satarupa22/MacromolecularLigandDB huggingface dataset:
Crystal structure of human Carbonic Anhydrase II in complex with 4-ethoxybenzenesulfonamide (PDB entry 4RUZ)
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): 1.63
R work: 0.1545
R free: 0.1922
Average B factor: 21.7759
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, 3mM 4-Ethoxybenzenesulfonamide, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Matthews coefficient: 2.07
Solvent content (%): 40.65
Ligand: 4-ethoxybenzenesulfonamide (3W8)
Ligand formula: C8 H11 N O3 S
Ligand molecular weight: 201.243
Ligand SMILES: CCOc1ccc(cc1)S(=O)(=O)N
Ligand InChI: InChI=1S/C8H11NO3S/c1-2-12-7-3-5-8(6-4-7)13(9,10)11/h3-6H,2H2,1H3,(H2,9,10,11)
Release date: 2015-04-22
Crystal structure of Ck2alpha with ZT0633 bound (PDB entry 5MOV)
Macromolecule: Casein kinase II subunit alpha
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 325 residues
Sequence: GPVPSRARVYTDVNTHRPSEYWDYESHVVEWGNQDDYQLVRKLGRGKYSEVFEAINITNNEKVVVKILKPVAAAKIKREIKILENLRGGPNIITLADIVKDPVSRTPALVFEHVNNTDFKQLYQTLTDYDIRFYMYEILKALDYCHSMGIMHRDVKPHNVMIDHEHRKLRLIDWGLAEFYHPGQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRKEPFFHGHDNYDQLVRIAKVLGTEDLYDYIDKYNIELDPRFNDILGRHSRKRWERFVHSENQHLVSPEALDFLDKLLRYDHQSRLTAREAMEHPYFYTV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.2
R work: 0.2057
R free: 0.2688
Average B factor: 33.6
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 298
Crystal growth procedure: 107mM Mes pH 6.5, 29% glycerol ethoxylate, 1 M ammonium acetate
Matthews coefficient: 1.98
Solvent content (%): 37.97
Ligand: 4'-HYDROXYCINNAMIC ACID (HC4)
Ligand formula: C9 H8 O3
Ligand molecular weight: 164.158
Ligand SMILES: c1cc(ccc1C=CC(=O)O)O
Ligand InChI: InChI=1S/C9H8O3/c10-8-4-1-7(2-5-8)3-6-9(11)12/h1-6,10H,(H,11,12)/b6-3+
Release date: 2017-05-24
Crystal structure of the catalytic domain of human PARP1 (apo) (PDB entry 7AAA)
Macromolecule: Poly [ADP-ribose] polymerase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.4.2.30
Sequence length: 352 residues
Sequence: GSKSKLPKPVQDLIKMIFDVESMKKAMVEYEIDLQKMPLGKLSKRQIQAAYSILSEVQQAVSQGSSDSQILDLSNRFYTLIPHDFGMKKPPLLNNADSVQAKAEMLDNLLDIEVAYSLLRGGSDDSSKDPIDVNYEKLKTDIKVVDRDSEEAEIIRKYVKNTHATTHNAYDLEVIDIFKIEREGECQRYKPFKQLHNRRLLWHGSRTTNFAGILSQGLRIAPPEAPVTGYMFGKGIYFADMVSKSANYCHTSQGDPIGLILLGEVALGNMYELKHASHISKLPKGKHSVKGLGKTTPDPSANISLDGVDVPLGTGISSGVNDTSLLYNEYIVYDIAQVNLKYLLKLKFNFKT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.74
R work: 0.204
R free: 0.227
Average B factor: 32.4
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 8.5
Crystallization temperature (K): 293
Crystal growth procedure: 2.45 M ammonium sulfate, 0.1 M Tris pH 8.5
Matthews coefficient: 2.34
Solvent content (%): 47.34
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: 2021-01-13
Notum_ARUK3001185 (PDB entry 7PK3)
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): 1.41
R work: 0.1747
R free: 0.2037
Average B factor: 24.8021
