satarupa22/MacromolecularLigandDB huggingface dataset:
Structure of the FKBP51FK1 domain in complex with the macrocyclic SAFit analogue 35-(E) (PDB entry 7B9Z)
Macromolecule: Peptidyl-prolyl cis-trans isomerase FKBP5
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 5.2.1.8
Sequence length: 130 residues
Sequence: HMGAPATVTEQGEDITSKKDRGVLKIVKRVGNGEETPMIGDKVYVHYKGKLSNGKKFDSSHDRNEPFVFSLGKGQVIKAWDIGVATMKKGEIAHLLIKPEYAYGSAGSLPKIPSNATLFFEIELLDFKGE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.44
R work: 0.1397
R free: 0.1663
Average B factor: 30.723
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 18% PEG3350, 0.1 M HEPES pH 7.5, 0.2 M ammoniumthiocyanat
Matthews coefficient: 2.46
Solvent content (%): 50.06
Ligand: 2-cyclohexyl-12-[2-(3,4-dimethoxyphenyl)ethyl]-25,26-dimethoxy-11,18,23-trioxa-4-azatetracyclo[22.3.1.113,17.04,9]nonacosa-1(27),13(29),14,16,20,24(28),25-heptaene-3,10-dione (T58)
Ligand formula: C43 H53 N O9
Ligand molecular weight: 727.882
Ligand SMILES: COc1ccc(cc1OC)CCC2c3cccc(c3)OCC=CCOc4cc(cc(c4OC)OC)C(C(=O)N5CCCCC5C(=O)O2)C6CCCCC6
Ligand InChI: InChI=1S/C43H53NO9/c1-47-36-21-19-29(25-37(36)48-2)18-20-35-31-15-12-16-33(26-31)51-23-10-11-24-52-39-28-32(27-38(49-3)41(39)50-4)40(30-13-6-5-7-14-30)42(45)44-22-9-8-17-34(44)43(46)53-35/h10-12,15-16,19,21,25-28,30,34-35,40H,5-9,13-14,17-18,20,22-24H2,1-4H3/b11-10+/t34-,35+,40-/m0/s1
Release date: 2021-03-17
The crystal structure of CK2alpha in complex with compound 18 (PDB entry 6EII)
Macromolecule: Casein kinase II subunit alpha
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 352 residues
Sequence: GSMDIEFDDDADDDGSGSGSGSGSSGPVPSRARVYTDVNTHRPSEYWDYESHVVEWGNQDDYQLVRKLGRGKYSEVFEAINITNNEKVVVKILKPVKKKKIKREIKILENLRGGPNIITLADIVKDPVSRTPALVFEHVNNTDFKQLYQTLTDYDIRFYMYEILKALDYCHSMGIMHRDVKPHNVMIDHEHRKLRLIDWGLAEFYHPGQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRKEPFFHGHDNYDQLVRIAKVLGTEDLYDYIDKYNIELDPRFNDILGRHSRKRWERFVHSENQHLVSPEALDFLDKLLRYDHQSRLTAREAMEHPYFYTVVK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.935
R work: 0.2077
R free: 0.2338
Average B factor: 45.19
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: 2.19
Solvent content (%): 43.89
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
Crystal structure of human DYRK1A in complex with compound 32 (PDB entry 6A1G)
Macromolecule: Dual specificity tyrosine-phosphorylation-regulated kinase 1A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.12.1
Sequence length: 360 residues
Sequence: GPMSSHKKERKVYNDGYDDDNYDYIVKNGEKWMDRYEIDSLIGKGSFGQVVKAYDRVEQEWVAIKIIKNKKAFLNQAQIEVRLLELMNKHDTEMKYYIVHLKRHFMFRNHLCLVFEMLSYNLYDLLRNTNFRGVSLNLTRKFAQQMCTALLFLATPELSIIHCDLKPENILLCNPKRSAIKIVDFGSSCQLGQRIYQYIQSRFYRSPEVLLGMPYDLAIDMWSLGCILVEMHTGEPLFSGANEVDQMNKIVEVLGIPPAHILDQAPKARKFFEKLPDGTWNLKKTKDGKREYKPPGTRKLHNILGVETGGPGGRRAGESGHTVADYLKFKDLILRMLDYDPKTRIQPYYALQHSFFKKTA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.15
R work: 0.22463
R free: 0.27232
Average B factor: 59.901
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 20% w/v Polyethylene glycol monomethyl ether 2000
Matthews coefficient: 2.37
Solvent content (%): 48.08
Ligand: 5,5-dimethyl-8-[1-(piperidin-4-yl)ethenyl]-5,6-dihydrobenzo[h]quinazolin-4-amine (9OL)
Ligand formula: C21 H26 N4
Ligand molecular weight: 334.458
Ligand SMILES: CC1(Cc2cc(ccc2-c3c1c(ncn3)N)C(=C)C4CCNCC4)C
