satarupa22/MacromolecularLigandDB huggingface dataset:
Identification of a New Zinc Binding Chemotype by Fragment Screening (PDB entry 5TY1)
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): 1.6
R work: 0.13726
R free: 0.18733
Average B factor: 13.386
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.3
Crystallization temperature (K): 281
Crystal growth procedure: the reservoir condition consisted of 2.9 M ammonium sulfate with 0.1 M Tris buffer at pH 8.3; concentrated CA II at ~10 mg mL-1 was set up with seeding; dry compound was added to crystals several days before harvesting and data collection
Matthews coefficient: 2.1
Solvent content (%): 41.47
Ligand: (5R)-5-(2,4-dimethoxyphenyl)-1,3-oxazolidine-2,4-dione (7QV)
Ligand formula: C11 H11 N O5
Ligand molecular weight: 237.209
Ligand SMILES: COc1ccc(c(c1)OC)C2C(=O)NC(=O)O2
Ligand InChI: InChI=1S/C11H11NO5/c1-15-6-3-4-7(8(5-6)16-2)9-10(13)12-11(14)17-9/h3-5,9H,1-2H3,(H,12,13,14)/t9-/m1/s1
Release date: 2017-10-04
DNA Polymerase Mu, 8-oxodGTP:At Product State Ternary Complex, 50 mM Mg2+ (960min) (PDB entry 7KT9)
Macromolecule: DNA-directed DNA/RNA polymerase mu
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 356 residues
Sequence: GSAAAPLSPAWMPAYACQRPTPLTHHNTGLSEALEILAEAAGFEGSEGRLLTFCRAASVLKALPSPVTTLSQLQGLPHFGEHSSRVVQELLEHGVCEEVERVRRSERYQTMKLFTQIFGVGVKTADRWYREGLRTLDDLREQPQKLTQQQKAGLQHHQDLSTPVLRSDVDALQQVVEEAVGQALPGATVTLTGGFRRGKLQGHDVDFLITHPKEGQEAGLLPRVMCRLQDQGLILYHQHQHSCCESPTRLAQQSHMDAFERSFCIFRLPQPGSWKAVRVDLVVAPVSQFPFALLGWTGSKLFQRELRRFSRKEKGLWLNSHGLFDPEQKTFFQAASEEDIFRHLGLEYLPPEQRNA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.482
R work: 0.1552
R free: 0.1755
Average B factor: 22.8378
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 85-90mM HEPES pH 7.5, 17-18% PEG4000
Matthews coefficient: 2.52
Solvent content (%): 51.18
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: 2021-12-15
Human TET2 in complex with unfavourable DNA substrate. (PDB entry 7NE6)
Macromolecule: Methylcytosine dioxygenase TET2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11
Sequence length: 463 residues
Sequence: GGSDFPSCRCVEQIIEKDEGPFYTHLGAGPNVAAIREIMEERFGQKGKAIRIERVIYTGKEGKSSQGCPIAKWVVRRSSSEEKLLCLVRERAGHTCEAAVIVILILVWEGIPLSLADKLYSELTETLRKYGTLTNRRCALNEERTCACQGLDPETCGASFSFGCSWSMYYNGCKFARSKIPRKFKLLGDDPKEEEKLESHLQNLSTLMAPTYKKLAPDAYNNQIEYEHRAPECRLGLKEGRPFSGVTACLDFCAHAHRDLHNMQNGSTLVCTLTREDNREFGGKPEDEQLHVLPLYKVSDVDEFGSVEAQEEKKRSGAIQVLSSFRRKVRMLAEPVKTCRQRKLEAKKAAAEKLSGGGGSGGGGSGGGGSDEVWSDSEQSFLDPDIGGVAVAPTHGSILIECAKRELHATTPLKNPNRNHPTRISLVFYQHKSMNEPKHGLALWEAKMAEKAREKEEECEKYG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.3
R work: 0.1951
R free: 0.227
Average B factor: 51.61
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.3
Crystallization temperature (K): 278