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: 1.93
Solvent content (%): 36.31
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: 2022-09-07
Crystal structure of caspase-7 DEVE peptide complex (PDB entry 5IC6)
Macromolecule: Caspase-7 subunit p20
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.22.60
Sequence length: 198 residues
Sequence: MADDQGCIEEQGVEDSANEDSVDAKPDRSSFVPSLFSKKKKNVTMRSIKTTRDRVPTYQYNMNFEKLGKCIIINNKNFDKVTGMGVRNGTDKDAEALFKCFRSLGFDVIVYNDCSCAKMQDLLKKASEEDHTNAACFACILLSHGEENVIYGKDGVTPIKDLTAHFRGDRCKTLLEKPKLFFIQACRGTELDDGIQAD
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.7
R work: 0.1972
R free: 0.241
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 4.6
Crystallization temperature (K): 298
Crystal growth procedure: 0.2 M ammonium fluoride, 0.1 M sodium acetate pH 4.6, 20% (w/v) PEG 10000
Matthews coefficient: 2.11
Solvent content (%): 41.62
Release date: 2016-07-20
CREBBP bromodomain in complex with Cpd17 (5-(7-(difluoromethyl)-6-(1-methyl-1H-pyrazol-4-yl)-3,4-dihydroquinolin-1(2H)-yl)-3-methylbenzo[d]thiazol-2(3H)-one) (PDB entry 6AY5)
Macromolecule: CREB-binding protein
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1.48
Sequence length: 115 residues
Sequence: KIFKPEELRQALMPTLEALYRQDPESLPFRQPVDPQLLGIPDYFDIVKNPMDLSTIKRKLDTGQYQEPWQYVDDVWLMFNNAWLYNRKTSRVYKFCSKLAEVFEQEIDPVMQSLG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.44
R work: 0.1632
R free: 0.1838
Average B factor: 25.0328
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 6.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.2M MgCl2, 0.1M Bis-Tris pH6.5, 22% PEG3350
Matthews coefficient: 2.5
Solvent content (%): 50.83
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: 2018-02-21
Crystal structure of catalytic fragment of human AlaRS in complex with Aze-SA (PDB entry 5V59)
Macromolecule: Alanine--tRNA ligase, cytoplasmic
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 6.1.1.7
Sequence length: 475 residues
Sequence: MGSSHHHHHHSSGLVPRGSHMDSTLTASEIRQRFIDFFKRNEHTYVHSSATIPLDDPTLLFANAGMNQFKPIFLNTIDPSHPMAKLSRAANTQKCIRAGGKHNDLDDVGKDVYHHTFFEMLGSWSFGDYFKELACKMALELLTQEFGIPIERLYVTYFGGDEAAGLEADLECKQIWQNLGLDDTKILPGNMKDNFWEMGDTGPCGPCSEIHYDRIGGRDAAHLVNQDDPNVLEIWNLVFIQYNREADGILKPLPKKSIDTGMGLERLVSVLQNKMSNYDTDLFVPYFEAIQKGTGARPYTGKVGAEDADGIDMAYRVLADHARTITVALADGGRPDNTGRGYVLRRILRRAVRYAHEKLNASRGFFATLVDVVVQSLGDAFPELKKDPDMVKDIINEEEVQFLKTLSRGRRILDRKIQSLGDSKTIPGDTAWLLYDTYGFPVDLTGLIAEEKGLVVDMDGFEEERKLAQLKSQGK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.03
R work: 0.1799
R free: 0.2146
Average B factor: 26.974
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 8
Crystallization temperature (K): 310
Crystal growth procedure: 25% PEG6000, 100 mM Tris-HCl, pH 8.0
Matthews coefficient: 2.04
Solvent content (%): 39.74
Ligand: 5'-O-{[(2S)-azetidine-2-carbonyl]sulfamoyl}adenosine (8X1)
Ligand formula: C14 H19 N7 O7 S
Ligand molecular weight: 429.408
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COS(=O)(=O)NC(=O)C4CCN4)O)O)N
