satarupa22/MacromolecularLigandDB huggingface dataset:
Atomic resolution structure of human Carbonic Anhydrase II in complex with (R)-5-phenyloxazolidine-2,4-dione (PDB entry 6SFQ)
Macromolecule: Carbonic anhydrase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 265 residues
Sequence: GSPEFMSHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHAFNVEFDDSQDKAVLKGGPLDGTYRLIQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDFGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTKGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLLECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1
R work: 0.1261
R free: 0.1468
Average B factor: 13.65
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.8
Crystallization temperature (K): 291
Crystal growth procedure: Sodium citrate 1.4 M, TRIS 0.1 M, saturated with para-Chloromercuribenzoic acid
Matthews coefficient: 2.13
Solvent content (%): 42.39
Ligand: SODIUM ION ()
Ligand formula: Na
Ligand molecular weight: 22.99
Ligand SMILES: [Na+]
Ligand InChI: InChI=1S/Na/q+1
Release date: 2020-08-26
DARPin_D5/Her3 domain 4 complex, monoclinic crystals (PDB entry 7BHE)
Macromolecule: DARPin_D5
Type: Protein, polypeptide(L)
Source organism: synthetic construct
Sequence length: 138 residues
Sequence: MRGSHHHHHHGPGSDLGKKLLEAARAGQDDEVRILMANGADVNAFDHNGSTPLHLAAAIGHLEIVEVLLKYGADVNAEDNWGNTPLHQAAWVGHLEIVEVLLKNGADVNAQDKFGKTAFDISIDNGNEDLAEILQKLN
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.297
R work: 0.184
R free: 0.2536
Average B factor: 34.4
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 4.83
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M Na citrate, 12% PEG4000, 0.2 M Li sulfate
Matthews coefficient: 2.66
Solvent content (%): 53.73
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: 2021-11-24
Crystal structure of human carbonic anhydrase isozyme II with 2,3,5,6-Tetrafluoro-4-(propylthio)benzenesulfonamide (PDB entry 4WW6)
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): 1.06
R work: 0.128
R free: 0.151
Average B factor: 15.737
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 291
Crystal growth procedure: Crystallization buffer was 0.1M sodium BICINE, pH 9, 0.25 M ammonium sulfate and 2M sodium malonate pH 7 made from 1M sodium BICINE and 3.4M sodium malonate
Matthews coefficient: 2
Solvent content (%): 38.2
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: 2015-07-01
Room-temperature Human Hsp90a-NTD bound to N6M (PDB entry 7S99)
Macromolecule: Heat shock protein HSP 90-alpha
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.4.10
Sequence length: 237 residues
Sequence: HMPEETQTQDQPMEEEEVETFAFQAEIAQLMSLIINTFYSNKEIFLRELISNSSDALDKIRYESLTDPSKLDSGKELHINLIPNKQDRTLTIVDTGIGMTKADLINNLGTIAKSGTKAFMEALQAGADISMIGQFGVGFYSAYLVAEKVTVITKHNDDEQYAWESSAGGSFTVRTDTGEPMGRGTKVILHLKEDQTEYLEERRIKEIVKKHSQFIGYPITLFVEKERDKEVSDDEAE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.52
