satarupa22/MacromolecularLigandDB huggingface dataset:
Crystal structure of human carbonic anhydrase isozyme II with 4-Propylthiobenzenesulfonamide (PDB entry 5LLG)
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): 1.12
R work: 0.138
R free: 0.1671
Average B factor: 17.787
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 291
Crystal growth procedure: Crystallization buffer: 0.1M sodium bicine (pH 9), 0.2M ammonium sulfate and 2M sodium malonate (pH 7)
Matthews coefficient: 2.01
Solvent content (%): 38.4
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: 2017-08-16
The structure of Stable-5-Lipoxygenase bound to AKBA (PDB entry 6NCF)
Macromolecule: Arachidonate 5-lipoxygenase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.13.11.34
Sequence length: 691 residues
Sequence: MGSSHHHHHHSSGLVPRGSHMPSYTVTVATGSQEHAGTDDYIYLSLVGSAGCSEKHLLDKGSFERGAVDSYDVTVDEELGEIQLVRIEKRKYGSNDDWYLKYITLKTPHGDYIEFPCYRWITGDVEVVLRDGRAKLARDDQIHILKQHRRKELETRQKQYRWMEWNPGFPLSIDAKCHKDLPRDIQFDSEKGVDFVLNYSKAMENLFINRFMHMFQSSWNDFADFEKIFVKISNTISERVMNHWQEDLMFGYQFLNGANPVLIRRCTELPEKLPVTTEMVECSLERQLSLEQEVQQGNIFIVDFELLDGIDANKTDPCTLQFLAAPICLLYKNLANKIVPIAIQLNQIPGDENPIFLPSDAKYDWLLAKIWVRSSDFHVHQTITHLLRTHLVSEVFGIAMYRQLPAVHPIFKLLVAHVRFTIAINTKAREQLICECGLFDKANATGGGGHVQMVQRAMKDLTYASLCFPEAIKARGMESKEDIPYYFYRDDGLLVWEAIRTFTAEVVDIYYEGDQVVEEDPELQDFVNDVYVYGMRGRKSSGFPKSVKSREQLSEYLTVVIFTASAQHAAVNFGQYDWASWIPNAPPTMRAPPPTAKGVVTIEQIVDTLPDRGRSCWHLGAVWALSQFQENELFLGMYPEEHFIEKPVKEAMARFRKNLEAIVSVIAERNENLQLPYYYLSPDRIPNSVAI
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.871
R work: 0.2747
R free: 0.2972
Average B factor: 33.7875
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6
Crystallization temperature (K): 295
Crystal growth procedure: 8-12% Tacsimate pH 6.0
Matthews coefficient: 2.56
Solvent content (%): 51.99
Ligand: FE (II) ION (FE2)
Ligand formula: Fe
Ligand molecular weight: 55.845
Ligand SMILES: [Fe+2]
Ligand InChI: InChI=1S/Fe/q+2
Release date: 2020-05-13
Human PI3Kdelta in complex with Compound 2-10 ((3S)-3-benzyl-3-methyl-5-[5-(2-methylpyrimidin-5-yl)pyrazolo[1,5-a]pyrimidin-3-yl]-1,3-dihydro-2H-indol-2-one) (PDB entry 6PYR)
Macromolecule: Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit delta isoform
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.1.153
Sequence length: 1018 residues
Sequence: NQSVVVDFLLPTGVYLNFPVSRNANLSTIKQLLWHRAQYEPLFHMLSGPEAYVFTCINQTAEQQELEDEQRRLCDVQPFLPVLRLVAREGDRVKKLINSQISLLIGKGLHEFDSLCDPEVNDFRAKMCQFCEEAAARRQQLGWEAWLQYSFPLQLEPSAQTWGPGTLRLPNRALLVNVKFEGSEESFTFQVSTKDVPLALMACALRKKATVFRQPLVEQPEDYTLQVNGRHEYLYGSYPLCQFQYICSCLHSGLTPHLTMVHSSSILAMRDEQSNPAPQVQKPRAKPPPIPAKKPSSVSLWSLEQPFRIELIQGSKVNADERMKLVVQAGLFHGNEMLCKTVSSSEVSVCSEPVWKQRLEFDINICDLPRMARLCFALYAVIEKAKKARSTKKKSKKADCPIAWANLMLFDYKDQLKTGERCLYMWPSVPDEKGELLNPTGTVRSNPNTDSAAALLICLPEVAPHPVYYPALEKILELGRHSECVHVTEEEQLQLREILERRGSGELYEHEKDLVWKLRHEVQEHFPEALARLLLVTKWNKHEDVAQMLYLLCSWPELPVLSALELLDFSFPDCHVGSFAIKSLRKLTDDELFQYLLQLVQVLKYESYLDCELTKFLLDRALANRKIGHFLFWHLRSEMHVPSVALRFGLILEAYCRGSTHHMKVLMKQGEALSKLKALNDFVKLSSQKTPKPQTKELMHLCMRQEAYLEALSHLQSPLDPSTLLAEVCVEQCTFMDSKMKPLWIMYSNEEAGSGGSVGIIFKNGDDLRQDMLTLQMIQLMDVLWKQEGLDLRMTPYGCLPTGDRTGLIEVVLRSDTIANIQLNKSNMAATAAFNKDALLNWLKSKNPGEALDRAIEEFTLSCAGYCVATYVLGIGDRHSDNIMIRESGQLFHIDFGHFLGNFKTKFGINRERVPFILTYDFVHVIQQGKTNNSEKFERFRGYCERAYTILRRHGLLFLHLFALMRAAGLPELSCSKDIQYLKDSLALGKTEEEALKHFRVKFNEALRESWKTKVNWL
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.21
R work: 0.2207
R free: 0.2591
Average B factor: 78.765
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 293
Crystal growth procedure: 12-14% PEG6000, 100 mM MES/NaOH, pH 5.75, 5 mM DTT
Matthews coefficient: 2.61
Solvent content (%): 52.91
Ligand: (3S)-3-benzyl-3-methyl-5-[5-(2-methylpyrimidin-5-yl)pyrazolo[1,5-a]pyrimidin-3-yl]-1,3-dihydro-2H-indol-2-one (P5J)
Ligand formula: C27 H22 N6 O
Ligand molecular weight: 446.503
Ligand SMILES: Cc1ncc(cn1)c2ccn3c(n2)c(cn3)c4ccc5c(c4)C(C(=O)N5)(C)Cc6ccccc6
Ligand InChI: InChI=1S/C27H22N6O/c1-17-28-14-20(15-29-17)23-10-11-33-25(31-23)21(16-30-33)19-8-9-24-22(12-19)27(2,26(34)32-24)13-18-6-4-3-5-7-18/h3-12,14-16H,13H2,1-2H3,(H,32,34)/t27-/m0/s1
Release date: 2019-08-28
The Crystal structure of RO4493940 bound to CK2alpha (PDB entry 7ZWG)
Macromolecule: Casein kinase II subunit alpha
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 328 residues
Sequence: SGPVPSRARVYTDVNTHRPSEYWDYESHVVEWGNQDDYQLVRKLGRGKYSEVFEAINITNNEKVVVKILKPVAAAKIKREIKILENLRGGPNIITLADIVKDPVSRTPALVFEHVNNTDFKQLYQTLTDYDIRFYMYEILKALDYCHSMGIMHRDVKPHNVMIDHEHRKLRLIDWGLAEFYHPGQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRKEPFFHGHDNYDQLVRIAKVLGTEDLYDYIDKYNIELDPRFNDILGRHSRKRWERFVHSENQHLVSPEALDFLDKLLRYDHQSRLTAREAMEHPYFYTVVK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.31
R work: 0.1881
R free: 0.2027
Average B factor: 24.7142
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 298
Crystal growth procedure: 112.5mM Mes, 35% glycerol ethoxylate, 180 mM ammonium acetate
Matthews coefficient: 1.99
Solvent content (%): 38.15
Ligand: SODIUM ION ()
Ligand formula: Na
Ligand molecular weight: 22.99
Ligand SMILES: [Na+]
Ligand InChI: InChI=1S/Na/q+1
Release date: 2023-05-31
Covalent fragment group deposition -- Crystal Structure of OUTB2 in complex with PCM-0102821 (PDB entry 5QIT)
Macromolecule: Ubiquitin thioesterase OTUB2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.19.12
Sequence length: 225 residues
Sequence: FNLISEKCDILSILRDHPENRIYRRKIEELSKRFTAIRKTKGDRNCFYRALGYSYLESLLGKSREIFKFKERVLQTPNDLLAAGFEEHKFRNFFNAFYSVVELVEKDGSVSSLLKVFNDQSASDHIVQFLRLLTSAFIRNRADFFRHFIDEEMDIKDFCTHEVEPMATECDHIQITALSQALSIALQVEYVDEMDTALNHHVFPEAATPSVYLLYKTSHYNILYA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.46
R work: 0.1415
R free: 0.1946
Average B factor: 17.96
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 293