Ligand InChI: InChI=1S/C14H19N7O7S/c15-11-8-12(18-4-17-11)21(5-19-8)14-10(23)9(22)7(28-14)3-27-29(25,26)20-13(24)6-1-2-16-6/h4-7,9-10,14,16,22-23H,1-3H2,(H,20,24)(H2,15,17,18)/t6-,7+,9+,10+,14+/m0/s1
Release date: 2018-01-10
Structure of human PARP1 catalytic domain bound to a phthalazinone inhibitor (PDB entry 5WRZ)
Macromolecule: Poly [ADP-ribose] polymerase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.4.2.30
Sequence length: 352 residues
Sequence: HMKSKLPKPVQDLIKMIFDVESMKKAMVEYEIDLQKMPLGKLSKRQIQAAYSILSEVQQAVSQGSSDSQILDLSNRFYTLIPHDFGMKKPPLLNNADSVQAKAEMLDNLLDIEVAYSLLRGGSDDSSKDPIDVNYEKLKTDIKVVDRDSEEAEIIRKYVKNTHATTHNAYDLEVIDIFKIEREGECQRYKPFKQLHNRRLLWHGSRTTNFAGILSQGLRIAPPEAPVTGYMFGKGIYFADMVSKSANYCHTSQGDPIGLILLGEVALGNMYELKHASHISKLPKGKHSVKGLGKTTPDPSANISLDGVDVPLGTGISSGVNDTSLLYNEYIVYDIAQVNLKYLLKLKFNFKT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.2
R work: 0.23042
R free: 0.27962
Average B factor: 22.801
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 298
Crystal growth procedure: 2.5M AMMONIUM SULFATE, 100mM TRIS
Matthews coefficient: 2.33
Solvent content (%): 47.2
Ligand: 7-fluoranyl-4-[[(3R)-pyrrolidin-3-yl]methoxy]-2H-phthalazin-1-one (7U3)
Ligand formula: C13 H14 F N3 O2
Ligand molecular weight: 263.268
Ligand SMILES: c1cc2c(cc1F)C(=O)NN=C2OCC3CCNC3
Ligand InChI: InChI=1S/C13H14FN3O2/c14-9-1-2-10-11(5-9)12(18)16-17-13(10)19-7-8-3-4-15-6-8/h1-2,5,8,15H,3-4,6-7H2,(H,16,18)/t8-/m1/s1
Release date: 2017-01-25
LINE-1 endonuclease domain complex with DNA (PDB entry 7N94)
Macromolecule: LINE-1 retrotransposable element ORF2 protein
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.49
Sequence length: 238 residues
Sequence: MTGSNSHITILTLNINGLNSAIKRHRLASWIKSQDPSVCCIQETHLTCRDTHRLKIKGWRKIYQANGKQKKAGVAILVSDKTDFKPTKIKRDKEGHYIMVKGSIQQEELTILNIYAPNTGAPRFIKQVLSDLQRDLDSHTLIMGAFNTPLSTLDRSTRQKVNKDTQELNSALHQADLIDIYRTLHPKSTEYTFFSAPHHTYSKIDHIVGSKALLSKCKRTEIITNKLSDHSAIKLELR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.85
R work: 0.2143
R free: 0.2803
Average B factor: 43.29
Crystallization method: EVAPORATION
Crystallization pH: 6
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M MES pH 6.0, 0.2M NaCl, 30% Jeffamine ED-2003
Matthews coefficient: 2.34
Solvent content (%): 47.54
Release date: 2021-10-13
Scaffold-ligand complex with ligand unmodelled (PDB entry 6Y3E)
Macromolecule: Peptidyl-prolyl cis-trans isomerase F, mitochondrial
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 5.2.1.8
Sequence length: 165 residues
Sequence: MGNPLVYLDVDANGKPLGRVVLELKADVVPKTAENFRALCTGEKGFGYKGSTFHRVIPSFMCQAGDFTNHNGTGGKSIYGSRFPDENFTLKHVGPGVLSMANAGPNTNGSQFFICTIKTDWLDGKHVVFGHVIEGMDVVKKIESFGSKSGRTSKKIVITDCGQLS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.45
R work: 0.1948
R free: 0.2342
Average B factor: 24.8851
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 298
Crystal growth procedure: 0.17 M Sodium acetate trihydrate,0.085 M Sodium cacodylate trihydrate pH 6.5,25.5% w/v Polyethylene glycol 8,000.
Matthews coefficient: 2.67
Solvent content (%): 53.86
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: 2020-03-04
FACTOR XIA IN COMPLEX WITH THE INHIBITOR N-[(1S)-1-benzyl-2-[2-[5-chloro-2-(tetrazol-1-yl)phenyl]ethylamino]-2-oxo-ethyl]-4-hydroxy-2-oxo-1H-quinoline-6-carboxamide (PDB entry 5E2P)
Macromolecule: Coagulation factor XIa light chain
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.27
Sequence length: 244 residues
Sequence: IVGGTASVRGEWPWQVTLHTTSPTQRHLCGGSIIGNQWILTAAHCFYGVESPKILRVYSGILNQSEIKEDTSFFGVQEIIIHDQYKMAESGYDIALLKLETTVGYGDSQRPICLPSKGDRNVIYTDCWVTGWGYRKLRDKIQNTLQKAKIPLVTNEECQKRYRGHKITHKMICAGYREGGKDACKGDSGGPLSCKHNEVWHLVGITSWGEGCAQRERPGVYTNVVEYVDWILEKTQAVHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.11
R work: 0.2273
R free: 0.2585
Average B factor: 34.75
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 4.6
Crystallization temperature (K): 277
Crystal growth procedure: 100 MM SODIUM ACETATE, PH 4.6, 26%(w/v) MEPEG2000, 200 MM AMMONIUM SULFATE
Matthews coefficient: 3.46
Solvent content (%): 64.47
Ligand: N-[(1S)-1-benzyl-2-[2-[5-chloro-2-(tetrazol-1-yl)phenyl]ethylamino]-2-oxo-ethyl]-4-hydroxy-2-oxo-1H-quinoline-6-carboxamide (7P0)
Ligand formula: C28 H24 Cl N7 O4
Ligand molecular weight: 557.988
Ligand SMILES: c1ccc(cc1)CC(C(=O)NCCc2cc(ccc2n3cnnn3)Cl)NC(=O)c4ccc5c(c4)C(=CC(=O)N5)O
Ligand InChI: InChI=1S/C28H24ClN7O4/c29-20-7-9-24(36-16-31-34-35-36)18(13-20)10-11-30-28(40)23(12-17-4-2-1-3-5-17)33-27(39)19-6-8-22-21(14-19)25(37)15-26(38)32-22/h1-9,13-16,23H,10-12H2,(H,30,40)(H,33,39)(H2,32,37,38)/t23-/m0/s1
Release date: 2015-12-09
Crystal structure of pIRE1alpha in complex with staurosporine (PDB entry 4YZC)
Macromolecule: Serine/threonine-protein kinase/endoribonuclease IRE1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 405 residues
Sequence: SVVIVGKISFCPKDVLGHGAEGTIVYRGMFDNRDVAVKRILPECFSFADREVQLLRESDEHPNVIRYFCTEKDRQFQYIAIELCAATLQEYVEQKDFAHLGLEPITLLQQTTSGLAHLHSLNIVHRDLKPHNILISMPNAHGKIKAMISDFGLCKKLAVGRHSFSRRSGVPGTEGWIAPEMLSEDCKENPTYTVDIFSAGCVFYYVISEGSHPFGKSLQRQANILLGACSLDCLHPEKHEDVIARELIEKMIAMDPQKRPSAKHVLKHPFFWSLEKQLQFFQDVSDRIEKESLDGPIVKQLERGGRAVVKMDWRENITVPLQTDLRKFRTYKGGSVRDLLRAMRNKKHHYRELPAEVRETLGSLPDDFVCYFTSRFPHLLAHTYRAMELCSHERLFQPYYFHEPP
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.494
R work: 0.2468
R free: 0.2892
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: The complex of pIRE1a (547-977) with staurosporine was prepared by mixing the protein with 0.5 mM staurosporine and incubated overnight on ice.  The crystals were grown at 20C by vapor diffusion in sitting drop containing 2 ul of protein (13 mg/ml in 50 mM Hepes, pH 7.5, 200 mM NaCl, 5 mM DTT, 1 mM EDTA) and 2ul reservoir solution containing PEG 300 (30%-40%), 100 mM Hepes pH 7.5, 200 mM KCl. Small hexagonal plates appeared over 5-10 days and reached full size (0.05 X 0.75 X 0.15 mm) in ~20 days. The crystals were flash-frozen in liquid N2 directly from the crystallization drop. All diffraction data was collected at the Advanced Photon Source, Argonne National Laboratories, Life Sciences CAT, Sector 21
