satarupa22/MacromolecularLigandDB huggingface dataset:
Crystal structure of c-Src in complex with covalent inhibitor DC-Srci-6668 (PDB entry 8JN8)
Macromolecule: Proto-oncogene tyrosine-protein kinase Src
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 536 residues
Sequence: MGSNKSKPKDASQRRRSLEPAENVHGAGGGAFPASQTPSKPASADGHRGPSAAFAPAAAEPKLFGGFNSSDTVTSPQRAGPLAGGVTTFVALYDYESRTETDLSFKKGERLQIVNNTEGDWWLAHSLSTGQTGYIPSNYVAPSDSIQAEEWYFGKITRRESERLLLNAENPRGTFLVRESETTKGAYCLSVSDFDNAKGLNVKHYKIRKLDSGGFYITSRTQFNSLQQLVAYYSKHADGLCHRLTTVCPTSKPQTQGLAKDAWEIPRESLRLEVKLGQGCFGEVWMGTWNGTTRVAIKTLKPGTMSPEAFLQEAQVMKKLRHEKLVQLYAVVSEEPIYIVTEYMSKGSLLDFLKGETGKYLRLPQLVDMAAQIASGMAYVERMNYVHRDLRAANILVGENLVCKVADFGLARLIEDNEYTARQGAKFPIKWTAPEAALYGRFTIKSDVWSFGILLTELTTKGRVPYPGMVNREVLDQVERGYRMPCPPECPESLHDLMCQCWRKEPEERPTFEYLQAFLEDYFTSTEPQYQPGENL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.902
R work: 0.2097
R free: 0.2535
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 289
Crystal growth procedure: 0.2M tri-Lithium citrate, 20%(w/v) PEG 3350
Matthews coefficient: 1.89
Solvent content (%): 34.78
Ligand: (2R)-N-cyclopentyl-2-[cyclopropyl(ethanoyl)amino]-2-(4-fluorophenyl)ethanamide (JA6)
Ligand formula: C18 H23 F N2 O2
Ligand molecular weight: 318.386
Ligand SMILES: CC(=O)N(C1CC1)C(c2ccc(cc2)F)C(=O)NC3CCCC3
Ligand InChI: InChI=1S/C18H23FN2O2/c1-12(22)21(16-10-11-16)17(13-6-8-14(19)9-7-13)18(23)20-15-4-2-3-5-15/h6-9,15-17H,2-5,10-11H2,1H3,(H,20,23)/t17-/m1/s1
Release date: 2024-06-12
DYRK1A IN COMPLEX WITH NITRO BENZOTHIAZOLE FRAGMENT (PDB entry 5A54)
Macromolecule: DUAL SPECIFICITY TYROSINE-PHOSPHORYLATION-REGULATED KINASE 1A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.12.1
Sequence length: 368 residues
Sequence: GASDSSHKKERKVYNDGYDDDNYDYIVKNGEKWMDRYEIDSLIGKGSFGQVVKAYDRVEQEWVAIKIIKNKKAFLNQAQIEVRLLELMNKHDTEMKYYIVHLKRHFMFRNHLCLVFEMLSYNLYDLLRNTNFRGVSLNLTRKFAQQMCTALLFLATPELSIIHCDLKPENILLCNPKRSAIKIVDFGSSCQLGQRIYQYIQSRFYRSPEVLLGMPYDLAIDMWSLGCILVEMHTGEPLFSGANEVDQMNKIVEVLGIPPAHILDQAPKARKFFEKLPDGTWNLKKTKDGKREYKPPGTRKLHNILGVETGGPGGRRAGESGHTVADYLKFKDLILRMLDYDPKTRIQPYYALQHSFFKKTADEGTNTS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.63
R work: 0.22232
R free: 0.25461
Average B factor: 59.49
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.8
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M KSCN; 0.1M KCL; 14% PEG 3350, PH 6.8, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K
Matthews coefficient: 2.6
Solvent content (%): 52.7
Ligand: N-(6-nitro-1,3-benzothiazol-2-yl)ethanamide (5PW)
Ligand formula: C9 H7 N3 O3 S
Ligand molecular weight: 237.235
Ligand SMILES: CC(=O)Nc1nc2ccc(cc2s1)[N+](=O)[O-]