Crystal growth procedure: 0.1M MES pH=6.3, 23% PEG2000MME
Matthews coefficient: 2.54
Solvent content (%): 51.64
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: 2022-03-02
Crystal structure of human MTH1 in complex with compound MI0639 (PDB entry 6JVG)
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: MGASRLYTLVLVLQPQRVLLGMKKRGFGAGRWNGFGGKVQEGETIEDGARRELQEESGLTVDALHKVGQIVFEFVGEPELMDVHVFCTDSIQGTPVESDEMRPCWFQLDQIPFKDMWPDDSYWFPLLLQKKKFHGYFKFQGQDTILDYTLREVDTV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.844
R work: 0.1855
R free: 0.2425
Average B factor: 20.9759
Crystallization method: EVAPORATION
Crystallization pH: 3.75
Crystallization temperature (K): 298
Crystal growth procedure: 30% PEG6000, 200 mM Lithium sulphate, 100 mM Sodium acetate pH 3.75
Matthews coefficient: 2.28
Solvent content (%): 46.06
Ligand: 5-ethyl-4-methyl-6-(morpholin-4-yl)pyrimidin-2-amine (95F)
Ligand formula: C11 H18 N4 O
Ligand molecular weight: 222.287
Ligand SMILES: CCc1c(nc(nc1N2CCOCC2)N)C
Ligand InChI: InChI=1S/C11H18N4O/c1-3-9-8(2)13-11(12)14-10(9)15-4-6-16-7-5-15/h3-7H2,1-2H3,(H2,12,13,14)
Release date: 2020-10-28
Crystal structure of the WDR domain of human DCAF1 in complex with CYCA-117-70 (PDB entry 7SSE)
Macromolecule: DDB1- and CUL4-associated factor 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 315 residues
Sequence: GASAFRPISVFREANEDESGFTCCAFSARERFLMLGTCTGQLKLYNVFSGQEEASYNCHNSAITHLEPSRDGSLLLTSATWSQPLSALWGMKSVFDMKHSFTEDHYVEFSKHSQDRVIGTKGDIAHIYDIQTGNKLLTLFNPDLANNYKRNCATFNPTDDLVLNDGVLWDVRSAQAIHKFDKFNMNISGVFHPNGLEVIINTEIWDLRTFHLLHTVPALDQCRVVFNHTGTVMYGAMLQADDEDDLMEERMKSPFGSSFRTFNATDYKPIATIDVKRNIFDLCTDTKDCYLAVIENQGSMDALNMDTVCRLYEVG
Oligomeric state: Homo 2-mer
Stoichiometry: A2
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.62
R work: 0.2056
R free: 0.2335
Average B factor: 26.441
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 291
Crystal growth procedure: 30% PEG3350 ,0.1M Ammonium Sulphate, 0.1M Bis-Tris pH5.5
Matthews coefficient: 2.21
Solvent content (%): 44.28
Ligand: N-[(3R)-1-(3-fluorophenyl)piperidin-3-yl]-6-(morpholin-4-yl)pyrimidin-4-amine (B1I)
Ligand formula: C19 H24 F N5 O
Ligand molecular weight: 357.425
Ligand SMILES: c1cc(cc(c1)F)N2CCCC(C2)Nc3cc(ncn3)N4CCOCC4
Ligand InChI: InChI=1S/C19H24FN5O/c20-15-3-1-5-17(11-15)25-6-2-4-16(13-25)23-18-12-19(22-14-21-18)24-7-9-26-10-8-24/h1,3,5,11-12,14,16H,2,4,6-10,13H2,(H,21,22,23)/t16-/m1/s1
Release date: 2021-12-15
Irak4-inhibitor co-structure (PDB entry 4ZTM)
Macromolecule: Interleukin-1 receptor-associated kinase 4
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 301 residues