Matthews coefficient: 3.2
Solvent content (%): 61.6
Ligand: STAUROSPORINE (STU)
Ligand formula: C28 H26 N4 O3
Ligand molecular weight: 466.531
Ligand SMILES: CC12C(C(CC(O1)n3c4ccccc4c5c3c6n2c7ccccc7c6c8c5C(=O)NC8)NC)OC
Ligand InChI: InChI=1S/C28H26N4O3/c1-28-26(34-3)17(29-2)12-20(35-28)31-18-10-6-4-8-14(18)22-23-16(13-30-27(23)33)21-15-9-5-7-11-19(15)32(28)25(21)24(22)31/h4-11,17,20,26,29H,12-13H2,1-3H3,(H,30,33)/t17-,20-,26-,28+/m1/s1
Release date: 2015-11-11
Human JAK2 JH1 domain in complex with PROTAC-intermediate linker handle 4 (PDB entry 6WTQ)
Macromolecule: Tyrosine-protein kinase JAK2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 309 residues
Sequence: MAFEDRDPTQFEERHLKFLQQLGKGNFGSVEMCRYDPLQDNTGEVVAVKKLQHSTEEHLRDFEREIEILKSLQHDNIVKYKGVCYSAGRRNLKLIMEYLPYGSLRDYLQKHKERIDHIKLLQYTSQICKGMEYLGTKRYIHRDLATRNILVENENRVKIGDFGLTKVLPQDKEYYKVKEPGESPIFWYAPESLTESKFSVASDVWSFGVVLYELFTYIEKSKSPPAEFMRMIGNDKQGQMIVFHLIELLKNNGRLPRPDGCPDEIYMIMTECWNNNVNQRPSFRDLALRVDQIRDNMAGGSGSENLYFQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.79968475557
R work: 0.191494477759
R free: 0.212725846763
Average B factor: 43.3181747434
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5
Crystallization temperature (K): 291
Crystal growth procedure: 0.1 M SODIUM CITRATE PH 6.5, 27% PEG 8000 AND 0.2 M AMMONIUM ACETATE.
REMARK 280  6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K
Matthews coefficient: 2.11
Solvent content (%): 41.79
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: 2021-05-05
Cdk2(F80C, C177A) with covalent adduct at C80 (PDB entry 5OSM)
Macromolecule: Cyclin-dependent kinase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.22
Sequence length: 303 residues
Sequence: GPLGSMENFQKVEKIGEGTYGVVYKARNKLTGEVVALKKIRLDTETEGVPSTAIREISLLKELNHPNIVKLLDVIHTENKLYLVCEFLHQDLKKFMDASALTGIPLPLIKSYLFQLLQGLAFCHSHRVLHRDLKPQNLLINTEGAIKLADFGLARAFGVPVRTYTHEVVTLWYRAPEILLGAKYYSTAVDIWSLGCIFAEMVTRRALFPGDSEIDQLFRIFRTLGTPDEVVWPGVTSMPDYKPSFPKWARQDFSKVVPPLDEDGRSLLSQMLHYDPNKRISAKAALAHPFFQDVTKPVPHLRL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.77
R work: 0.16217
R free: 0.20611
Average B factor: 22.042
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 298
Crystal growth procedure: 15% w/v Jeffamine ED-2003, 50 mM HEPES, 50 mM sodium/potassium phosphate
Matthews coefficient: 1.98
Solvent content (%): 37.82
Ligand: methyl 1-propanoyl-3,4-dihydro-2~{H}-quinoline-6-carboxylate (AEQ)
Ligand formula: C14 H17 N O3
Ligand molecular weight: 247.29
Ligand SMILES: CCC(=O)N1CCCc2c1ccc(c2)C(=O)OC
