satarupa22/MacromolecularLigandDB huggingface dataset:
Crystal structure of N-terminal domain of human protein O-mannose beta-1,2-N-acetylglucosaminyltransferase in complex with GalNac-beta1,3-GlcNAc-beta-pNP (PDB entry 5GGO)
Macromolecule: Protein O-linked-mannose beta-1,2-N-acetylglucosaminyltransferase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.4.1
Sequence length: 164 residues
Sequence: GPLGSGSGPRRVLDVEVYSSRSKVYVAVDGTTVLEDEAREQGRGIHVIVLNQATGHVMAKRVFDTYSPHEDEAMVLFLNMVAPGRVLICTVKDEGSFHLKDTAKALLRSLGSQAGPALGWRDTWAFVGRKGGPVFGEKHSKSPALSSWGDPVLLKTDVPLSSAE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.502
R work: 0.1752
R free: 0.2081
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8.8
Crystallization temperature (K): 293
Crystal growth procedure: Tris-HCl, PEG-6000
Matthews coefficient: 2.38
Solvent content (%): 48.26
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: 2016-08-10
Complex structure of PCNA with UHRF2 (PDB entry 5YCO)
Macromolecule: Proliferating cell nuclear antigen
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 269 residues
Sequence: MFEARLVQGSILKKVLEALKDLINEACWDISSSGVNLQSMDSSHVSLVQLTLRSEGFDTYRCDRNLAMGVNLTSMSKILKCAGNEDIITLRAEDNADTLALVFEAPNQEKVSDYEMKLMDLDVEQLGIPEQEYSCVVKMPSGEFARICRDLSHIGDAVVISCAKDGVKFSASGELGNGNIKLSQTSNVDKEEEAVTIEMNEPVQLTFALRYLNFFTKATPLSSTVTLSMSADVPLVVEYKIADMGHLKYYLAPKIEDEEGSLEHHHHHH
Oligomeric state: Hetero 4-mer
Stoichiometry: A3, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.199
R work: 0.2039
R free: 0.2201
Average B factor: 48.4451
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 289
Crystal growth procedure: 2 M ammonium sulfate, 0.1 M Tris pH 8.0
Matthews coefficient: 4.27
Solvent content (%): 71.18
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: 2017-11-15
The crystal structure of CK2alpha in complex with CAM4712 and compound 37 (PDB entry 6EHK)
Macromolecule: Casein kinase II subunit alpha
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 342 residues
Sequence: SGPVPSRARVYTDVNTHRPSEYWDYESHVVEWGNQDDYQLVRKLGRGKYSEVFEAINITNNEKVVVKILKPVAAAKIKREIKILENLRGGPNIITLADIVKDPVSRTPALVFEHVNNTDFKQLYQTLTDYDIRFYMYEILKALDYCHSMGIMHRDVKPHNVMIDHEHRKLRLIDWGLAEFYHPGQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRKEPFFHGHDNYDQLVRIAKVLGTEDLYDYIDKYNIELDPRFNDILGRHSRKRWERFVHSENQHLVSPEALDFLDKLLRYDHQSRLTAREAMEHPYFYTVVKREAMEHPYFYTVVK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.4
R work: 0.1778
R free: 0.1939
Average B factor: 24.56
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: 1.93
Solvent content (%): 36.42
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
Unc-51-Like Kinase 3 (ULK3) In Complex With Momelotinib (PDB entry 6FDZ)
Macromolecule: Serine/threonine-protein kinase ULK3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 276 residues
Sequence: AGPGWGPPRLDGFILTERLGSGTYATVYKAYAKKDTREVVAIKCVAKKSLNKASVENLLTEIEILKGIRHPHIVQLKDFQWDSDNIYLIMEFCAGGDLSRFIHTRRILPEKVARVFMQQLASALQFLHERNISHLDLKPQNILLSSLEKPHLKLADFGFAQHMSPWDEKHVLRGSPLYMAPEMVCQRQYDARVDLWSMGVILYEALFGQPPFASRSFSELEEKIRSNRVIELPLRPLLSRDCRDLLQRLLERDPSRRISFQDFFAHPWVDLEHMPS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.55