R work: 0.167
R free: 0.1809
Average B factor: 36.4
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 1.8 M Malic acid, pH 7
Matthews coefficient: 2.79
Solvent content (%): 55.95
Ligand: N-METHYL-9H-PURIN-6-AMINE (N6M)
Ligand formula: C6 H7 N5
Ligand molecular weight: 149.153
Ligand SMILES: CNc1c2c([nH]cn2)ncn1
Ligand InChI: InChI=1S/C6H7N5/c1-7-5-4-6(10-2-8-4)11-3-9-5/h2-3H,1H3,(H2,7,8,9,10,11)
Release date: 2022-08-03
IRAK4 in complex with inhibitor (PDB entry 7QG3)
Macromolecule: Interleukin-1 receptor-associated kinase 4
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 308 residues
Sequence: GENKSLEVSDTRFHSFSFYELKNVTNNFDERPISVGGNKMGEGGFGVVYKGYVNNTTVAVKKLAAMVDITTEELKQQFDQEIKVMAKCQHENLVELLGFSSDGDDLCLVYVYMPNGSLLDRLSCLDGTPPLSWHMRCKIAQGAANGINFLHENHHIHRDIKSANILLDEAFTAKISDFGLARASEKFAQTVMTSRIVGTTAYMAPEALRGEITPKSDIYSFGVVLLEIITGLPAVDEHREPQLLLDIKEEIEDEEKTIEDYIDKKMNDADSTSVEAMYSVASQCLHEKKNKRPDIKKVQQLLQEMTAS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.11
R work: 0.272
R free: 0.304
Crystallization method: EVAPORATION
Crystallization temperature (K): 298
Crystal growth procedure: 2.7 M AMS 0.1 M Hepes pH 7.1-7.7
Matthews coefficient: 2.48
Solvent content (%): 50.35
Ligand: 6-[(2~{S})-2-fluoranylpropyl]-4-[(1-methylcyclopropyl)amino]-2-[[1-(1-methylpiperidin-4-yl)pyrazol-4-yl]amino]pyrido[4,3-d]pyrimidin-5-one (B4U)
Ligand formula: C23 H31 F N8 O
Ligand molecular weight: 454.544
Ligand SMILES: CC(CN1C=Cc2c(c(nc(n2)Nc3cnn(c3)C4CCN(CC4)C)NC5(CC5)C)C1=O)F
Ligand InChI: InChI=1S/C23H31FN8O/c1-15(24)13-31-11-6-18-19(21(31)33)20(29-23(2)7-8-23)28-22(27-18)26-16-12-25-32(14-16)17-4-9-30(3)10-5-17/h6,11-12,14-15,17H,4-5,7-10,13H2,1-3H3,(H2,26,27,28,29)/t15-/m0/s1
Release date: 2022-05-04
MEK1 bound to DS94070624 (PDB entry 7XNC)
Macromolecule: Dual specificity mitogen-activated protein kinase kinase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.12.2
Sequence length: 348 residues
Sequence: GLEELELDEQQRKRLEAFLTQKQKVGELKDDDFEKISELGAGNGGVVFKVSHKPSGLVMARKLIHLEIKPAIRNQIIRELQVLHECNSPYIVGFYGAFYSDGEISICMEHMDGGSLDQVLKKAGRIPEQILGKVSIAVIKGLTYLREKHKIMHRDVKPSNILVNSRGEIKLCDFGVSGQLIDSMANSFVGTRSYMSPERLQGTHYSVQSDIWSMGLSLVEMAVGRYPIPPPDAKELELMFGCQVEGDAAETPPRPRTPGRPLNKKGMDSRPPMAIFELLDYIVNEPPPKLPSGVFSLEFQDFVNKCLIKNPAERADLKQLMVHAFIKRSDAEEVDFAGWLCSTIGLNQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.1
R work: 0.2252
R free: 0.2512
Average B factor: 53.8059
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.75
Crystallization temperature (K): 277
Crystal growth procedure: 100 mM Tris (pH 7.75), 200 mM calcium chloride, 2% DMSO, 18-20% PEG 3350
Matthews coefficient: 2.47
Solvent content (%): 50.18