Ligand InChI: InChI=1S/C9H7N3O3S/c1-5(13)10-9-11-7-3-2-6(12(14)15)4-8(7)16-9/h2-4H,1H3,(H,10,11,13)
Release date: 2016-06-29
Pre-catalytic quaternary complex of DNA Polymerase Lambda with bound mismatched DSB and incoming dUMPNPP (PDB entry 7M0B)
Macromolecule: DNA (5'-D(*CP*GP*GP*CP*AP*G)-3')
Type: DNA, polydeoxyribonucleotide
Source organism: synthetic construct
Sequence length: 6 residues
Sequence: CGGCAG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2
R work: 0.1705
R free: 0.2004
Average B factor: 24.95
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 277
Crystal growth procedure: 76.5mM Na cacodylate pH 6.5, 0.153M ammonium sulfate, 22.95% (w/v) PEG8000, 13.5% (v/v) glycerol, 0.2M NDSB-201
Matthews coefficient: 3.03
Solvent content (%): 59.4
Ligand: 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE (DUP)
Ligand formula: C9 H16 N3 O13 P3
Ligand molecular weight: 467.157
Ligand SMILES: C1C(C(OC1N2C=CC(=O)NC2=O)COP(=O)(NP(=O)(O)OP(=O)(O)O)O)O
Ligand InChI: InChI=1S/C9H16N3O13P3/c13-5-3-8(12-2-1-7(14)10-9(12)15)24-6(5)4-23-26(16,17)11-27(18,19)25-28(20,21)22/h1-2,5-6,8,13H,3-4H2,(H,10,14,15)(H2,20,21,22)(H3,11,16,17,18,19)/t5-,6+,8+/m0/s1
Release date: 2022-03-16
Unphosphorylated CaMKK2 in complex with CC-8977 (PDB entry 8TUC)
Macromolecule: Calcium/calmodulin-dependent protein kinase kinase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.17
Sequence length: 291 residues
Sequence: SMQLNQYTLKDEIGKGSYGVVKLAYNENDNTYYAMKVLSKKKLIRQAGFPRRPPPRGTRPAPGGCIQPRGPIEQVYQEIAILKKLDHPNVVKLVEVLDDPNEDHLYMVFELVNQGPVMEVPTLKPLSEDQARFYFQDLIKGIEYLHYQKIIHRDIKPSNLLVGEDGHIKIADFGVSNEFKGSDALLSNTVGTPAFMAPESLSETRKIFSGKALDVWAMGVTLYCFVFGQCPFMDERIMCLHSKIKSQALEFPDQPDIAEDLKDLITRMLDKNPESRIVVPEIKLHPWVTRH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.5
R work: 0.16692
R free: 0.20678
Average B factor: 25.645
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 2.0 M (NH4)2S04, 2 M NaCl, 0.1 NaCacodylate
Matthews coefficient: 2.62
Solvent content (%): 49.22
Ligand: (4M)-2-cyclopentyl-4-(7-ethoxyquinazolin-4-yl)benzoic acid (O7I)
Ligand formula: C22 H22 N2 O3
Ligand molecular weight: 362.422
Ligand SMILES: CCOc1ccc2c(c1)ncnc2c3ccc(c(c3)C4CCCC4)C(=O)O
Ligand InChI: InChI=1S/C22H22N2O3/c1-2-27-16-8-10-18-20(12-16)23-13-24-21(18)15-7-9-17(22(25)26)19(11-15)14-5-3-4-6-14/h7-14H,2-6H2,1H3,(H,25,26)
Release date: 2023-12-13
Crystal Structure of 5-(trifluoromethoxy)indoline-2,3-dione covalently bound to the PH domain of Bruton's tyrosine kinase mutant R28C (PDB entry 6YYG)
Macromolecule: Tyrosine-protein kinase BTK
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 169 residues