R work: 0.23043
R free: 0.30109
Average B factor: 58.642
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.1 M HEPES pH 7.5, 0.2 M MgCl2, 30% 2-propanol
Matthews coefficient: 2.79
Solvent content (%): 55.91
Ligand: Momelotinib (C87)
Ligand formula: C23 H22 N6 O2
Ligand molecular weight: 414.46
Ligand SMILES: c1cc(ccc1c2ccnc(n2)Nc3ccc(cc3)N4CCOCC4)C(=O)NCC#N
Ligand InChI: InChI=1S/C23H22N6O2/c24-10-12-25-22(30)18-3-1-17(2-4-18)21-9-11-26-23(28-21)27-19-5-7-20(8-6-19)29-13-15-31-16-14-29/h1-9,11H,12-16H2,(H,25,30)(H,26,27,28)
Release date: 2018-08-01
Crystal structure of (3aR,4S,9bS)-4-(4-hydroxyphenyl)-3a,4,5,9b-tetrahydro-3H-cyclopenta[c]quinoline-8-sulfonamide with carbonic anhydrase 2 (PDB entry 6SYS)
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): 1.3
R work: 0.1194
R free: 0.1644
Average B factor: 15.857
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8
Crystallization temperature (K): 296
Crystal growth procedure: 1.5 M sodium citrate, 50 mM Tris pH 8.0
Matthews coefficient: 2.1
Solvent content (%): 41.49
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: 2020-10-14
EGFR(T790M/V948R) kinase in complex with benzimidazole allosteric inhibitor (PDB entry 8GB4)
Macromolecule: Epidermal growth factor receptor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 331 residues
Sequence: GSTSGEAPNQALLRILKETEFKKIKVLGSGAFGTVYKGLWIPEGEKVKIPVAIKELREATSPKANKEILDEAYVMASVDNPHVCRLLGICLTSTVQLIMQLMPFGCLLDYVREHKDNIGSQYLLNWCVQIAKGMNYLEDRRLVHRDLAARNVLVKTPQHVKITDFGLAKLLGAEEKEYHAEGGKVPIKWMALESILHRIYTHQSDVWSYGVTVWELMTFGSKPYDGIPASEISSILEKGERLPQPPICTIDVYMIMRKCWMIDADSRPKFRELIIEFSKMARDPQRYLVIQGDERMHLPSPTDSNFYRALMDEEDMDDVVDADEYLIPQQG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.59
R work: 0.2291
R free: 0.2535
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M Bis-Tris pH 5.5, 30% (w/v) PEG 3350
Matthews coefficient: 2.15
Solvent content (%): 42.71
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: 2024-03-13
Structure of the MAGEA4 MHD-RAD18 R6BD Complex (PDB entry 9BD3)
Macromolecule: E3 ubiquitin-protein ligase RAD18
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2.27
Sequence length: 28 residues
Sequence: HSKYRKKHKSEFQLLVDQARKGYKKIAG
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.58
R work: 0.1912
R free: 0.2255
Average B factor: 61.65
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: 20% (w/v) PEG 8000 100 mM HEPES/ Sodium hydroxide, pH 7.5, 200 mM Ammonium sulfate, 10% (v/v) 2-propanol
Matthews coefficient: 3.81
Solvent content (%): 67.7
Release date: 2024-06-05
The STK17A (DRAK1) Kinase Domain Bound to CK156 (PDB entry 7QUF)
Macromolecule: Serine/threonine-protein kinase 17A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 275 residues
Sequence: SMVRTEPFQDGYSLCPGRELGRGKFAVVRKCIKKDSGKEFAAKFMRKRRKGQDCRMEIIHEIAVLELAQDNPWVINLHEVYETASEMILVLEYAAGGEIFDQCVADREEAFKEKDVQRLMRQILEGVHFLHTRDVVHLDLKPQNILLTSESPLGDIKIVDFGLSRILKNSEELREIMGTPEYVAPEILSYDPISMATDMWSIGVLTYVMLTGISPFLGNDKQETFLNISQMNLSYSEEEFDVLSESAVDFIRTLLVKKPEDRATAEECLKHPWLT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.6
