDSERMDFELLPDDERQCVKCKTTCFMSAISCSCKPGLLVCLHHVKELCSCPPYKYKLRYRYTLDDLYPMMNALKLRAESYNEWALNVNEALEAKI
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.15
R work: 0.1825
R free: 0.2266
Crystallization pH: 7.5
Crystal growth procedure: 0.1M HEPES PH 7.5 -- 0.8M POTASSIUM PHOSPHATE DIBASIC -- 0.8M SODIUM PHOSPHATE MONOBASIC
Matthews coefficient: 2.01
Solvent content (%): 38.94
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: 2016-03-23
Crystal structure of the G391V variant of human PGM-1 (PDB entry 7S77)
Macromolecule: Phosphoglucomutase-1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 5.4.2.2
Sequence length: 585 residues
Sequence: MHHHHHHSSGVDLGTENLYFQSNMVKIVTVKTQAYQDQKPGTSGLRKRVKVFQSSANYAENFIQSIISTVEPAQRQEATLVVGGDGRFYMKEAIQLIARIAAANGIGRLVIGQNGILSTPAVSCIIRKIKAIGGIILTASHNPGGPNGDFGIKFNISNGGPAPEAITDKIFQISKTIEEYAVCPDLKVDLGVLGKQQFDLENKFKPFTVEIVDSVEAYATMLRSIFDFSALKELLSGPNRLKIRIDAMHGVVGPYVKKILCEELGAPANSAVNCVPLEDFGGHHPDPNLTYAADLVETMKSGEHDFGAAFDGDGDRNMILGKHGFFVNPSDSVAVIAANIFSIPYFQQTGVRGFARSMPTSGALDRVASATKIALYETPTGWKFFGNLMDASKLSLCGEESFGTGSDHIREKDVLWAVLAWLSILATRKQSVEDILKDHWQKYGRNFFTRYDYEEVEAEGANKMMKDLEALMFDRSFVGKQFSANDKVYTVEKADNFEYSDPVDGSISRNQGLRLIFTDGSRIVFRLSGTGSAGATIRLYIDSYEKDVAKINQDPQVMLAPLISIALKVSQLQERTGRTAPTVIT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.8
R work: 0.1927
R free: 0.2518
Average B factor: 82.28
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 293
Crystal growth procedure: condition 2-33 of the Morpheus crystal screen (Molecular Dimensions) at a protein concentration of 10 mg/mL from a hanging drop of 1 ml protein and 4 ml well buffer.  Condition 2-33 contains 0.1 M of a carboxylic acid mixture (0.2 M sodium formate, 0.2 M ammonium acetate, 0.2 M sodium citrate tribasic dihydrate, 0.2 M sodium potassium tartrate tetrahydrate, and 0.2 M sodium oxamate), 0.1 M of a buffer system at pH 8.5 (Tris base and BICINE), and a 30% v/v precipitant mix (40% v/v PEG 500 MME and 20% w/v PEG 20000)
Matthews coefficient: 2.86
Solvent content (%): 56.98
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: 2022-05-04
Human DNA polymerase beta crosslinked complex, 40 s Ca to Mg exchange (PDB entry 7RBK)
Macromolecule: DNA polymerase beta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 341 residues
Sequence: MSKRKAPQETLNGGITDMLTELANFEKNVSQAIHKYNAYRKAASVIAKYPHKIKSGAEAKKLPGVGTKIAEKIDEFLATGKLRKLEKIRQDDTSSSINFLTRVSGIGPSAARKFVDEGIKTLEDLRKNEDKLNHHQRIGLKYFGDFEKRIPREEMLQMQDIVLNEVKKVDSEYIATVCGSFRRGAESSGDMDVLLTHPSFTSESTKQPKLLHQVVEQLQKVHFITDTLSKGETKFMGVCQLPSKNDEKEYPHRRIDIRLIPKDQYYCGVLYFTGSDIFNKNMRAHALEKGFTINEYTIRPLGVTGVAGEPLPVDSEKDIFDYIQWKYREPKDRSEHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.2
R work: 0.1977
R free: 0.2513
Average B factor: 31.515