Sequence: VSDTRFHSFSFYELKNVTNNFDERPISVGGNKMGEGGFGVVYKGYVNNTTVAVKKLAAMVDITTEELKQQFDQEIKVMAKCQHENLVELLGFSSDGDDLCLVYVYMPNGSLLDRLSCLDGTPPLSWHMRCKIAQGAANGINFLHENHHIHRDIKSANILLDEAFTAKISDFGLARASEKFAQTVMTSRIVGTTAYMAPEALRGEITPKSDIYSFGVVLLEIITGLPAVDEHREPQLLLDIKEEIEDEEKTIEDYIDKKMNDADSTSVEAMYSVASQCLHEKKNKRPDIKKVQQLLQEMTAS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.66
R work: 0.1934
R free: 0.2259
Average B factor: 54.04
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.4
Crystallization temperature (K): 289
Crystal growth procedure: 1.80 to 2.0 M Sodium Malonate, 0.2 M Sodium Acetate, 25 mM Hexamminecobalt(III)chloride, 0.05%w/v Pluronic-F-68
Matthews coefficient: 2.64
Solvent content (%): 53.39
Ligand: 5-(1,3-benzothiazol-2-yl)-2-(cyclopropylamino)-6-{[(1R,2S,3R,4R)-2,3-dihydroxy-4-(hydroxymethyl)cyclopentyl]amino}pyrimidin-4(3H)-one (4S2)
Ligand formula: C20 H23 N5 O4 S
Ligand molecular weight: 429.493
Ligand SMILES: c1ccc2c(c1)nc(s2)C3=C(N=C(NC3=O)NC4CC4)NC5CC(C(C5O)O)CO
Ligand InChI: InChI=1S/C20H23N5O4S/c26-8-9-7-12(16(28)15(9)27)22-17-14(18(29)25-20(24-17)21-10-5-6-10)19-23-11-3-1-2-4-13(11)30-19/h1-4,9-10,12,15-16,26-28H,5-8H2,(H3,21,22,24,25,29)/t9-,12-,15-,16+/m1/s1
Release date: 2015-09-02
PanDDA analysis group deposition -- Crystal Structure of JMJD1B in complex with FM001700a (PDB entry 5RB1)
Macromolecule: Lysine-specific demethylase 3B
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11
Sequence length: 372 residues
Sequence: MHHHHHHSSGVDLGTENLYFQSMTSHSWLCDGRLLCLHDPSNKNNWKIFRECWKQGQPVLVSGVHKKLKSELWKPEAFSQEFGDQDVDLVNCRNCAIISDVKVRDFWDGFEIICKRLRSEDGQPMVLKLKDWPPGEDFRDMMPTRFEDLMENLPLPEYTKRDGRLNLASRLPSYFVRPDLGPKMYNAYGLITAEDRRVGTTNLHLDVSDAVNVMVYVGIPIGEGAHDEEVLKTIDEGDADEVTKERIHDHKEKPGALWHIYAAKDAEKIRELLRKVGEEQGQENPPDHDPIHDQSWYLDQTLRKRLYEEYGVQGWAIVQFLGDAVFIPAGAPHQVHNLYSCIKVAEDFVSPEHVKHCFRLTQEFRHLSNTHT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.76
R work: 0.1813
R free: 0.2139
Average B factor: 32.61
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.1M bis-tris pH 5.5 21% PEG3350  0.3M magnesium chloride
Matthews coefficient: 2.79
Solvent content (%): 55.85
Ligand: ~{N}2-pyridin-2-ylbenzene-1,2-diamine (S4V)
Ligand formula: C11 H11 N3
Ligand molecular weight: 185.225
Ligand SMILES: c1ccc(c(c1)N)Nc2ccccn2
Ligand InChI: InChI=1S/C11H11N3/c12-9-5-1-2-6-10(9)14-11-7-3-4-8-13-11/h1-8H,12H2,(H,13,14)
Release date: 2020-04-22
Structural and mechanistical studies of the nuclear import by Importin-alpha (PDB entry 5H43)
Macromolecule: Importin subunit alpha-1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 429 residues
Sequence: SNQGTVNWSVDDIVKGINSSNVENQLQATQAARKLLSREKQPPIDNIIRAGLIPKFVSFLGRTDCSPIQFESAWALTNIASGTSEQTKAVVDGGAIPAFISLLASPHAHISEQAVWALGNIAGDGSVFRDLVIKYGAVDPLLALLAVPDMSSLACGYLRNLTWTLSNLCRNKNPAPPIDAVEQILPTLVRLLHHDDPEVLADTCWAISYLTDGPNERIGMVVKTGVVPQLVKLLGASELPIVTPALRAIGNIVTGTDEQTQVVIDAGALAVFPSLLTNPKTNIQKEATWTMSNITAGRQDQIQQVVNHGLVPFLVSVLSKADFKTQKEAVWAVTNYTSGGTVEQIVYLVHCGIIEPLMNLLTAKDTKIILVILDAISNIFQAAEKLGETEKLSIMIEECGGLDKIEALQNHENESVYKASLSLIEKYFS