Ligand InChI: InChI=1S/C14H17NO3/c1-3-13(16)15-8-4-5-10-9-11(14(17)18-2)6-7-12(10)15/h6-7,9H,3-5,8H2,1-2H3
Release date: 2018-03-14
Crystal structure of human cathepsin D in complex with macrocyclic inhibitor 33 (PDB entry 6QBH)
Macromolecule: Cathepsin D
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.23.5
Sequence length: 97 residues
Sequence: GPIPEVLKNYMDAQYYGEIGIGTPPQCFTVVFDTGSSNLWVPSIHCKLLDIACWIHHKYNSDKSSTYVKNGTSFDIHYGSGSLSGYLSQDTVSVPCQ
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.85
R work: 0.1753
R free: 0.2072
Average B factor: 20.035
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 291.15
Crystal growth procedure: 25 % PEG 3350
0.2 M lithium sulphate
0.1 M Bis-Tris Ph 5.5
Matthews coefficient: 3
Solvent content (%): 58.94
Ligand: (4~{S},5~{S},9~{S})-5-oxidanyl-4-(phenylmethyl)-9-propan-2-yl-1-oxa-3,8,11-triazacyclodocosane-2,7,10-trione (S43)
Ligand formula: C28 H45 N3 O5
Ligand molecular weight: 503.674
Ligand SMILES: CC(C)C1C(=O)NCCCCCCCCCCCOC(=O)NC(C(CC(=O)N1)O)Cc2ccccc2
Ligand InChI: InChI=1S/C28H45N3O5/c1-21(2)26-27(34)29-17-13-8-6-4-3-5-7-9-14-18-36-28(35)30-23(24(32)20-25(33)31-26)19-22-15-11-10-12-16-22/h10-12,15-16,21,23-24,26,32H,3-9,13-14,17-20H2,1-2H3,(H,29,34)(H,30,35)(H,31,33)/t23-,24-,26-/m0/s1
Release date: 2020-01-29
Crystal structure of MAP2K6 with a covalent compound GCL96 (PDB entry 8P7J)
Macromolecule: Dual specificity mitogen-activated protein kinase kinase 6
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.12.2
Sequence length: 290 residues
Sequence: SMEVKADDLEPIMELGRGAYGVVEKMRHVPSGQIMAVKRIRATVNSQEQKRLLMDLDISMRTVDCPFTVTFYGALFREGDVWICMELMDTSLDKFYKQVIDKGQTIPEDILGKIAVSIVKALEHLHSKLSVIHRDVKPSNVLINALGQVKMCDFGISGYLVDDVAKDIDAGCKPYMAPERINPELNQKGYSVKSDIWSLGITMIELAILRFPYDSWGTPFQQLKQVVEEPSPQLPADKFSAEFVDFTSQCLKKNSKERPTYPELMQHPFFTLHESKGTDVASFVKLILGD
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.4
R work: 0.19557
R free: 0.25744
Average B factor: 55.382
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293.15
Crystal growth procedure: 0.05M magnesium chloride -- 30% PEG500MME -- 0.1M HEPES pH 7.5
Matthews coefficient: 2.57
Solvent content (%): 52.18
Ligand: N-[3-(1H-pyrrolo[2,3-b]pyridin-4-yl)phenyl]prop-2-enamide (X3K)
Ligand formula: C16 H13 N3 O
Ligand molecular weight: 263.294
Ligand SMILES: C=CC(=O)Nc1cccc(c1)c2ccnc3c2cc[nH]3
Ligand InChI: InChI=1S/C16H13N3O/c1-2-15(20)19-12-5-3-4-11(10-12)13-6-8-17-16-14(13)7-9-18-16/h2-10H,1H2,(H,17,18)(H,19,20)
Release date: 2023-07-05
PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with FMOOA000637a (PDB entry 7GTH)
Macromolecule: Tyrosine-protein phosphatase non-receptor type 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 321 residues