Ligand: ~{N}-[4-[[6-(3-chloranylpyridin-4-yl)-3-methyl-1~{H}-indazol-4-yl]oxy]cyclohexyl]ethanamide (GIK)
Ligand formula: C21 H23 Cl N4 O2
Ligand molecular weight: 398.886
Ligand SMILES: Cc1c2c(cc(cc2OC3CCC(CC3)NC(=O)C)c4ccncc4Cl)[nH]n1
Ligand InChI: InChI=1S/C21H23ClN4O2/c1-12-21-19(26-25-12)9-14(17-7-8-23-11-18(17)22)10-20(21)28-16-5-3-15(4-6-16)24-13(2)27/h7-11,15-16H,3-6H2,1-2H3,(H,24,27)(H,25,26)/t15-,16-
Release date: 2023-03-01
Crystal structure of PML B-box2 mutant (PDB entry 8J25)
Macromolecule: Maltose/maltodextrin-binding periplasmic protein,Protein PML
Type: Protein, polypeptide(L)
Source organism: Escherichia coli K-12
EC number: 2.3.2
Sequence length: 428 residues
Sequence: MGKIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGPDIIFWAHDRFGGYAQSGLLAEITPDKAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYNKDLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYENGKYDIKDVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNIDTSKVNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNKDKPLGAVALKSYEEELAKDPRIAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTVDEALKDAQTNAAAEFKTNNIFCSNPNHRTPTLTSIYCRGCSKPLCASCVLLDSSHSELKCDISAEIQQR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.6
R work: 0.2042
R free: 0.2478
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 291
Crystal growth procedure: 22% PEG 3350
Matthews coefficient: 2.5
Solvent content (%): 50.85
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: 2023-09-20
INPP5D PanDDA analysis group deposition -- Crystal Structure of the phosphatase and C2 domains of SHIP1 in complex with Z2856434821 (PDB entry 5RXB)
Macromolecule: Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.86
Sequence length: 463 residues
Sequence: SMEQPEPDMITIFIGTWNMGNAPPPKKITSWFLSKGQGKTRDDSADYIPHDIYVIGTQEDPLSEKEWLEILKHSLQEITSVTFKTVAIHTLWNIRIVVLAKPEHENRISHICTDNVKTGIANTLGNKGAVGVSFMFNGTSLGFVNSHLTSGSEKKLRRNQNYMNILRFLALGDKKLSPFNITHRFTHLFWFGDLNYRVDLPTWEAETIIQKIKQQQYADLLSHDQLLTERREQKVFLHFEEEEITFAPTYRFERLTRDKYAYTKQKATGMKYNLPSWCDRVLWKSYPLVHVVCQSYGSTSDIMTSDHSPVFATFEAGVTSQFVSKNGPGTVDSQGQIEFLRCYATLKTKSQTKFYLEFHSSCLESFVKSQEGENEEGSEGELVVKFGETLPKLKPIISDPEYLLDQHILISIKSSDSDESYGEGCIALRLEATETQLPIYTPLTHHGELTGHFQGEIKLQTSQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.58
R work: 0.1828
R free: 0.213
Average B factor: 17.845
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 30 mM sodium nitrate, 30 mM dibasic sodium phosphate, 30 mM ammonium sulfate, 100 mM MES/imidazole, pH 6.5, 20% PEG500 MME, 10% PEG20000
Matthews coefficient: 2.11
Solvent content (%): 41.57
Ligand: 2-methyl-2-{[(3-methylthiophen-2-yl)methyl]amino}propan-1-ol (RX7)
Ligand formula: C10 H17 N O S
Ligand molecular weight: 199.313
Ligand SMILES: Cc1ccsc1CNC(C)(C)CO
Ligand InChI: InChI=1S/C10H17NOS/c1-8-4-5-13-9(8)6-11-10(2,3)7-12/h4-5,11-12H,6-7H2,1-3H3