R work: 0.2315
R free: 0.2937
Average B factor: 75.82
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 24% PEG3350, 0.2 M ammonium chloride
Matthews coefficient: 2.75
Solvent content (%): 55.3
Ligand: ~{N}-~{tert}-butyl-7,10-dioxa-13,17,18,21-tetrazatetracyclo[12.5.2.1^{2,6}.0^{17,20}]docosa-1(20),2(22),3,5,14(21),15,18-heptaene-5-carboxamide (F8I)
Ligand formula: C21 H25 N5 O3
Ligand molecular weight: 395.455
Ligand SMILES: CC(C)(C)NC(=O)c1ccc-2cc1OCCOCCNc3ccn4c(c2cn4)n3
Ligand InChI: InChI=1S/C21H25N5O3/c1-21(2,3)25-20(27)15-5-4-14-12-17(15)29-11-10-28-9-7-22-18-6-8-26-19(24-18)16(14)13-23-26/h4-6,8,12-13H,7,9-11H2,1-3H3,(H,22,24)(H,25,27)
Release date: 2022-02-02
CRYSTAL STRUCTURE OF HUMAN MYT1 KINASE DOMAIN IN COMPLEX WITH Pelitinib (PDB entry 5VCW)
Macromolecule: Membrane-associated tyrosine- and threonine-specific cdc2-inhibitory kinase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 311 residues
Sequence: MHHHHHHSSGVDLGTENLYFQSMHQLQPRRVSFRGEASETLQSPGYDPSRPESFFQQSFQRLSRLGHGSYGEVFKVRSKEDGRLYAVKRSMSPFRGPKDRARKLAEVGSHEKVGQHPCCVRLEQAWEEGGILYLQTELCGPSLQQHCEAWGASLPEAQVWGYLRDTLLALAHLHSQGLVHLDVKPANIFLGPRGRCKLGDFGLLVELGTAGAGEVQEGDPRYMAPELLQGSYGTAADVFSLGLTILEVACNMELPHGGEGWQQLRQGYLPPEFTAGLSSELRSVLVMMLEPDPKLRATAEALLALPVLRQP
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.25
R work: 0.1956
R free: 0.2457
Average B factor: 69.7286
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 291
Crystal growth procedure: 6.9 MG/ML MYT1, 25 mM HEPES, 100 MM SODIUM CHLORIDE, 0.5 mM DTT, 0.05 M MES pH 6.5, 0.8 M Magnesium sulfate, 2 mM Pelitinib
Matthews coefficient: 2.84
Solvent content (%): 56.64
Ligand: (2E)-N-{4-[(3-chloro-4-fluorophenyl)amino]-3-cyano-7-ethoxyquinolin-6-yl}-4-(dimethylamino)but-2-enamide (93J)
Ligand formula: C24 H23 Cl F N5 O2
Ligand molecular weight: 467.923
Ligand SMILES: CCOc1cc2c(cc1NC(=O)C=CCN(C)C)c(c(cn2)C#N)Nc3ccc(c(c3)Cl)F
Ligand InChI: InChI=1S/C24H23ClFN5O2/c1-4-33-22-12-20-17(11-21(22)30-23(32)6-5-9-31(2)3)24(15(13-27)14-28-20)29-16-7-8-19(26)18(25)10-16/h5-8,10-12,14H,4,9H2,1-3H3,(H,28,29)(H,30,32)/b6-5+
Release date: 2017-08-23
Human Aldose Reductase complexed with a ligand with an IDD structure (2-[5-fluoro-2-(prop-2-ynylcarbamoyl)phenoxy]acetic acid) at 1.12 A (PDB entry 4PUW)
Macromolecule: Aldose reductase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.1.1.21
Sequence length: 316 residues
Sequence: MASRILLNNGAKMPILGLGTWKSPPGQVTEAVKVAIDVGYRHIDCAHVYQNENEVGVAIQEKLREQVVKREELFIVSKLWCTYHEKGLVKGACQKTLSDLKLDYLDLYLIHWPTGFKPGKEFFPLDESGNVVPSDTNILDTWAAMEELVDEGLVKAIGISNFNHLQVEMILNKPGLKYKPAVNQIECHPYLTQEKLIQYCQSKGIVVTAYSPLGSPDRPWAKPEDPSLLEDPRIKAIAAKHNKTTAQVLIRFPMQRNLVVIPKSVTPERIAENFKVFDFELSSQDMTTLLSYNRNWRVCALLSCTSHKDYPFHEEF
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.12
R work: 0.137
R free: 0.1568
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5
Crystallization temperature (K): 291
Crystal growth procedure: Crystallization solution: 50 mM di-Ammoniumhydrogen citrate pH 5.0 PEG6000= 5 % (m/V) DTT= 5.15 g/L NADP+= 0.66 g/L and Human Aldose Reductase= 15 mg/ml.        