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 298
Crystal growth procedure: 0.1 M Citrate pH 5.5, 18% PEG6000
Matthews coefficient: 2.2
Solvent content (%): 44.2
Ligand: 2-deoxy-3,5-di-O-phosphono-D-erythro-pentitol (QPJ)
Ligand formula: C5 H14 O10 P2
Ligand molecular weight: 296.106
Ligand SMILES: C(CO)C(C(COP(=O)(O)O)O)OP(=O)(O)O
Ligand InChI: InChI=1S/C5H14O10P2/c6-2-1-5(15-17(11,12)13)4(7)3-14-16(8,9)10/h4-7H,1-3H2,(H2,8,9,10)(H2,11,12,13)/t4-,5+/m1/s1
Release date: 2022-03-09
The crystal structure of CK2alpha in complex with compound 19 (PDB entry 5OT6)
Macromolecule: Casein kinase II subunit alpha
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 352 residues
Sequence: GSMDIEFDDDADDDGSGSGSGSGSSGPVPSRARVYTDVNTHRPSEYWDYESHVVEWGNQDDYQLVRKLGRGKYSEVFEAINITNNEKVVVKILKPVKKKKIKREIKILENLRGGPNIITLADIVKDPVSRTPALVFEHVNNTDFKQLYQTLTDYDIRFYMYEILKALDYCHSMGIMHRDVKPHNVMIDHEHRKLRLIDWGLAEFYHPGQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRKEPFFHGHDNYDQLVRIAKVLGTEDLYDYIDKYNIELDPRFNDILGRHSRKRWERFVHSENQHLVSPEALDFLDKLLRYDHQSRLTAREAMEHPYFYTVVK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.94
R work: 0.219
R free: 0.241
Average B factor: 53.78
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 298
Crystal growth procedure: 112.5mM Mes pH 6.5, 35% glycerol ethoxylate, 180 mM ammonium acetate
Matthews coefficient: 2.23
Solvent content (%): 44.87
Ligand: ACETATE ION (ACT)
Ligand formula: C2 H3 O2
Ligand molecular weight: 59.044
Ligand SMILES: CC(=O)[O-]
Ligand InChI: InChI=1S/C2H4O2/c1-2(3)4/h1H3,(H,3,4)/p-1
Release date: 2018-02-28
X-ray structure of human G166D PGK-1 mutant (PDB entry 5M1R)
Macromolecule: Phosphoglycerate kinase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.2.3
Sequence length: 416 residues
Sequence: SLSNKLTLDKLDVKGKRVVMRVDFNVPMKNNQITNNQRIKAAVPSIKFCLDNGAKSVVLMSHLGRPDGVPMPDKYSLEPVAVELKSLLGKDVLFLKDCVGPEVEKACANPAAGSVILLENLRFHVEEEGKGKDASGNKVKAEPAKIEAFRASLSKLGDVYVNDAFDTAHRAHSSMVGVNLPQKAGGFLMKKELNYFAKALESPERPFLAILGGAKVADKIQLINNMLDKVNEMIIGGGMAFTFLKVLNNMEIGTSLFDEEGAKIVKDLMSKAEKNGVKITLPVDFVTADKFDENAKTGQATVASGIPAGWMGLDCGPESSKKYAEAVTRAKQIVWNGPVGVFEWEAFARGTKALMDEVVKATSRGCITIIGGGDTATCCAKWNTEDKVSHVSTGGGASLELLEGKVLPGVDALSNI
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.64
R work: 0.16425
R free: 0.20095
Average B factor: 21.517
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 294
Crystal growth procedure: Sodium Citrate, 1.6 M
Matthews coefficient: 1.93
Solvent content (%): 35.83
Ligand: ADENOSINE-5'-DIPHOSPHATE (ADP)
Ligand formula: C10 H15 N5 O10 P2
Ligand molecular weight: 427.201
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
Ligand InChI: InChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
Release date: 2017-12-20