Sequence: AAVILESIFLKRSQQKKKTSPLNFKKRLFLLTVHKLSYYEYDFERGRRGSKKGSIDVEKITCVETVVPEKNPPPERQIPRRGEESSEMEQISIIERFPYPFQVVYDEGPLYVFSPTEELRKRWIHQLKNVIRYNSDLVQKYHPCFWIDGQYLCCSQTAKNAMGCQILEN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.95
R work: 0.2304
R free: 0.2988
Average B factor: 41.561
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 298
Crystal growth procedure: 0.1 M TRIS 8.5 pH, 32.5% w/v PEG 3350, 200mM MgCl2 500 mM NaCl
Matthews coefficient: 2.27
Solvent content (%): 45.71
Ligand: 5-(trifluoromethyloxy)-1,3-dihydroindol-2-one (Q1B)
Ligand formula: C9 H6 F3 N O2
Ligand molecular weight: 217.145
Ligand SMILES: c1cc2c(cc1OC(F)(F)F)CC(=O)N2
Ligand InChI: InChI=1S/C9H6F3NO2/c10-9(11,12)15-6-1-2-7-5(3-6)4-8(14)13-7/h1-3H,4H2,(H,13,14)
Release date: 2021-05-12
Crystal structure of WNK3 kinase domain in a monophosphorylated apo state (PDB entry 5O23)
Macromolecule: Serine/threonine-protein kinase WNK3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 285 residues
Sequence: SMEAEMKAVATSPSGRFLKFDIELGRGAFKTVYKGLDTETWVEVAWCELQDRKLTKAEQQRFKEEAEMLKGLQHPNIVRFYDSWESILKGKKCIVLVTELMTSGTLKTYLKRFKVMKPKVLRSWCRQILKGLQFLHTRTPPIIHRDLKCDNIFITGPTGSVKIGDLGLATLMRTSFAKSVIGTPEFMAPEMYEEHYDESVDVYAFGMCMLEMATSEYPYSECQNAAQIYRKVTSGIKPASFNKVTDPEVKEIIEGCIRQNKSERLSIRDLLNHAFFAEDTGLRVE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.25
R work: 0.2052
R free: 0.2387
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 30% PEG Smear Medium, 0.2 M lithium sulfate, 0.1 M ADA pH 6.5
Matthews coefficient: 3.64
Solvent content (%): 66.22
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: 2017-06-28
Monoclinic complex structure of human protein kinase CK2 catalytic subunit (isoform CK2alpha') with the inhibitor 4'-carboxy-6,8-chloro-flavonol (FLC21) (PDB entry 5M56)
Macromolecule: Casein kinase II subunit alpha'
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 364 residues
Sequence: MGSSHHHHHHSQDPMPGPAAGSRARVYAEVNSLRSREYWDYEAHVPSWGNQDGYQLVRKLGRGKYSEVFEAINITNNERVVVKILKPVKKKKIKREVKILENLRGGTNIIKLIDTVKDPVSKTPALVFEYINNTDFKQLYQILTDFDIRFYMYELLKALDYCHSKGIMHRDVKPHNVMIDHQQKKLRLIDWGLAEFYHPAQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRREPFFHGQDNYDQLVRIAKVLGTEELYGYLKKYHIDLDPHFNDILGQHSRKRWENFIHSENRHLVSPEALDLLDKLLRYDHQQRLTAKEAMEHPYFYPVVKEQSQPSADNAVLSSGLTAAR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.237
R work: 0.1635
R free: 0.2063
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277
Crystal growth procedure: PROTEIN STOCK SOLUTION: 5.5 MG/ML CK2ALPHA'-D39G-C336S IN 0.5 M NACL, 25 MM TRIS/HCL, PH 8.5;
INHIBITOR STOCK SOLUTION: 10 MM INHIBITOR IN DMSO;
PROTEIN/INHIBITOR COMPLEX SOLUTION: 90 MICROLITER PROTEIN STOCK SOLUTION + 10 MICROLITER INHIBITOR STOCK SOLUTION; 
RESERVOIR SOLUTION: 25 % PEG4000, 15 % glycerol, 0.17 M sodium acetate, 0.08 M Tris/HCl, pH 8.5;