Crystal growth procedure: 16% PEG4K, 0.1M HEPES pH 7.0, 8% 2-propanol, 5 mM DTT
Matthews coefficient: 2.34
Solvent content (%): 47.54
Ligand: N-[(E)-(3-methylphenyl)methylidene]acetamide (J5J)
Ligand formula: C10 H11 N O
Ligand molecular weight: 161.2
Ligand SMILES: Cc1cccc(c1)C=NC(=O)C
Ligand InChI: InChI=1S/C10H11NO/c1-8-4-3-5-10(6-8)7-11-9(2)12/h3-7H,1-2H3/b11-7+
Release date: 2019-12-18
Peptide QLRQQE in complex with human cathepsin V C25A mutant (PDB entry 7QHK)
Macromolecule: Cathepsin L2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.22.43
Sequence length: 221 residues
Sequence: LPKSVDWRKKGYVTPVKNQKQCGSAWAFSATGALEGQMFRKTGKLVSLSEQNLVDCSRPQGNQGCNGGFMARAFQYVKENGGLDSEESYPYVAVDEICKYRPENSVAQDTGFTVVAPGKEKALMKAVATVGPISVAMDAGHSSFQFYKSGIYFEPDCSSKNLDHGVLVVGYGFEGANSQNSKYWLVKNSWGPEWGSNGYVKIAKDKNNHCGIATAASYPNV
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.83
R work: 0.1731
R free: 0.2
Average B factor: 29.9
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 278
Crystal growth procedure: 77 % MPD, 23 % of 60 mM TRIS, pH 8
Matthews coefficient: 2.76
Solvent content (%): 55.39
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: 2022-12-21
PIM1 kinase in complex with Compound 1s (PDB entry 4XHK)
Macromolecule: Serine/threonine-protein kinase pim-1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 315 residues
Sequence: GPMLLSKINSLAHLRAAPCNDLHATKLAPGKEKEPLESQYQVGPLLGSGGFGSVYSGIRVSDNLPVAIKHVEKDRISDWGELPNGTRVPMEVVLLKKVSSGFSGVIRLLDWFERPDSFVLILERPEPVQDLFDFITERGALQEELARSFFWQVLEAVRHCHNCGVLHRDIKDENILIDLNRGELKLIDFGSGALLKDTVYTDFDGTRVYSPPEWIRYHRYHGRSAAVWSLGILLYDMVCGDIPFEHDEEIIRGQVFFRQRVSSECQHLIRWCLALRPSDRPTFEEIQNHPWMQDVLLPQETAEIHLHSLSPGPSK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.9
R work: 0.1561
R free: 0.1842
Average B factor: 30.688
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 5.5
Crystallization temperature (K): 298
Crystal growth procedure: 0.1M BisTRIS pH 5.5, 0.2M NaCl, 1.5M Ammonium Sulfate
Matthews coefficient: 3.06
Solvent content (%): 59.75
Ligand: 2-(2,6-difluorophenyl)-N-{4-[(3S)-pyrrolidin-3-yloxy]pyridin-3-yl}-1,3-thiazole-4-carboxamide (3YR)
Ligand formula: C19 H16 F2 N4 O2 S
Ligand molecular weight: 402.418
Ligand SMILES: c1cc(c(c(c1)F)c2nc(cs2)C(=O)Nc3cnccc3OC4CCNC4)F
Ligand InChI: InChI=1S/C19H16F2N4O2S/c20-12-2-1-3-13(21)17(12)19-25-15(10-28-19)18(26)24-14-9-23-7-5-16(14)27-11-4-6-22-8-11/h1-3,5,7,9-11,22H,4,6,8H2,(H,24,26)/t11-/m0/s1
Release date: 2015-02-11
Crystal structure of NTMT1 in complex with PPKRIA peptide (PDB entry 5E1M)
Macromolecule: N-terminal Xaa-Pro-Lys N-methyltransferase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1.244
Sequence length: 241 residues
Sequence: MGSSHHHHHHSSGLVPRGSTSEVIEDEKQFYSKAKTYWKQIPPTVDGMLGGYGHISSIDINSSRKFLQRFLREGPNKTGTSCALDCGAGIGRITKRLLLPLFREVDMVDITEDFLVQAKTYLGEEGKRVRNYFCCGLQDFTPEPDSYDVIWIQWVIGHLTDQHLAEFLRRCKGSLRPNGIIVIKDNMAQEGVILDDVDSSVCRDLDVVRRIICSAGLSLLAEERQENLPDEIYHVYSFALR