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.3
R work: 0.21144
R free: 0.24253
Average B factor: 68.447
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293.15
Crystal growth procedure: 3%(v/v) Tacsimate pH5.0, 0.1M Sodium citrate tribasic dehydrate pH5.6, 16%(w/v) PEG 3350
Matthews coefficient: 2.89
Solvent content (%): 57.38
Release date: 2017-10-25
Notum Fragment 690 (PDB entry 7BC9)
Macromolecule: Palmitoleoyl-protein carboxylesterase NOTUM
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.1.98
Sequence length: 383 residues
Sequence: ETGSAQQLNEDLRLHLLLNTSVTCNDGSPAGYYLKESRGSRRWLLFLEGGWYCFNRENCDSRYDTMRRLMSSRDWPRTRTGTGILSSQPEENPYWWNANMVFIPYCSSDVWSGASSKSEKNEYAFMGALIIQEVVRELLGRGLSGAKVLLLAGSSAGGTGVLLNVDRVAEQLEKLGYPAIQVRGLADSGWFLDNKQYRHTDCVDTITCAPTEAIRRGIRYWNGVVPERCRRQFQEGEEWNCFFGYKVYPTLRSPVFVVQWLFDEAQLTVDNVHLTGQPVQEGLRLYIQNLGRELRHTLKDVPASFAPACLSHEIIIRSHWTDVQVKGTSLPRALHCWDRSLHDSHKASKTPLKGCPVHLVDSCPWPHCNPSCPTGTKHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.73
R work: 0.2271
R free: 0.2521
Average B factor: 26.9878
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 296
Crystal growth procedure: 1.5 M Ammonium Sulphate
0.1 M Sodium Citrate, pH4.2
Matthews coefficient: 1.97
Solvent content (%): 37.68
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: 2022-01-12
Highly Potent and Selective Plasmin Inhibitors Based on the Sunflower Trypsin Inhibitor-1 Scaffold Attenuate Fibrinolysis in Plasma (PDB entry 6D40)
Macromolecule: Plasminogen
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.7
Sequence length: 248 residues
Sequence: PSFDCGKPQVEPKKCPGRVVGGCVAHPHSWPWQVSLRTRFGMHFCGGTLISPEWVLTAAHCLEKSPRPSSYKVILGAHQEVNLEPHVQEIEVSRLFLEPTRKDIALLKLSSPAVITDKVIPACLPSPNYVVADRTECFITGWGETQGTFGAGLLKEAQLPVIENKVCNRYEFLNGRVQSTELCAGHLAGGTDSCQGDSGGPLVCFEKDKYILQGVTSWGLGCARPNKPGVYVRVSRFVTWIEGVMRNN
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.43
R work: 0.1856
R free: 0.21
Average B factor: 24.9964
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 293
Crystal growth procedure: 15% PEG4000, 0.1 M MES, 0.15 M ammonium sulfate
Matthews coefficient: 2.3
Solvent content (%): 46.58
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: 2019-01-23
Carbonic Anhydrase IX mimic complexed with benzene sulfonamide MB11-710A (PDB entry 6OUI)
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): 1.528
R work: 0.1767
R free: 0.2067
Average B factor: 22.5232
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 298
Crystal growth procedure: 1.6M sodium citrate, 50mM Tris HCl, pH 7.8
Matthews coefficient: 2.15
Solvent content (%): 42.86
Ligand: 3-{[(4-hydroxybutyl)carbamoyl]amino}benzene-1-sulfonamide (N7D)
Ligand formula: C11 H17 N3 O4 S