DROP SOLUTION BEFORE EQULIBRATION: 0.3 MICROLITER PROTEIN/INHIBITOR COMPLEX SOLUTION + 0.3 MICROLITER RESERVOIR SOLUTION
Matthews coefficient: 2.48
Solvent content (%): 50.46
Ligand: 4-[6,8-bis(chloranyl)-3-oxidanyl-4-oxidanylidene-chromen-2-yl]benzoic acid (7FC)
Ligand formula: C16 H8 Cl2 O5
Ligand molecular weight: 351.138
Ligand SMILES: c1cc(ccc1C2=C(C(=O)c3cc(cc(c3O2)Cl)Cl)O)C(=O)O
Ligand InChI: InChI=1S/C16H8Cl2O5/c17-9-5-10-12(19)13(20)14(23-15(10)11(18)6-9)7-1-3-8(4-2-7)16(21)22/h1-6,20H,(H,21,22)
Release date: 2017-01-18
Human DNA polymerase eta-DNA ternary mismatch complex:reaction with 0.5 mM Mn2+ for 1800s then with 10 mM Mn2+ for 300s (PDB entry 7U76)
Macromolecule: DNA (5'-D(*CP*AP*TP*TP*AP*TP*GP*AP*CP*GP*CP*T)-3')
Type: DNA, polydeoxyribonucleotide
Source organism: synthetic construct
Sequence length: 12 residues
Sequence: CATTATGACGCT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.69
R work: 0.1825
R free: 0.2192
Average B factor: 37.3805
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6
Crystallization temperature (K): 298
Crystal growth procedure: 10% PEG 2000MME, 0.1 M MES
Matthews coefficient: 2.04
Solvent content (%): 39.64
Ligand: MANGANESE (II) ION (MN)
Ligand formula: Mn
Ligand molecular weight: 54.938
Ligand SMILES: [Mn+2]
Ligand InChI: InChI=1S/Mn/q+2
Release date: 2022-05-04
Crystal structure of haspin (GSG2) in complex with MU1668 (PDB entry 9FLC)
Macromolecule: Serine/threonine-protein kinase haspin
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 357 residues
Sequence: MHHHHHHSSGVDLGTENLYFQSMGECSQKGPVPFSHCLPTEKLQRCEKIGEGVFGEVFQTIADHTPVAIKIIAIEGPDLVNGSHQKTFEEILPEIIISKELSLLSGEVCNRTEGFIGLNSVHCVQGSYPPLLLKAWDHYNSTKGSANDRPDFFKDDQLFIVLEFEFGGIDLEQMRTKLSSLATAKSILHQLTASLAVAEASLRFEHRDLHWGNVLLKKTSLKKLHYTLNGKSSTIPSCGLQVSIIDYTLSRLERDGIVVFCDVSMDEDLFTGDGDYQFDIYRLMKKENNNRWGEYHPYSNVLWLHYLTDKMLKQMTFKTKCNTPAMKQIKRKIQEFHRTMLNFSSATDLLCQHSLFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.18
R work: 0.16485
R free: 0.19705
Average B factor: 39.187
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 63% MPD, 0.1M SPG 7.0
Matthews coefficient: 3.03
Solvent content (%): 59.37
Ligand: 5-(1-methylpyrazol-3-yl)-3-pyridin-4-yl-thieno[3,2-b]pyridine (A1IDA)
Ligand formula: C16 H12 N4 S
Ligand molecular weight: 292.358
Ligand SMILES: Cn1ccc(n1)c2ccc3c(n2)c(cs3)c4ccncc4
Ligand InChI: InChI=1S/C16H12N4S/c1-20-9-6-14(19-20)13-2-3-15-16(18-13)12(10-21-15)11-4-7-17-8-5-11/h2-10H,1H3
Release date: 2024-09-11
INPP5D PanDDA analysis group deposition -- Crystal Structure of the phosphatase and C2 domains of SHIP1 in complex with Z2177153697 (PDB entry 5RYJ)