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.75
R work: 0.1611
R free: 0.1882
Average B factor: 18.374
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 26% PEG3350, 16% tacsimate
Matthews coefficient: 3.06
Solvent content (%): 59.76
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: 2015-10-28
UbcH5a-Ub isopeptide conjugate (PDB entry 5TUT)
Macromolecule: Ubiquitin-conjugating enzyme E2 D1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2.23
Sequence length: 150 residues
Sequence: GSHMALKRIQKELSDLQRDPPAHCSAGPVGDDLFHWQATIMGPPDSAYQGGVFFLTVHFPTDYPFKPPKIAFTTKIYHPNINSNGSIKLDILRSQWSPALTVSKVLLSICSLLCDPNPDDPLVPDIAQIYKSDKEKYNRHAREWTQKYAM
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.604
R work: 0.2002
R free: 0.2426
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystal growth procedure: Hampton PEG/Ion F10
Matthews coefficient: 2.2
Solvent content (%): 44.17
Release date: 2017-11-08
EGFR kinase domain mutant "TMLR" with a imidazopyridinyl-aminopyrimidine inhibitor (PDB entry 5HIC)
Macromolecule: Epidermal growth factor receptor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 331 residues
Sequence: GSGEAPNQALLRILKETEFKKIKVLGSGAFGTVYKGLWIPEGEKVKIPVAIKELREATSPKANKEILDEAYVMASVDNPHVCRLLGICLTSTVQLIMQLMPFGCLLDYVREHKDNIGSQYLLNWCVQIAKGMNYLEDRRLVHRDLAARNVLVKTPQHVKITDFGRAKLLGAAAAEYHAEGGKVPIKWMALESILHRIYTHQSDVWSYGVTVWELMTFGSKPYDGIPASEISSILEKGERLPQPPICTIDVYMIMVKCWMIDADSRPKFRELIIEFSKMARDPQRYLVIQGDERMHLPSPTDSNFYRALMDEEDMDDVVDADEYLIPQQGNS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.6
R work: 0.1894
R free: 0.2325
Average B factor: 61.33
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 292
Crystal growth procedure: PEG 10K, ethylene glycol
Matthews coefficient: 3.48
Solvent content (%): 64.7
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: 2016-04-06
Structure of ULK1 LIR motif bound to GABARAP (PDB entry 6HYO)
Macromolecule: Serine/threonine-protein kinase ULK1,Gamma-aminobutyric acid receptor-associated protein
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 137 residues
Sequence: GPTMGTDDFVMVPAQFPGGSMKFVYKEEHPFEKRRSEGEKIRKKYPDRVPVIVEKAPKARIGDLDKKKYLVPSDLTVGQFYFLIRKRIHLRAEDALFFFVNNVIPPTSATMGQLYQEHHEEDFFLYIAYSDESVYGL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.07
R work: 0.1416
R free: 0.1608
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.2M MgCl2. 0.1 M Na cacodylate pH 6.5, 20% PEG1000
Matthews coefficient: 2.67
Solvent content (%): 53.96
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: 2019-05-08
Crystal structure of AF10-DOT1L complex (PDB entry 7EDP)
Macromolecule: Histone-lysine N-methyltransferase, H3 lysine-79 specific
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1.360
Sequence length: 40 residues
Sequence: DWATLSLEKLLKEKQALKSQISEKQRHCLELQISIVELEK
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.2
R work: 0.2213