9 microliter of the crystallization  solution were mixed with 3 microliter of a 5 mM solution of the inhibitor in 120 mM di-Ammoniumhydrogen citrate pH 5.0 with 25 % (m/V) PEG 6000 and 5 % DMSO, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Matthews coefficient: 2.17
Solvent content (%): 43.37
Ligand: [5-fluoro-2-(prop-2-yn-1-ylcarbamoyl)phenoxy]acetic acid (2WQ)
Ligand formula: C12 H10 F N O4
Ligand molecular weight: 251.211
Ligand SMILES: C#CCNC(=O)c1ccc(cc1OCC(=O)O)F
Ligand InChI: InChI=1S/C12H10FNO4/c1-2-5-14-12(17)9-4-3-8(13)6-10(9)18-7-11(15)16/h1,3-4,6H,5,7H2,(H,14,17)(H,15,16)
Release date: 2015-04-08
Structure of the Smurf2 HECT Domain with a High Affinity Ubiquitin Variant (UbV) (PDB entry 7M3Q)
Macromolecule: E3 ubiquitin-protein ligase SMURF2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2.26
Sequence length: 387 residues
Sequence: GAMAPRYKRDLVQKLKILRQELSQQQPQAGHCRIEVSREEIFEESYRQVMKMRPKDLWKRLMIKFRGEEGLDYGGVAREWLYLLSHEMLNPYYGLFQYSRDDIYTLQINPDSAVNPEHLSYFHFVGRIMGMAVFHGHYIDGGFTLPFYKQLLGKSITLDDMELVDPDLHNSLVWILENDITGVLDHTFCVEHNAYGEIIQHELKPNGKSIPVNEENKKEYVRLYVNWRFLRGIEAQFLALQKGFNEVIPQHLLKTFDEKELELIICGLGKIDVNDWKVNTRLKHCTPDSNIVKWFWKAVEFFDEERRARLLQFVTGSSRVPLQGFKALQGAAGPRLFTIHQIDACTNNLPKAHTCFNRIDIPPYESYEKLYEKLLTAIEETCGFAVE
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.5
R work: 0.2029
R free: 0.2349
Average B factor: 70.6
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6
Crystallization temperature (K): 298
Crystal growth procedure: 1.5 M Ammonium Sulphate and 100 mM MES pH 6.0. Trypsin was added to the protein complex at a final concentration of 10 microgram per mL
Matthews coefficient: 3.11
Solvent content (%): 60.47
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: 2021-04-21
POLYADPRIBOSYL GLYCOHYDROLASE IN COMPLEX WITH PDD00016690 (PDB entry 6HMK)
Macromolecule: Poly(ADP-ribose) glycohydrolase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.2.1.143
Sequence length: 531 residues
Sequence: GSSPDKKWLGTPIEEMRRMPRCGIRLPLLRPSANHTVTIRVDLLRAGEVPKPFPTHYKDLWDNKHVKMPCSEQNLYPVEDENGERTAGSRWELIQTALLNKFTRPQNLKDAILKYNVAYSKKWDFTALIDFWDKVLEEAEAQHLYQSILPDMVKIALCLPNICTQPIPLLAAAMNHSITMSQEQIASLLANAFFCTFPRRNAKMKSEYSSYPDINFNRLFEGRSSRKPEKLKTLFCYFRRVTAAAPTGLVTFTRQSLEDFPEWERCEKPLTRLHVTYEGTIEENGQGMLQVDFANRFVGGGVTSAGLVQEEIRFLINPELIISRLFTEVLDHNECLIITGTEQYSEYTGYAETYRWSRSHEDGSERDDWQRRCTEIVAIDALHFRRYLDQFVPEKMRRELNKAYCGFLRPGVSSENLSAVATGNWGCGAFGGDARLKALIQILAAAAAERDVVYFTFGDSELMRDIYSMHIFLTERKLTVGDVYKLLLRYYNEECRNCSTPGPDIKLYPFIYHAVESCAETADHSGQRTGT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.06
R work: 0.1536
R free: 0.1888
Average B factor: 33.03