Release date: 2020-11-11
CATHEPSIN L IN COMPLEX WITH 4-[1,3-benzodioxol-5-ylmethyl(2-phenoxyethyl)amino]-5-fluoropyrimidine-2-carbonitrile (PDB entry 5MQY)
Macromolecule: Cathepsin L1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.22.15
Sequence length: 220 residues
Sequence: APRSVDWREKGYVTPVKNQGQCGSCWAFSATGALEGQMFRKTGRLISLSEQNLVDCSGPQGNEGCNGGLMDYAFQYVQDNGGLDSEESYPYEATEESCKYNPKYSVANDTGFVDIPKQEKALMKAVATVGPISVAIDAGHESFLFYKEGIYFEPDCSSEDMDHGVLVVGYGFESTESDNNKYWLVKNSWGEEWGMGGYVKMAKDRRNHCGIASAASYPTV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.13
R work: 0.14869
R free: 0.19898
Average B factor: 23.934
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 294
Crystal growth procedure: 25% PEG3350, 0.1M Bis-Tris
Matthews coefficient: 2.06
Solvent content (%): 40.15
Ligand: 4-[1,3-benzodioxol-5-ylmethyl(2-phenoxyethyl)amino]-5-fluoropyrimidine-2-carbonitrile (GH4)
Ligand formula: C21 H19 F N4 O3
Ligand molecular weight: 394.399
Ligand SMILES: c1ccc(cc1)OCCN(Cc2ccc3c(c2)OCO3)c4c(cnc(n4)C=N)F
Ligand InChI: InChI=1S/C21H19FN4O3/c22-17-12-24-20(11-23)25-21(17)26(8-9-27-16-4-2-1-3-5-16)13-15-6-7-18-19(10-15)29-14-28-18/h1-7,10-12,23H,8-9,13-14H2/b23-11+
Release date: 2017-03-22
PanDDA analysis group deposition of models with modelled events (e.g. bound ligands) -- Crystal Structure of NUDT7 in complex with NUOOA000259a (PDB entry 5QH6)
Macromolecule: Peroxisomal coenzyme A diphosphatase NUDT7
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.1
Sequence length: 196 residues
Sequence: SMLDDAKARLRKYDIGGKYSHLPYNKYSVLLPLVAKEGKLHLLFTVRSEKLRRAPGEVCFPGGKRDPTDMDDAATALREAQEEVGLRPHQVEVVCCLVPCLIDTDTLITPFVGLIDHNFQAQPNPAEVKDVFLVPLAYFLHPQVHDQHYVTRLGHRFINHIFEYTNPEDGVTYQIKGMTANLAVLVAFIILEKKPT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.0
R work: 0.1849
R free: 0.2152
Average B factor: 32.872
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M bis-tris pH 5.5 -- 0.1M ammonium acetate -- 5%(w/v) PEG10K
Matthews coefficient: 4.11
Solvent content (%): 70.08
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: 2019-03-27
CRYSTAL STRUCTURE OF GLYCOGEN SYNTHASE KINASE 3 BETA COMPLEXED WITH 3-[(CYCLOPROPYLMETHYL)AMINO] -N-(4-PHENYLPYRIDIN-3-YL)IMIDAZO[1,2-B]PYRIDAZINE-8-CARBOX AMIDE (PDB entry 8DJD)
Macromolecule: Glycogen synthase kinase-3 beta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.26
Sequence length: 441 residues
Sequence: MHSSHHHHHHSSGENLYFQGHMSGRPRTTSFAESCKPVQQPSAFGSMKVSRDKDGSKVTTVVATPGQGPDRPQEVSYTDTKVIGNGSFGVVYQAKLCDSGELVAIKKVLQDKRFKNRELQIMRKLDHCNIVRLRYFFYSSGEKKDEVYLNLVLDYVPETVYRVARHYSRAKQTLPVIYVKLYMYQLFRSLAYIHSFGICHRDIKPQNLLLDPDTAVLKLCDFGSAKQLVRGEPNVSYICSRYYRAPELIFGATDYTSSIDVWSAGCVLAELLLGQPIFPGDSGVDQLVEIIKVLGTPTREQIREMNPNYTEFKFPQIKAHPWTKVFRPRTPPEAIALCSRLLEYTPTARLTPLEACAHSFFDELRDPNVKLPNGRDTPALFNFTTQELSSNPPLATILIPPHARIQAAASTPTNATAASDANTGDRGQTNNAASASASNST