R free: 0.2682
Average B factor: 57.0047
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 25% Ethylene glycol
Matthews coefficient: 3.29
Solvent content (%): 62.62
Release date: 2021-04-28
Bioreductive 4-hydroxy-3-nitro-5-ureido-benzenesulfonamides selectively target the tumor-associated carbonic anhydrase isoforms IX and XII and show hypoxia-enhanced cytotoxicity against human cancer cell lines. (PDB entry 6EEO)
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): 1.719
R work: 0.1729
R free: 0.2069
Average B factor: 24.4039
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.8
Crystallization temperature (K): 298
Crystal growth procedure: 1.6 M Sodium citrate, 50 mM Tris-HCl
Matthews coefficient: 2.19
Solvent content (%): 43.71
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: 2018-11-28
BACE crystal structure with tricyclic aminothiazine inhibitor (PDB entry 4ZSQ)
Macromolecule: Beta-secretase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.23.46
Sequence length: 442 residues
Sequence: MAGVLPAHGTQHGIRLPLRSGLGGAPLGLRLPRETDEEPEEPGRRGSFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHPFLHRYYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTVRANIAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTHVPNLFSLQLCGAGFPLNQSEVLASVGGSMIIGGIDHSLYTGSLWYTPIRREWYYEVIIVRVEINGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVKSIKAASSTEKFPDGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRITILPQQYLRPVEDVATSQDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSACHVHDEFRTAAVEGPFVTLDMEDCGYNIPQTDEST
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.3
R work: 0.20191
R free: 0.25798
Average B factor: 54.488
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 277
Crystal growth procedure: PEG8000, sodium cacodylate, ammonium sulfate
Matthews coefficient: 2.69
Solvent content (%): 54.2
Ligand: N-[(4S,4aS,6S,8aR)-10-aminohexahydro-3H-4,8a-(epithiomethenoazeno)isochromen-6(1H)-yl]-3-chlorobenzamide (4RX)
Ligand formula: C17 H20 Cl N3 O2 S
Ligand molecular weight: 365.878
Ligand SMILES: c1cc(cc(c1)Cl)C(=O)NC2CCC34COCC(C3C2)SC(=N4)N
Ligand InChI: InChI=1S/C17H20ClN3O2S/c18-11-3-1-2-10(6-11)15(22)20-12-4-5-17-9-23-8-14(13(17)7-12)24-16(19)21-17/h1-3,6,12-14H,4-5,7-9H2,(H2,19,21)(H,20,22)/t12-,13+,14+,17-/m0/s1
Release date: 2015-06-10
A crystal form of a human CDK2-CDK7 chimera (PDB entry 8RU8)
Macromolecule: Cyclin-dependent kinase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.22
Sequence length: 306 residues
Sequence: GPLGSPEFMENFQKVEKLGEGQYGVVYKARNKLTGEVVALKKIRLDTETEGVPSTAIREISLLKELNHPNIIKLLDVIHTENKLYLVFEFLHQDLEVFMKASALTGIPLPLIKSYLFQLLQGLAFCHSHRVLHRDLKPNNLLINTEGAIKLADFGLARAFGVPVRTYTHEVVTLWYRAPEILLGCKYYSTAVDIWSLGCIFAEMVTRRALFPGDSEIDQLFRIFRTLGTPDEVVWPGVTSMPDYKPSFPKWARQDFSKVVPPLDEDGRSLLSQMLHYDPNKRISAKAALAHPFFQDVTKPVPHLRL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.51
R work: 0.2033
R free: 0.2408