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: 750 nL purified protein at 7.5 mg/mL in 50 mM HEPES, pH 7.0, 150 mM NaCl, 2 mM DTT was mixed with 250 nL of seed stock and 1000 nL of a  precipitant consisting of 18-23 % (w/v) PEG-3350, 0.2 M ammonium sulphate, 0.1 M PCTP pH 7.5.  Seed stock was prepared using a Seed BeadTM (Hampton Research) from a co-crystal of GS-PARG(448-976 [K617A, Q618A, K619A, E688A, K689A, K690A]) with ADP-ribose, with co-crystallisation mother liquor (19 % (w/v) PEG-3350, 0.2 M ammonium sulphate, 0.1 M PCTP pH 7.5) as the stabilising solution. The final volume of the seed stock was 100 microL.
Matthews coefficient: 2.47
Solvent content (%): 50.22
Ligand: DIMETHYL SULFOXIDE (DMS)
Ligand formula: C2 H6 O S
Ligand molecular weight: 78.133
Ligand SMILES: CS(=O)C
Ligand InChI: InChI=1S/C2H6OS/c1-4(2)3/h1-2H3
Release date: 2018-11-14
STRUCTURE OF HUMAN HDAC2 IN COMPLEX WITH APICIDIN (PDB entry 7LTG)
Macromolecule: Histone deacetylase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.5.1.98
Sequence length: 376 residues
Sequence: MAYSQGGGKKKVCYYYDGDIGNYYYGQGHPMKPHRIRMTHNLLLNYGLYRKMEIYRPHKATAEEMTKYHSDEYIKFLRSIRPDNMSEYSKQMQRFNVGEDCPVFDGLFEFCQLSTGGSVAGAVKLNRQQTDMAVNWAGGLHHAKKSEASGFCYVNDIVLAILELLKYHQRVLYIDIDIHHGDGVEEAFYTTDRVMTVSFHKYGEYFPGTGDLRDIGAGKGKYYAVNFPMRDGIDDESYGQIFKPIISKVMEMYQPSAVVLQCGADSLSGDRLGCFNLTVKGHAKCVEVVKTFNLPLLMLGGGGYTIRNVARCWTYETAVALDCEIPNELPYNDYFEYFGPDFKLHISPSNMTNQNTPEYMEKIKQRLFENLRMLPH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.168
R free: 0.198
Average B factor: 29.5
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 25% PEG 3350, 0.2 M ammonium sulfate, 0.1 M Hepes pH 7.5
Matthews coefficient: 2.44
Solvent content (%): 49.66
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: 2021-05-05
Crystal structure of HERC2 ZZ domain in complex with histone H3 tail (PDB entry 6WW4)
Macromolecule: Histone H3.1,E3 ubiquitin-protein ligase HERC2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2.26
Sequence length: 56 residues
Sequence: ARTKQTIHPGVTCDGCQMFPINGSRFKCRNCDDFDFCETCFKTKKHNTRHTFGRIN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.252
R work: 0.1985
R free: 0.2434
Average B factor: 29.9424
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 298
Crystal growth procedure: 0.1 M ammonium acetate, 0.1 M Bis-Tris, pH 5.5, and 17% PEG 10000
Matthews coefficient: 2.35
Solvent content (%): 47.72
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: 2020-08-05
LOW-SALT STRUCTURE OF PROTEIN KINASE CK2 CATALYTIC SUBUNIT (ISOFORM CK2ALPHA; CSNK2A1 gene product) IN COMPLEX WITH THE INDENOINDOLE-TYPE INHIBITOR THN27 (PDB entry 6HME)
Macromolecule: Casein kinase II subunit alpha
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 349 residues