Ligand molecular weight: 287.335
Ligand SMILES: c1cc(cc(c1)S(=O)(=O)N)NC(=O)NCCCCO
Ligand InChI: InChI=1S/C11H17N3O4S/c12-19(17,18)10-5-3-4-9(8-10)14-11(16)13-6-1-2-7-15/h3-5,8,15H,1-2,6-7H2,(H2,12,17,18)(H2,13,14,16)
Release date: 2020-05-06
Crystal Structure of p38alpha in Complex with Lipid Pocket Ligand 9g (PDB entry 5N64)
Macromolecule: Mitogen-activated protein kinase 14
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.24
Sequence length: 360 residues
Sequence: MSQERPTFYRQELNKTIWEVPERYQNLSPVGSGAYGSVCAAFDTKTGLRVAVKKLSRPFQSIIHAKRTYRELRLLKHMKHENVIGLLDVFTPARSLEEFNDVYLVTHLMGADLNNIVKCQKLTDDHVQFLIYQILRGLKYIHSADIIHRDLKPSNLAVNEDCELKILDFGLARHTDDEMTGYVATRWYRAPEIMLNWMHYNQTVDIWSVGCIMAELLTGRTLFPGTDHIDQLKLILRLVGTPGAELLKKISSESARNYIQSLTQMPKMNFANVFIGANPLAVDLLEKMLVLDSDKRITAAQALAHAYFAQYHDPDDEPVADPYDQSFESRDLLIDEWKSLTYDEVISFVPPPLDQEEMES
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.4
R work: 0.2043
R free: 0.2407
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293.15
Crystal growth procedure: 100 mM MES pH 5.6-6.2
20-30 % PEG4000
50 mM BOG
Matthews coefficient: 2.34
Solvent content (%): 47.33
Ligand: 2-phenyl-~{N}4-(thiophen-2-ylmethyl)quinazoline-4,7-diamine (8OH)
Ligand formula: C19 H16 N4 S
Ligand molecular weight: 332.422
Ligand SMILES: c1ccc(cc1)c2nc3cc(ccc3c(n2)NCc4cccs4)N
Ligand InChI: InChI=1S/C19H16N4S/c20-14-8-9-16-17(11-14)22-18(13-5-2-1-3-6-13)23-19(16)21-12-15-7-4-10-24-15/h1-11H,12,20H2,(H,21,22,23)
Release date: 2017-09-20
Human biliverdin IX beta reductase: NADP/Erythrosin extra bluish ternary complex (PDB entry 5OOH)
Macromolecule: Flavin reductase (NADPH)
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.5.1.30
Sequence length: 206 residues
Sequence: MAVKKIAIFGATGQTGLTTLAQAVQAGYEVTVLVRDSSRLPSEGPRPAHVVVGDVLQAADVDKTVAGQDAVIVLLGTRNDLSPTTVMSEGARNIVAAMKAHGVDKVVACTSAFLLWDPTKVPPRLQAVTDDHIRMHKVLRESGLKYVAVMPPHIGDQPLTGAYTVTLDGRGPSRVISKHDLGHFMLRCLTTDEYDGHSTYPSHQYQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.2
R work: 0.122
R free: 0.1474
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 30% PEG 3350, 0.2 M AMMONIUM SULFATE, 0.1 M SODIUM CACODYLATE PH 6.5. NADP ADDED TO A FINAL CONCENTRATION OF 2.5 MM
Matthews coefficient: 2.4
Solvent content (%): 48.76
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: 2018-03-07
Structure of human Nocturnin C-terminal domain (PDB entry 6MAL)
Macromolecule: Nocturnin
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.13.4
Sequence length: 312 residues
Sequence: GPPPRFQRDFVDLRTDCPSTHPPIRVMQWNILAQALGEGKDNFVQCPVEALKWEERKCLILEEILAYQPDILCLQEVDHYFDTFQPLLSRLGYQGTFFPKPWSPCLDVEHNNGPDGCALFFLQNRFKLVNSANIRLTAMTLKTNQVAIAQTLECKESGRQFCIAVTHLKARTGWERFRSAQGCDLLQNLQNITQGAKIPLIVCGDFNAEPTEEVYKHFASSSLNLNSAYKLLSADGQSEPPYTTWKIRTSGECRHTLDYIWYSKHALNVRSALDLLTEEQIGPNRLPSFNYPSDHLSLVCDFSFTEESDGLS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.6