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.205
R work: 0.2083
R free: 0.2218
Average B factor: 45.77
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 295
Crystal growth procedure: 0.1 M HEPES pH 7.0, 20.0 %w/v PEG6K, 0.2 M LiCl
Matthews coefficient: 3.03
Solvent content (%): 59.47
Ligand: 2-[(cyclopropanecarbonyl)amino]-N-(5-phenylpyridin-3-yl)pyridine-4-carboxamide (U3E)
Ligand formula: C21 H18 N4 O2
Ligand molecular weight: 358.393
Ligand SMILES: c1ccc(cc1)c2cc(cnc2)NC(=O)c3ccnc(c3)NC(=O)C4CC4
Ligand InChI: InChI=1S/C21H18N4O2/c26-20(15-6-7-15)25-19-11-16(8-9-23-19)21(27)24-18-10-17(12-22-13-18)14-4-2-1-3-5-14/h1-5,8-13,15H,6-7H2,(H,24,27)(H,23,25,26)
Release date: 2023-03-22
Reversible lysine-targeted probes reveal residence time-based kinase selectivity in vivo (PDB entry 7FIC)
Macromolecule: Aurora kinase A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 265 residues
Sequence: QWALEDFEIGRPLGKGKFGNVYLAREKQSKFILALKVLFKAQLEKAGVEHQLRREVEIQSHLRHPNILRLYGYFHDATRVYLILEYAPLGTVYRELQKLSKFDEQRTATYITELANALSYCHSKRVIHRDIKPENLLLGSAGELKIADFGWSVHAPSSRRTTLAGTLDYLPPEMIEGRMHDEKVDLWSLGVLCYEFLVGKPPFEANTYQETYKRISRVEFTFPDFVTEGARDLISRLLKHNPSQRPMLREVLEHPWITANSSKPS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.32
R work: 0.2356
R free: 0.274
Average B factor: 90.24
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7
Crystallization temperature (K): 298
Crystal growth procedure: 0.2 M lithium sulfate, 0.1 M BIS-TRIS pH 5.5, 25% w/v PEG 3350
Matthews coefficient: 2.88
Solvent content (%): 57.34
Ligand: 6-[(5-cyclopropyl-1~{H}-pyrazol-3-yl)amino]-2-[4-[(3-methyl-4-oxidanyl-phenyl)methyl]piperazin-1-yl]-~{N}-prop-2-ynyl-pyrimidine-4-carboxamide (5YZ)
Ligand formula: C26 H30 N8 O2
Ligand molecular weight: 486.569
Ligand SMILES: Cc1cc(ccc1O)CN2CCN(CC2)c3nc(cc(n3)Nc4cc([nH]n4)C5CC5)C(=O)NCC#C
Ligand InChI: InChI=1S/C26H30N8O2/c1-3-8-27-25(36)21-15-23(29-24-14-20(31-32-24)19-5-6-19)30-26(28-21)34-11-9-33(10-12-34)16-18-4-7-22(35)17(2)13-18/h1,4,7,13-15,19,35H,5-6,8-12,16H2,2H3,(H,27,36)(H2,28,29,30,31,32)
Release date: 2022-06-08
Crystal structure of the human TRIM25 PRYSPRY domain (PDB entry 6FLM)
Macromolecule: E3 ubiquitin/ISG15 ligase TRIM25
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 6.3.2
Sequence length: 199 residues
Sequence: GMASLKAKVLETFLAKSRPELLEYYIKVILDYNTAHNKVALSECYTVASVAEMPQNYRPHPQRFTYCSQVLGLHCYKKGIHYWEVELQKNNFCGVGICYGSMNRQGPESRLGRNSASWCVEWFNTKISAWHNNVEKTLPSTKATRVGVLLNCDHGFVIFFAVADKVHLMYKFRVDFTEALYPAFWVFSAGATLSICSPK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.009
R work: 0.1649
R free: 0.2061
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 15 mg/ml protein mixed in 1:1 ratio with reservoir containing 0.1 M bis-TRIS pH 6.5 and 2M ammonium sulphate.