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): 1.42
R work: 0.1779
R free: 0.203
Average B factor: 16.984
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: 2.09
Solvent content (%): 41.13
Ligand: 3-cyclopropyl-5-[(3R)-pyrrolidin-3-yl]-1,2,4-oxadiazole (WOD)
Ligand formula: C9 H13 N3 O
Ligand molecular weight: 179.219
Ligand SMILES: C1CC1c2nc(on2)C3CCNC3
Ligand InChI: InChI=1S/C9H13N3O/c1-2-6(1)8-11-9(13-12-8)7-3-4-10-5-7/h6-7,10H,1-5H2/t7-/m1/s1
Release date: 2020-11-11
PanDDA analysis group deposition -- Crystal structure of PTP1B in complex with compound_FMOOA000523a (PDB entry 5QFG)
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): 1.654
R work: 0.1934
R free: 0.2226
Average B factor: 34.4744
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: well solution: 0.3 M magnesium acetate, 0.1 M HEPES pH 7.5, 0.1% beta-mercaptoethanol, 13-14% PEG 8000, 2% ethanol
Matthews coefficient: 3.33
Solvent content (%): 63.01
Ligand: (1R,4R,5R,6R)-4,6-dimethoxy-2-(methylsulfonyl)-2-azabicyclo[3.3.1]nonane (JOA)
Ligand formula: C11 H21 N O4 S
Ligand molecular weight: 263.354
Ligand SMILES: COC1CCC2CC1C(CN2S(=O)(=O)C)OC
Ligand InChI: InChI=1S/C11H21NO4S/c1-15-10-5-4-8-6-9(10)11(16-2)7-12(8)17(3,13)14/h8-11H,4-7H2,1-3H3/t8-,9-,10-,11+/m1/s1
Release date: 2018-10-10
Crystal Structure of CK2alpha with a novel closed conformation of the aD loop (PDB entry 5CVG)
Macromolecule: Casein kinase II subunit alpha
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 351 residues
Sequence: GSMDIEFDDDADDDGSGSGSGSGSGPVPSRARVYTDVNTHRPSEYWDYESHVVEWGNQDDYQLVRKLGRGKYSEVFEAINITNNEKVVVKILKPVKKKKIKREIKILENLRGGPNIITLADIVKDPVSRTPALVFEHVNNTDFKQLYQTLTDYDIRFYMYEILKALDYCHSMGIMHRDVKPHNVMIDHEHRKLRLIDWGLAEFYHPGQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRKEPFFHGHDNYDQLVRIAKVLGTEDLYDYIDKYNIELDPRFNDILGRHSRKRWERFVHSENQHLVSPEALDFLDKLLRYDHQSRLTAREAMEHPYFYTVVK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.25
R work: 0.1532
R free: 0.1698
Average B factor: 18.75
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 298
Crystal growth procedure: 92mM Mes pH 6.5, 33% glycerol ethoxylate, 750mM ammonium acetate
Matthews coefficient: 1.78
Solvent content (%): 31.05
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: 2016-07-27
Crystal structure of Importin alpha 2 in complex with LSD1 NLS S111E mutant (PDB entry 7JK7)
Macromolecule: Lysine-specific histone demethylase 1A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.99.66
Sequence length: 26 residues
Sequence: TPEGRRTERRKRAKVEYREMDESLAN
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.96
R work: 0.1812
R free: 0.2063
Average B factor: 52.9818
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 295