R work: 0.2522
R free: 0.3069
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: Magnesium Chloride, HEPES pH 7.5, PEG 400
Matthews coefficient: 2.11
Solvent content (%): 41.76
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: 2018-09-05
Crystal structure of the human NK1 substance P receptor (PDB entry 6J20)
Macromolecule: Substance-P receptor,Endolysin
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.2.1.17
Sequence length: 441 residues
Sequence: DNVLPVDSDLSPNISTNTSEPNQFVQPAWQIVLWAAAYTVIVVTSVVGNVVVMWIILAHKRMRTVTNYFLVNLAFANASMAAFNTVVNFTYAVHNEWYYGLFYCKFHNFFPIAAVFASIWSMTAVAFDRYMAIIHPLQPRLSATATKVVICVIWVLALLLAFPQGYYSTTETMPSRVVCMIEWPEHPNKIYEKVYHICVTVLIYFLPLLVIGYAYTVVGIRLWASNIFEMLRIDEGGGSGGDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDAYHEQVSAKRKVVKMMIVVVCTFAICWLPFHIFFLLPYINPDLYLKKFIQQVYLAIMWLAMSSTMYNPIIYCCLNDRFRLGFKHAFRCCPFISAGDYEGLE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.7
R work: 0.233
R free: 0.26
Average B factor: 114.89
Crystallization method: LIPIDIC CUBIC PHASE
Crystallization temperature (K): 293
Crystal growth procedure: 100mM MES, pH 6.0-6.6, 25-35% PEG 400, 200-350mM ammonium tartrate dibasic
Matthews coefficient: 4.08
Solvent content (%): 69.88
Ligand: 5-[[(2~{R},3~{S})-2-[(1~{R})-1-[3,5-bis(trifluoromethyl)phenyl]ethoxy]-3-(4-fluorophenyl)morpholin-4-yl]methyl]-1,2-dihydro-1,2,4-triazol-3-one (GBQ)
Ligand formula: C23 H21 F7 N4 O3
Ligand molecular weight: 534.427
Ligand SMILES: CC(c1cc(cc(c1)C(F)(F)F)C(F)(F)F)OC2C(N(CCO2)CC3=NC(=O)NN3)c4ccc(cc4)F
Ligand InChI: InChI=1S/C23H21F7N4O3/c1-12(14-8-15(22(25,26)27)10-16(9-14)23(28,29)30)37-20-19(13-2-4-17(24)5-3-13)34(6-7-36-20)11-18-31-21(35)33-32-18/h2-5,8-10,12,19-20H,6-7,11H2,1H3,(H2,31,32,33,35)/t12-,19+,20-/m1/s1
Release date: 2019-03-06
Crystal Structure of double mutant Y115E Y117E human Secretory Glutaminyl Cyclase (PDB entry 7CP0)
Macromolecule: Glutaminyl-peptide cyclotransferase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2.5
Sequence length: 327 residues
Sequence: AWPEEKNYHQPAILNSSALRQIAEGTSISEMWQNDLQPLLIERYPGSPGSYAARQHIMQRIQRLQADWVLEIDTFLSQTPEGERSFSNIISTLNPTAKRHLVLACHYDSKYFSHWNNRVFVGATDSAVPCAMMLELARALDKKLLSLKTVSDSKPDLSLQLIFFDGEEAFLHWSPQDSLYGSRHLAAKMASTPHPPGARGTSQLHGMDLLVLLDLIGAPNPTFPNFFPNSARWFERLQAIEHELHELGLLKDHSLEGRYFQNYSYGGVIQDDHIPFLRRGVPVLHLIPSPFPEVWHTMDDNEENLDESTIDNLNKILQVFVLEYLHL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.7
R work: 0.2054
R free: 0.2228
Average B factor: 17.651
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6
Crystallization temperature (K): 277.15
Crystal growth procedure: 100 mM MES buffer pH 6.5, 46-67 mM NaOH, 100 mM ammonium sulfate
Matthews coefficient: 2.75
Solvent content (%): 55.23