Matthews coefficient: 3.41
Solvent content (%): 63.94
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: 2018-05-23
Ternary trans-complex of phospho-parkin with cis ACT and pUb (PDB entry 8IKT)
Macromolecule: E3 ubiquitin-protein ligase parkin
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2.31
Sequence length: 312 residues
Sequence: SGQEMNATGGDDPRNAAGGCEREPQSLTRVDLSSSVLPGDSVGLAVILHTDSRKDSPPAGSPAGRSIYNSFYVYCKGPCQRVQPGKLRVQCSTCRQATLTLTQGPSCWDDVLIPNRMSGECQSPHCPGTSAEFFFKCGAHPTSDKETSVALHLIATNSRNITCITCTDVRSPVLVFQCNSRHVICLDCFHLYCVTRLNDRQFVHDPQLGYSLPCVAGCPNSLIKELHHFRILGEEQYNRYQQYGAEECVLQMGGVLCPRPGCGAGLLPEPDCRKVTCEGGNGLGCGFAFCRECKEAYHEGECSAVFENLYFQ
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.6
R work: 0.2125
R free: 0.2358
Average B factor: 63.575
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 0.3 M Sodium nitrate, 0.3 Sodium phosphate dibasic, 0.3 M Ammonium sulfate, Imidazole, MES monohydrate (acid), 25% v/v MPD, 25% PEG 1000, 25% w/v PEG 3350
Matthews coefficient: 1.98
Solvent content (%): 38.02
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: 2024-09-11
PanDDA analysis group deposition of models with modelled events (e.g. bound ligands) -- Crystal Structure of NUDT7 in complex with FMOPL000476a (PDB entry 5QGS)
Macromolecule: Peroxisomal coenzyme A diphosphatase NUDT7
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.1
Sequence length: 196 residues
Sequence: SMLDDAKARLRKYDIGGKYSHLPYNKYSVLLPLVAKEGKLHLLFTVRSEKLRRAPGEVCFPGGKRDPTDMDDAATALREAQEEVGLRPHQVEVVCCLVPCLIDTDTLITPFVGLIDHNFQAQPNPAEVKDVFLVPLAYFLHPQVHDQHYVTRLGHRFINHIFEYTNPEDGVTYQIKGMTANLAVLVAFIILEKKPT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.55
R work: 0.1642
R free: 0.1951
Average B factor: 32.119
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M bis-tris pH 5.5 -- 0.1M ammonium acetate -- 5%(w/v) PEG10K
Matthews coefficient: 4.28
Solvent content (%): 71.23
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: 2019-03-27
Human protein kinase CK2 alpha in complex with CK2-TN02 (PDB entry 8C6M)
Macromolecule: Casein kinase II subunit alpha
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 336 residues
Sequence: MSGPVPSRARVYTDVNTHRPREYWDYESHVVEWGNQDDYQLVRKLGRGKYSEVFEAINITNNEKVVVKILKPVKKKKIKREIKILENLRGGPNIITLADIVKDPVSRTPALVFEHVNNTDFKQLYQTLTDYDIRFYMYEILKALDYCHSMGIMHRDVKPHNVMIDHEHRKLRLIDWGLAEFYHPGQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRKEPFFHGHDNYDQLVRIAKVLGTEDLYDYIDKYNIELDPRFNDILGRHSRKRWERFVHSENQHLVSPEALDFLDKLLRYDHQSRLTAREAMEHPYFYTVVKDQARMGS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.1594
R free: 0.2021
Average B factor: 23.9737
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 293
Crystal growth procedure: 32% PEG4000, 0.2 M Lithium Sulfate
Matthews coefficient: 2
Solvent content (%): 38.5
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: 2024-04-24
c-KIT kinase domain in complex with avapritinib derivative 12 (PDB entry 8PQF)
Macromolecule: Mast/stem cell growth factor receptor Kit
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 327 residues