Average B factor: 28.809
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 12% 1,2-Propanediol
.12% 1,3-Propanediol
.12% 1,4-Butanediol
.12M 1,6-Hexanediol
.12% 1-Butanol
.12% 2-Propanol
30% MPEG 500
10% PEG 20000
.1M pH=7.5 MOPS/NaHEPES
Matthews coefficient: 2.04
Solvent content (%): 39.6
Ligand: (3R,4R)-4-[[[7-[(phenylmethyl)amino]-3-propan-2-yl-pyrazolo[1,5-a]pyrimidin-5-yl]amino]methyl]piperidin-3-ol (I74)
Ligand formula: C22 H30 N6 O
Ligand molecular weight: 394.513
Ligand SMILES: CC(C)c1cnn2c1nc(cc2NCc3ccccc3)NCC4CCNCC4O
Ligand InChI: InChI=1S/C22H30N6O/c1-15(2)18-13-26-28-21(25-11-16-6-4-3-5-7-16)10-20(27-22(18)28)24-12-17-8-9-23-14-19(17)29/h3-7,10,13,15,17,19,23,25,29H,8-9,11-12,14H2,1-2H3,(H,24,27)/t17-,19+/m1/s1
Release date: 2024-06-26
Structure of Get3 bound to the transmembrane domain of Sec22 (PDB entry 4XWO)
Macromolecule: Antibody heavy chain
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 230 residues
Sequence: EISEVQLVESGGGLVQPGGSLRLSCAASGFNLYYYSIHWVRQAPGKGLEWVASISPYSSSTSYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARGRWYRRALDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHT
Oligomeric state: Hetero 7-mer
Stoichiometry: A2, B2, C2, D1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.75
R work: 0.1956
R free: 0.2472
Average B factor: 75.163
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 298
Crystal growth procedure: 13% PEG 3350, 25 mM succinic acid pH 7.0
Matthews coefficient: 2.4
Solvent content (%): 48.7
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: 2015-03-25
Structure of phospho-Parkin bound to phospho-ubiquitin (PDB entry 6GLC)
Macromolecule: E3 ubiquitin-protein ligase parkin
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2.31
Sequence length: 389 residues
Sequence: GPMIVFVRFNSSHGFPVEVDSDTSIFQLKEVVAKRQGVPADQLRVIFAGKELRNDWTVQNCDLDQQSIVHIVQRPWRKGQEMNATGGDDPRNAAGGCEREPQSLTRVDLSSSVLPGDSVGLAVILHTDSRKDSPPAGSPAGRSIYNSFYVYCKGPCQRVQPGKLRVQCSTCRQATLTLTQGPSCWDDVLIPNRMSGECQSPHCPGTSAEFFFKCGAHPTSDKETSVALHLIATNSRNITCITCTDVRSPVLVFQCNSRHVICLDCFHLYCVTRLNDRQFVHDPQLGYSLPCVAGCPNSLIKELHHFRILGEEQYNRYQQYGAEECVLQMGGVLCPRPGCGAGLLPEPDCRKVTCEGGNGLGCGFAFCRECKEAYHEGECSAVFENLYFQ
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.1799
R free: 0.2054
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 291
Crystal growth procedure: 12.5% (w/v) PEG 1000, 12.5% (w/v) PEG 3350, 12.5% (v/v) MPD, 0.03 M of each sodium nitrate, disodium hydrogen phosphate, ammonium sulphate, 0.1 M MOPS/HEPES-Na (pH 7.5)
Matthews coefficient: 2.32
Solvent content (%): 40.56
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: 2018-06-13
Human Sirt2 in complex with ADP-ribose and the inhibitor quercetin (PDB entry 6QCN)
Macromolecule: NAD-dependent protein deacetylase sirtuin-2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.5.1
Sequence length: 304 residues