Sequence: MGSSHHHHHHSQDPMSGPVPSRARVYTDVNTHRPREYWDYESHVVEWGNQDDYQLVRKLGRGKYSEVFEAINITNNEKVVVKILKPVKKKKIKREIKILENLRGGPNIITLADIVKDPVSRTPALVFEHVNNTDFKQLYQTLTDYDIRFYMYEILKALDYCHSMGIMHRDVKPHNVMIDHEHRKLRLIDWGLAEFYHPGQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRKEPFFHGHDNYDQLVRIAKVLGTEDLYDYIDKYNIELDPRFNDILGRHSRKRWERFVHSENQHLVSPEALDFLDKLLRYDHQSRLTAREAMEHPYFYTVVKDQARMG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.85
R work: 0.1749
R free: 0.197
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293.15
Crystal growth procedure: 180 MICROLITERS OF ENZYME SOLUTION (6 MG/ML CK2ALPHA, 0.025 M TRIS/HCL, PH 8.5, 0.5 M NACL) WERE MIXED WITH 20 MICROLITERS OF INHIBITOR STOCK SOLUTION (0.010 M INHIBITOR THN27 IN DMSO). THIS MIXTURE WAS INCUBATED FOR 30 MIN AT ROOM TEMPERATURE. THE RESERVOIR SOLUTION OF THE CRYSTALLIZATION EXPERIMENT WAS 0.2 M AMMONIUM SULFATE, 0.1 M SODIUM CACODYLATE TRIHYDRATE, PH 6.5, 30% (W/V) PEG 8,000. PRIOR TO EQUILIBRATION THE CRYSTALLIZATION DROP WAS COMPOSED OF 10 MICROLITERS RESERVOIR SOLUTION PLUS 20 MICROLITERS ENZYME/INHIBITOR MIXTURE.
Matthews coefficient: 3.11
Solvent content (%): 60.39
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
TNNI3K complexed with a 4,6-diaminopyrimidine (PDB entry 6B5J)
Macromolecule: Serine/threonine-protein kinase TNNI3K
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 311 residues
Sequence: GGDGSYVSVPSPLGKIKSMTKEKADILLLRAGLPSHFHLQLSEIEFHEIIGSGSFGKVYKGRCRNKIVAIKRYRANTYCSKSDVDMFCREVSILCQLNHPCVIQFVGACLNDPSQFAIVTQYISGGSLFSLLHEQKRILDLQSKLIIAVDVAKGMEYLHNLTQPIIHRDLNSHNILLYEDGHAVVADFGESRFLQSLDEDNMTKQPGNLRWMAPEVFTQCTRYTIKADVFSYALCLWEILTGEIPFAHLKPAAAAADMAYHHIRPPIGYSIPKPISSLLIRGWNACPEGRPEFSEVVMKLEECLCNIELMS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.97
R work: 0.201
R free: 0.2579
Average B factor: 59.083
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7
Crystallization temperature (K): 283
Crystal growth procedure: 15% tascimate, 0.1M Hepes pH 7, 2% PEG3350
Matthews coefficient: 3.06
Solvent content (%): 59.84
Ligand: N-methyl-3-[(6-{[4-(trifluoromethyl)phenyl]amino}pyrimidin-4-yl)amino]benzene-1-sulfonamide (CV4)
Ligand formula: C18 H16 F3 N5 O2 S
Ligand molecular weight: 423.412
Ligand SMILES: CNS(=O)(=O)c1cccc(c1)Nc2cc(ncn2)Nc3ccc(cc3)C(F)(F)F
Ligand InChI: InChI=1S/C18H16F3N5O2S/c1-22-29(27,28)15-4-2-3-14(9-15)26-17-10-16(23-11-24-17)25-13-7-5-12(6-8-13)18(19,20)21/h2-11,22H,1H3,(H2,23,24,25,26)
Release date: 2018-04-04
Crystal structure of human Sirt5 in complex with an internally quenched fluorescent substrate GluIQF (PDB entry 6LJK)
Macromolecule: NAD-dependent protein deacylase sirtuin-5, mitochondrial
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1