Sequence: MEMEKEFEQIDKSGSWAAIYQDIRHEASDFPSRVAKLPKNKNRNRYRDVSPFDHSRIKLHQEDNDYINASLIKMEEAQRSYILTQGPLPNTVGHFWEMVWEQKSRGVVMLNRVMEKGSLKCAQYWPQKEEKEMIFEDTNLKLTLISEDIKSYYTVRQLELENLTTQETREILHFHYTTWPDFGVPESPASFLNFLFKVRESGSLSPEHGPVVVHCSAGIGRSGTFCLADTCLLLMDKRKDPSSVDIKKVLLEMRKFRMGLIQTADQLRFSYLAVIEGAKFIMGDSSVQDQWKELSHEDLEPPPEHIPPPPRPPKRILEPHN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.66
R work: 0.2004
R free: 0.2347
Average B factor: 36.552
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.3 M magnesium acetate, 0.1 M HEPES pH 7.5, 0.1% beta-mercaptoethanol, 13-14% PEG 8000, 2% ethanol
Matthews coefficient: 3.35
Solvent content (%): 63.28
Ligand: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL (TRS)
Ligand formula: C4 H12 N O3
Ligand molecular weight: 122.143
Ligand SMILES: C(C(CO)(CO)[NH3+])O
Ligand InChI: InChI=1S/C4H11NO3/c5-4(1-6,2-7)3-8/h6-8H,1-3,5H2/p+1
Release date: 2024-01-24
Crystal structure of TREX1 in complex with a inosine contained ssDNA (PDB entry 5YWV)
Macromolecule: Three-prime repair exonuclease 1
Type: Protein, polypeptide(L)
Source organism: Mus musculus
EC number: 3.1.11.2
Sequence length: 259 residues
Sequence: GSHMASMTGGQQMGRGSMGSQTLPHGHMQTLIFLDLEATGLPSSRPEVTELCLLAVHRRALENTSISQGHPPPVPRPPRVVDKLSLCIAPGKACSPGASEITGLSKAELEVQGRQRFDDNLAILLRAFLQRQPQPCCLVAHNGDRYDFPLLQTELARLSTPSPLDGTFCVDSIAALKALEQASSPSGNGSRKSYSLGSIYTRLYWQAPTDSHTAEGDVLTLLSICQWKPQALLQWVDEHARPFSTVKPMYGTPATTGTT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.3
R work: 0.159
R free: 0.22
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M MES MONOHYDRATE PH 6.0, 20%(W/V)
 POLYETHYLENE GLYCOL MONOMETHYL ETHER 2,000, VAPOR DIFFUSION,
 HANGING DROP, TEMPERATURE 293K
Matthews coefficient: 1.86
Solvent content (%): 33.91
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: 2018-05-23
Structure of the catalytic domain of USP28 (insertion deleted) (PDB entry 6HEH)
Macromolecule: Ubiquitin carboxyl-terminal hydrolase 28,Ubiquitin carboxyl-terminal hydrolase 28
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.19.12
Sequence length: 382 residues
Sequence: GPNPNDWRRVDGWPVGLKNVGNTCWFSAVIQSLFQLPEFRRLVLSYSLPQNVLENCRSHTEKRNIMFMQELQYLFALMMGSNRKFVDPSAALDLLKGAFRSSEEQQQDVSEFTHKLLDWLEDAFQLAVNVNSPRNKSENPMVQLFYGTFLTEGVREGKPFCNNETFGQYPLQVNGYRNLDECLEGAMVEGDVELLPSDHSVKYGQERWFTKLPPVLTFELSRFEFNQSLGQPEKIHNKLEFPQIIYMDRYMYGSGSGSRQVPYRLHAVLVHEGQANAGHYWAYIYNQPRQSWLKYNDISVTESSWEEVERDSYGGLRNVSAYCLMYINDKLPYFNAEAAPTESDQMSEVEALSVELKHYIQEDNWRFEQEVEEWEEEQSCKI
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.26
R work: 0.1956
R free: 0.2161
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.6
Crystallization temperature (K): 291
Crystal growth procedure: 12% (w/v) PEG 8000, 100 mM sodium chloride, 200 mM lithium sulfate, 100 mM MES pH 6.6
Matthews coefficient: 3.16
Solvent content (%): 61.1
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: 2019-03-27