Crystal growth procedure: 0.7 M sodium citrate, 0.01M DTT, 0.1M sodium HEPES pH 7
Matthews coefficient: 3.2
Solvent content (%): 61.51
Ligand: GLYCEROL (GOL)
Ligand formula: C3 H8 O3
Ligand molecular weight: 92.094
Ligand SMILES: C(C(CO)O)O
Ligand InChI: InChI=1S/C3H8O3/c4-1-3(6)2-5/h3-6H,1-2H2
Release date: 2020-08-05
Crystal structure of covalent inhibitor 2-chloro-N'-(N-(4-chlorophenyl)-N-methylglycyl)acetohydrazide bound to Ubiquitin C-terminal Hydrolase-L1 (PDB entry 8EDE)
Macromolecule: Ubiquitin carboxyl-terminal hydrolase isozyme L1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.19.12
Sequence length: 223 residues
Sequence: MQLKPMEINPEMLNKVLSRLGVAGQWRFVDVLGLEEESLGSVPAPACALLLLFPLTAQHENFRKKQIEELKGQEVSPKVYFMKQTIGNSCGTIGLIHAVANNQDKLGFEDGSVLKQFLSETEKMSPEDRAKCFEKNEAIQAAHDAVAQEGQCRVDDKVNFHFILFNNVDGHLYELDGRMPFPVNHGASSEDTLLKDAAKVCREFTEREQGEVRFSAVALCKAA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.799
R work: 0.1928
R free: 0.2267
Average B factor: 47.1589
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 294.15
Crystal growth procedure: 0.1M tri-Sodium citrate
2.4M Ammonium sulfate
Matthews coefficient: 2.35
Solvent content (%): 48.38
Ligand: 2-[(4-chlorophenyl)-methyl-amino]-~{N}'-ethanoyl-ethanehydrazide (WEU)
Ligand formula: C11 H14 Cl N3 O2
Ligand molecular weight: 255.701
Ligand SMILES: CC(=O)NNC(=O)CN(C)c1ccc(cc1)Cl
Ligand InChI: InChI=1S/C11H14ClN3O2/c1-8(16)13-14-11(17)7-15(2)10-5-3-9(12)4-6-10/h3-6H,7H2,1-2H3,(H,13,16)(H,14,17)
Release date: 2023-09-20
Human GIVD cytosolic phospholipase A2 in complex with Methyl gamma-Linolenyl Fluorophosphonate (PDB entry 5IXC)
Macromolecule: Cytosolic phospholipase A2 delta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.1.4
Sequence length: 814 residues
Sequence: GAMGSESLSPGGPPGHPYQGEASTCWQLTVRVLEARNLRWADLLSEADPYVILQLSTAPGMKFKTKTLTDTSHPVWNEAFRFLIQSQVKNVLELSIYDEDSVTEDDICFKVLYDISEVLPGKLLRKTFSQSPQGEEELDVEFLMEETSDRPENLITNKVIVARELSCLDVHLDSTGSTAVVADQDKLELELVLKGSYEDTQTSFLGTASAFRFHYMAALETELSGRLRSSRSNGWNGDNSAGYLTVPLRPLTIGKEVTMDVPAPNAPGVRLQLKAEGCPEELAVHLGFNLCAEEQAFLSRRKQVVAKALKQALQLDRDLQEDEVPVVGIMATGGGARAMTSLYGHLLALQKLGLLDCVTYFSGISGSTWTMAHLYGDPEWSQRDLEGPIRYAREHLAKSKLEVFSPERLASYRRELELRAEQGHPTTFVDLWALVLESMLHGQVMDQKLSGQRAALERGQNPLPLYLSLNVKENNLETLDFKEWVEFSPYEVGFLKYGAFVPPELFGSEFFMGRLMRRIPEPRICFLEAIWSNIFSLNLLDAWYDLTSSGESWKQHIKDKTRSLEKEPLTTSGTSSRLEASWLQPGTALAQAFKGFLTGRPLHQRSPNFLQGLQLHQDYCSHKDFSTWADYQLDSMPSQLTPKEPRLCLVDAAYFINTSSPSMFRPGRRLDLILSFDYSLSAPFEALQQTELYCRARGLPFPRVEPSPQDQHQPRECHLFSDPACPEAPILLHFPLVNASFKDHSAPGVQRSPAELQGGQVDLTGATCPYTLSNMTYKEEDFERLLRLSDYNVQTSQGAILQALRTALKHRTLE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.65
R work: 0.23659
R free: 0.25068