Sequence length: 272 residues
Sequence: QASARPSSSMADFRKFFAKAKHIVIISGAGVSAESGVPTFRGAGGYWRKWQAQDLATPLAFAHNPSRVWEFYHYRREVMGSKEPNAGHRAIAECETRLGKQGRRVVVITQNIDELHRKAGTKNLLEIHGSLFKTRCTSCGVVAENYKSPICPALSGKGAPEPGTQDASIPVEKLPRCEEAGCGGLLRPHVVWFGENLDPAILEEVDRELAHCDLCLVVGTSSVVYPAAMFAPQVAARGVPVAEFNTETTPATNRFRFHFQGPCGTTLPEALA
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.394
R work: 0.1222
R free: 0.1582
Average B factor: 15.0322
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 25%-27% (v/v) PEG 3350, 0.1 M MES, pH 5.5-6.0, 0.1-0.2 M NaCl
Matthews coefficient: 2.33
Solvent content (%): 47.25
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: 2020-12-23
HUMAN SPLEEN TYROSINE KINASE KINASE DOMAIN IN COMPLEX WITH AZANAPHTHYRIDINE INHIBITOR (PDB entry 5LMB)
Macromolecule: Tyrosine-protein kinase SYK
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 277 residues
Sequence: GPKEVYLDRKLLTLEDKELGSGNFGTVKKGYYQMKKVVKTVAVKILKNEANDPALKDELLAEANVMQQLDNPYIVRMIGICEAESWMLVMEMAELGPLNKYLQQNRHVKDKNIIELVHQVSMGMKYLEESNFVHRDLAARNVLLVTQHYAKISDFGLSKALRADENYYKAQTHGKWPVKWYAPECINYYKFSSKSDVWSFGVLMWEAFSYGQKPYRGMKGSEVTAMLEKGERMGCPAGCPREMYDLMNLCWTYDVENRPGFAAVELRLRNYYYDVVN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.95
R work: 0.1751
R free: 0.2281
Average B factor: 43.673
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.8
Crystallization temperature (K): 293
Crystal growth procedure: PEG1500, HEPES, TACSIMATE, GLYCEROL
Matthews coefficient: 2.18
Solvent content (%): 43.66
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: 2016-09-14
Human PARP14 (ARTD8), catalytic fragment in complex with an N-aryl piperazine inhibitor (PDB entry 5NQE)
Macromolecule: Poly [ADP-ribose] polymerase 14
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.4.2.30
Sequence length: 193 residues
Sequence: SMDMKQQNFCVVELLPSDPEYNTVASKFNQTCSHFRIEKIERIQNPDLWNSYQAKKKTMDAKNGQTMNEKQLFHGTDAGSVPHVNRNGFNRSYAGKNAVAYGKGTYFAVNANYSANDTYSRPDANGRKHVYYVRVLTGIYTHGNHSLIVPPSKNPQNPTDLYDTVTDNVHHPSLFVAFYDYQAYPEYLITFRK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.71
R work: 0.227
R free: 0.258
Average B factor: 40.21
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 20% PEG3350, 0.2M Sodium-malonate
Matthews coefficient: 3.06
Solvent content (%): 57.8
Ligand: 3-[[4-[4-(4-fluorophenyl)piperazin-1-yl]-4-oxidanylidene-butanoyl]amino]benzamide (94Z)
Ligand formula: C21 H23 F N4 O3
Ligand molecular weight: 398.431
Ligand SMILES: c1cc(cc(c1)NC(=O)CCC(=O)N2CCN(CC2)c3ccc(cc3)F)C(=O)N
Ligand InChI: InChI=1S/C21H23FN4O3/c22-16-4-6-18(7-5-16)25-10-12-26(13-11-25)20(28)9-8-19(27)24-17-3-1-2-15(14-17)21(23)29/h1-7,14H,8-13H2,(H2,23,29)(H,24,27)
Release date: 2017-05-24