Sequence: GSMPMYEVQWKVVEESNGNNYSYIDPTQLPYDHKWEFPRNRLSFGKTLGAGAFGKVVEATAQGLIKSDAAMTVAVKMLKPSAHSTEREALMSELKVLSYLGNHENIVNLLGACTHGGPTLVITEYCCYGDLLNFLRRKRDEFVPYKVAPEDLYKDFLTLEHLLSFSYQVAKGMAFLASKNCIHRDLAARNILLTHGNITKICDFGLARDIKNDSNYVDKGNARLPVKWMAPESIFNSVYTFESDVWSYGIFLWELFSLGSSPYPGMPVDSKFYKMIKEGFRMSSPEYAPAEMYDIMKTCWDADPDKRPTFKQIVQDIEKQISESTNH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.9
R work: 0.1957
R free: 0.2186
Average B factor: 47.66
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 285.15
Crystal growth procedure: 3 mg/mL, 21% PEG3350, 125 mM Li3-citrate
Matthews coefficient: 1.9
Solvent content (%): 35.35
Ligand: methyl ~{N}-[(1~{S})-1-(4-fluorophenyl)-1-[2-[4-[6-(1-methylpyrazol-4-yl)pyrrolo[2,1-f][1,2,4]triazin-4-yl]piperazin-1-yl]pyrimidin-5-yl]ethyl]carbamate (9KI)
Ligand formula: C28 H29 F N10 O2
Ligand molecular weight: 556.594
Ligand SMILES: CC(c1ccc(cc1)F)(c2cnc(nc2)N3CCN(CC3)c4c5cc(cn5ncn4)c6cnn(c6)C)NC(=O)OC
Ligand InChI: InChI=1S/C28H29FN10O2/c1-28(35-27(40)41-3,21-4-6-23(29)7-5-21)22-14-30-26(31-15-22)38-10-8-37(9-11-38)25-24-12-19(17-39(24)34-18-32-25)20-13-33-36(2)16-20/h4-7,12-18H,8-11H2,1-3H3,(H,35,40)/t28-/m0/s1
Release date: 2023-12-27
Carborane closo-butyl-sulfonamide in complex with CA II (PDB entry 6YZQ)
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): 1.04
R work: 0.141
R free: 0.1596
Average B factor: 18.645
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.8
Crystallization temperature (K): 291
Crystal growth procedure: 1.6 M sodium citrate, 50 mM Tris-H2SO4
Matthews coefficient: 2.08
Solvent content (%): 40.85
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: 2020-10-28
Application of Off-Rate Screening in the Identification of Novel Pan-Isoform Inhibitors of Pyruvate Dehydrogenase Kinase (PDB entry 5M4P)
Macromolecule: [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.2
Sequence length: 408 residues
Sequence: MRWVWALLKNASLAGSAPKYIEHFSKFSPSPLSMKQFLDFGSSNACEKTSFTFLRQELPVRLANIMKEINLLPDRVLSTPSVQLVQSWYVQSLLDIMEFLDKDPEDHRTLSQFTDALVTIRNRHNDVVPTMAQGVLEYKDTYGDDPVSNQNIQYFLDRFYLSRISIRMLINQHTLIFDGSTNPAHPKHIGSIDPNCNVSEVVKDAYDMAKLLCDKYYMASPDLEIQEINAANSKQPIHMVYVPSHLYHMLFELFKNAMRATVESHESSLILPPIKVMVALGEEDLSIKMSDRGGGVPLRKIERLFSYMYSTAPTPQPGTGGTPLAGFGYGLPISRLYAKYFQGDLQLFSMEGFGTDAVIYLKALSTDSVERLPVYNKSAWRHYQTIQEAGDWCVPSTEPKNTSTYRVS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.3
R work: 0.19951
R free: 0.25178
Average B factor: 54.98
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 5.8
Crystallization temperature (K): 277
Crystal growth procedure: 0.1 M SODIUM ACETATE PH 5.8
0.125 M MAGNESIUM CHLORIDE
6% ISOPROPANOL
Matthews coefficient: 3.16
Solvent content (%): 61.03
Ligand: ~{N}-[4-(2-chloranyl-5-methyl-pyrimidin-4-yl)phenyl]-2,4-bis(oxidanyl)-~{N}-[[4-(pyrrolidin-1-ylmethyl)phenyl]methyl]benzamide (7FE)
Ligand formula: C30 H29 Cl N4 O3
Ligand molecular weight: 529.029
Ligand SMILES: Cc1cnc(nc1c2ccc(cc2)N(Cc3ccc(cc3)CN4CCCC4)C(=O)c5ccc(cc5O)O)Cl
Ligand InChI: InChI=1S/C30H29ClN4O3/c1-20-17-32-30(31)33-28(20)23-8-10-24(11-9-23)35(29(38)26-13-12-25(36)16-27(26)37)19-22-6-4-21(5-7-22)18-34-14-2-3-15-34/h4-13,16-17,36-37H,2-3,14-15,18-19H2,1H3
Release date: 2017-02-22