Average B factor: 65.842
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 100 mM MES (pH 6.0-6.2), 50 mM sodium acetate, and 10-14% (v/v) PEG20K
Matthews coefficient: 2.4
Solvent content (%): 48.7
Ligand: BARIUM ION (BA)
Ligand formula: Ba
Ligand molecular weight: 137.327
Ligand SMILES: [Ba+2]
Ligand InChI: InChI=1S/Ba/q+2
Release date: 2016-06-08
Structure of human PARP1 catalytic domain bound to a benzoimidazole inhibitor (PDB entry 5WS0)
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): 2.6
R work: 0.21225
R free: 0.27713
Average B factor: 25.776
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: 2.32
Solvent content (%): 47.04
Ligand: 2-piperazin-1-ylcarbonyl-1H-benzimidazole-4-carboxamide (7U6)
Ligand formula: C13 H15 N5 O2
Ligand molecular weight: 273.291
Ligand SMILES: c1cc(c2c(c1)[nH]c(n2)C(=O)N3CCNCC3)C(=O)N
Ligand InChI: InChI=1S/C13H15N5O2/c14-11(19)8-2-1-3-9-10(8)17-12(16-9)13(20)18-6-4-15-5-7-18/h1-3,15H,4-7H2,(H2,14,19)(H,16,17)
Release date: 2017-01-25
Notum Inhibitor ARUK3004470 (PDB entry 8BTE)
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): 1.62
R work: 0.2042
R free: 0.2334
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 (%): 36.19
Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose (NAG)
Ligand formula: C8 H15 N O6
Ligand molecular weight: 221.208
Ligand SMILES: CC(=O)NC1C(C(C(OC1O)CO)O)O
Ligand InChI: InChI=1S/C8H15NO6/c1-3(11)9-5-7(13)6(12)4(2-10)15-8(5)14/h4-8,10,12-14H,2H2,1H3,(H,9,11)/t4-,5-,6-,7-,8-/m1/s1
Release date: 2022-12-14
Pim1 in complex with 6-bromobenzo[d]oxazol-2-amine and Pimtide (PDB entry 8R1P)
Macromolecule: Serine/threonine-protein kinase pim-1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 313 residues
Sequence: SMLLSKINSLAHLRAAPCNDLHATKLAPGKEKEPLESQYQVGPLLGSGGFGSVYSGIRVSDNLPVAIKHVEKDRISDWGELPNGTRVPMEVVLLKKVSSGFSGVIRLLDWFERPDSFVLILERPEPVQDLFDFITERGALQEELARSFFWQVLEAVRHCHNCGVLHRDIKDENILIDLNRGELKLIDFGSGALLKDTVYTDFDGTRVYSPPEWIRYHRYHGRSAAVWSLGILLYDMVCGDIPFEHDEEIIGGQVFFRQRVSSECQHLIRWCLALRPSDRPTFEEIQNHPWMQDVLLPQETAEIHLHSLSPGPS
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.45
R work: 0.1764
R free: 0.2058
Average B factor: 48.38
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 291.15
Crystal growth procedure: 100 mM bis-tris-propane (pH 7.0), 10% ethylene glycol, 0.3% DMSO, 20% PEG3350, 200 mM Mg(OAc)2
Matthews coefficient: 3.1
Solvent content (%): 60.5
Ligand: 4-(4-aminostyryl)benzoic acid (XIP)
Ligand formula: C15 H13 N O2
Ligand molecular weight: 239.269
Ligand SMILES: c1cc(ccc1C=Cc2ccc(cc2)N)C(=O)O
Ligand InChI: InChI=1S/C15H13NO2/c16-14-9-5-12(6-10-14)2-1-11-3-7-13(8-4-11)15(17)18/h1-10H,16H2,(H,17,18)
Release date: 2024-03-20