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: 2021-01-13
Human angiogenin ALS variant V103I (PDB entry 5M9S)
Macromolecule: Angiogenin
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.27
Sequence length: 124 residues
Sequence: MQDNSRYTHFLTQHYDAKPQGRDDRYCESIMRRRGLTSPCKDINTFIHGNKRSIKAICENKNGNPHRENLRISKSSFQVTTCKLHGGSPWPPCQYRATAGFRNIVVACENGLPVHLDQSIFRRP
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.85
R work: 0.20824
R free: 0.26447
Average B factor: 33.444
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 289
Crystal growth procedure: 0.2 M Na/K tartrate
0.1 M MES
20% PEG 4000
Matthews coefficient: 3.12
Solvent content (%): 60.62
Ligand: D(-)-TARTARIC ACID (TAR)
Ligand formula: C4 H6 O6
Ligand molecular weight: 150.087
Ligand SMILES: C(C(C(=O)O)O)(C(=O)O)O
Ligand InChI: InChI=1S/C4H6O6/c5-1(3(7)8)2(6)4(9)10/h1-2,5-6H,(H,7,8)(H,9,10)/t1-,2-/m0/s1
Release date: 2017-02-22
Cocrystal structure of human CaMKII-alpha (CAMK2A)kinase domain and GluA1 (PDB entry 6X5Q)
Macromolecule: Calcium/calmodulin-dependent protein kinase type II subunit alpha
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.17
Sequence length: 268 residues
Sequence: TRFTEEYQLFEELGKGAFSVVRRCVKVLAGQEYAAKIINTKKLSARDHQKLEREARICRLLKHPNIVRLHDSISEEGHHYLIFDLVTGGELFEDIVAREYYSEADASHCIQQILEAVLHCHQMGVVHRNLKPENLLLASKLKGAAVKLADFGLAIEVEGEQQAWFGFAGTPGYLSPEVLRKDPYGKPVDLWACGVILYILLVGYPPFWDEDQHRLYKQIKAGAYDFPSPEWDTVTPEAKDLINKMLTINPSKRITAAEALKHPWISHR
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.14
R work: 0.1893
R free: 0.235
Average B factor: 15.884
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8
Crystallization temperature (K): 277
Crystal growth procedure: 0.1 M Tris, 28% w/v PEG 4000
Matthews coefficient: 2.01
Solvent content (%): 38.69
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: 2020-12-23
Crystal structure of human MTH1 in complex with compound MI1012 (PDB entry 6JVK)
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: MGASRLYTLVLVLQPQRVLLGMKKRGFGAGRWNGFGGKVQEGETIEDGARRELQEESGLTVDALHKVGQIVFEFVGEPELMDVHVFCTDSIQGTPVESDEMRPCWFQLDQIPFKDMWPDDSYWFPLLLQKKKFHGYFKFQGQDTILDYTLREVDTV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.1
R work: 0.1825
R free: 0.2499
Average B factor: 27.003
Crystallization method: EVAPORATION
Crystallization pH: 3.75
Crystallization temperature (K): 298
Crystal growth procedure: 30% PEG6000, 200 mM Lithium sulphate, 100 mM Sodium acetate pH 3.75
Matthews coefficient: 2.26
Solvent content (%): 45.5
Ligand: N4-methyl-6-(4-methylpiperazin-1-yl)pyrimidine-2,4-diamine (CEU)
Ligand formula: C10 H18 N6
Ligand molecular weight: 222.29
Ligand SMILES: CNc1cc(nc(n1)N)N2CCN(CC2)C
Ligand InChI: InChI=1S/C10H18N6/c1-12-8-7-9(14-10(11)13-8)16-5-3-15(2)4-6-16/h7H,3-6H2,1-2H3,(H3,11,12,13,14)
Release date: 2020-10-28