Sequence: HMKERLLDELTLEGVARYMQSERCRRVICLVGAGISTSAGIPDFRSPSTGLYDNLEKYHLPYPEAIFEISYFKKHPEPFFALAKELYPGQFKPTICHYFMRLLKDKGLLLRCYTQNIDTLERIAGLEQEDLVEAHGTFYTSHCVSASCRHEYPLSWMKEKIFSEVTPKCEDCQSLVKPDIVFFGESLPARFFSCMQSDFLKVDLLLVMGTSLQVQPFASLISKAPLSTPRLLINKEKAGQSDPFLGMIMGLGGGMDFDSKKAYRDVAWLGECDQGCLALAELLGWKKELEDLVRREHASIDAQS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.23
R work: 0.20926
R free: 0.23405
Average B factor: 49.105
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.8
Crystallization temperature (K): 293
Crystal growth procedure: 14% PEG 10,000, 0.1M ammonium acetate pH 5.8
Matthews coefficient: 2.66
Solvent content (%): 53.73
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: 2019-12-25
Human kallikrein-related peptidase 7 (KLK7) in the unliganded state (PDB entry 6Y4S)
Macromolecule: Kallikrein-7
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.117
Sequence length: 224 residues
Sequence: IIDGAPCARGSHPWQVALLSGNQLHCGGVLVNERWVLTAAHCKMNEYTVHLGSDTLGDRRAQRIKASKSFRHPGYSTQTHVNDLMLVKLNSQARLSSMVKKVRLPSRCEPPGTTCTVSGWGTTTSPDVTFPSDLMCVDVKLISPQDCTKVYKDLLENSMLCAGIPDSKKNACNGDSGGPLVCRGTLQGLVSWGTFPCGQPNDPGVYTQVCKFTKWINDTMKKHR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.23
R work: 0.219
R free: 0.242
Average B factor: 56.26
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 292
Crystal growth procedure: 2.9 M ammonium sulphate, 0.1 M HEPES, pH 8.5 and 0.5-2 %
PEG 3350
Matthews coefficient: 2.74
Solvent content (%): 55.03
Ligand: TRIETHYLENE GLYCOL (PGE)
Ligand formula: C6 H14 O4
Ligand molecular weight: 150.173
Ligand SMILES: C(COCCOCCO)O
Ligand InChI: InChI=1S/C6H14O4/c7-1-3-9-5-6-10-4-2-8/h7-8H,1-6H2
Release date: 2020-05-20
Crystal structure of RNA dioxygenase bound with an inhibitor (PDB entry 6AKW)
Macromolecule: Alpha-ketoglutarate-dependent dioxygenase FTO
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11
Sequence length: 492 residues
Sequence: MGSSHHHHHHSSGLVPRGSHMTPKDDEFYQQWQLKYPKLILREASSVSEELHKEVQEAFLTLHKHGCLFRDLVRIQGKDLLTPVSRILIGNPGCTYKYLNTRLFTVPWPVKGSNIKHTEAEIAAACETFLKLNDYLQIETIQALEELAAKEKANEDAVPLCMSADFPRVGMGSSYNGQDEVDIKSRAAYNVTLLNFMDPQKMPYLKEEPYFGMGKMAVSWHHDENLVDRSAVAVYSYSCEGPEEESEDDSHLEGRDPDIWHVGFKISWDIETPGLAIPLHQGDCYFMLDDLNATHQHCVLAGSQPRFSSTHRVAECSTGTLDYILQRCQLALQNVCDDVDNDDVSLKSFEPAVLKQGEEIHNEVEFEWLRQFWFQGNRYRKCTDWWCQPMAQLEALWKKMEGVTNAVLHEVKREGLPVEQRNEILTAILASLTARQNLRREWHARCQSRIARTLPADQKPECRPYWEKDDASMPLPFDLTDIVSELRGQLLE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.2
R work: 0.2122
R free: 0.2544
Crystallization method: EVAPORATION
Crystallization temperature (K): 293
Crystal growth procedure: 100 mM sodium citrate, 12% PEG 3350, 8% isopropanol
Matthews coefficient: 2.85
Solvent content (%): 56.77
Ligand: 2-OXOGLUTARIC ACID (AKG)
Ligand formula: C5 H6 O5
Ligand molecular weight: 146.098
Ligand SMILES: C(CC(=O)O)C(=O)C(=O)O
Ligand InChI: InChI=1S/C5H6O5/c6-3(5(9)10)1-2-4(7)8/h1-2H2,(H,7,8)(H,9,10)
Release date: 2019-05-29