Ligand InChI: InChI=1S/C21H26N4/c1-13(14-6-8-23-9-7-14)15-4-5-17-16(10-15)11-21(2,3)18-19(17)24-12-25-20(18)22/h4-5,10,12,14,23H,1,6-9,11H2,2-3H3,(H2,22,24,25)
Release date: 2018-10-03
Structure of human DNA polymerase beta complexed with N7BG in the template base paired with incoming non-hydrolyzable CTP (PDB entry 4YMN)
Macromolecule: DNA polymerase beta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 335 residues
Sequence: MSKRKAPQETLNGGITDMLTELANFEKNVSQAIHKYNAYRKAASVIAKYPHKIKSGAEAKKLPGVGTKIAEKIDEFLATGKLRKLEKIRQDDTSSSINFLTRVSGIGPSAARKFVDEGIKTLEDLRKNEDKLNHHQRIGLKYFGDFEKRIPREEMLQMQDIVLNEVKKVDSEYIATVCGSFRRGAESSGDMDVLLTHPSFTSESTKQPKLLHQVVEQLQKVHFITDTLSKGETKFMGVCQLPSKNDEKEYPHRRIDIRLIPKDQYYCGVLYFTGSDIFNKNMRAHALEKGFTINEYTIRPLGVTGVAGEPLPVDSEKDIFDYIQWKYREPKDRSE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.591
R work: 0.1998
R free: 0.2692
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 297
Crystal growth procedure: 14% to 23% PEG3400, and 350 mM sodium acetate in 50 mM imidazole (pH 7.5)
Matthews coefficient: 2.37
Solvent content (%): 48.2
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: 2016-03-09
Crystal structure of the catalytic domains of Mettl3/Mettl14 complex with SAM (PDB entry 5K7U)
Macromolecule: N6-adenosine-methyltransferase 70 kDa subunit
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1.62
Sequence length: 225 residues
Sequence: MQSVGGDSSADRLFPPQWICCDIRYLDVSILGKFAVVMADPPWDIHMELPYGTLTDDEMRRLNIPVLQDDGFLFLWVTGRAMELGRECLNLWGYERVDEIIWVKTNQLQRIIRTGRTGHWLNHGKEHCLVGVKGNPQGFNQGLDCDVIVAEVRSTSHKPDEIYGMIERLSPGTRKIELFGRPHNVQPNWITLGNQLDGIHLLDPDVVARFKQRYPDGIISKPKNL
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.7
R work: 0.1634
R free: 0.1873
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8
Crystallization temperature (K): 291
Crystal growth procedure: 0.1M Tris pH 8.0, 20% PEG3350
Matthews coefficient: 2.31
Solvent content (%): 46.84
Ligand: S-ADENOSYLMETHIONINE (SAM)
Ligand formula: C15 H22 N6 O5 S
Ligand molecular weight: 398.437
Ligand SMILES: C[S+](CCC(C(=O)[O-])N)CC1C(C(C(O1)n2cnc3c2ncnc3N)O)O
Ligand InChI: InChI=1S/C15H22N6O5S/c1-27(3-2-7(16)15(24)25)4-8-10(22)11(23)14(26-8)21-6-20-9-12(17)18-5-19-13(9)21/h5-8,10-11,14,22-23H,2-4,16H2,1H3,(H2-,17,18,19,24,25)/t7-,8+,10+,11+,14+,27-/m0/s1
Release date: 2016-07-06
Binary complex of human DNA Polymerase Mu with MndGTP (PDB entry 5ZLC)
Macromolecule: DNA-directed DNA/RNA polymerase mu
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 356 residues
Sequence: GSAAAPLSPAWMPAYACQRPTPLTHHNTGLSEALEILAEAAGFEGSEGRLLTFCRAASVLKALPSPVTTLSQLQGLPHFGEHSSRVVQELLEHGVCEEVERVRRSERYQTMKLFTQIFGVGVKTADRWYREGLRTLDDLREQPQKLTQQQKAGLQHHQDLSTPVLRSDVDALQQVVEEAVGQALPGATVTLTGGFRRGKLQGHDVDFLITHPKEGQEAGLLPRVMCRLQDQGLILYHQHQHSCCESPTRLAQQSHMDAFERSFCIFRLPQPGSWKAVRVDLVVAPVSQFPFALLGWTGSKLFQRELRRFSRKEKGLWLNSHGLFDPEQKTFFQAASEEDIFRHLGLEYLPPEQRNA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2
R work: 0.20153
R free: 0.2406
Average B factor: 29.824
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 7.5
Crystallization temperature (K): 298
Crystal growth procedure: 0.1 M HEPES pH 7.5, 1.5 M Li2SO4
Matthews coefficient: 2.45
Solvent content (%): 49.83
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: 2019-05-29
Structure of CaMKK2 in complex with CKI-009 (PDB entry 5YV9)
Macromolecule: Calcium/calmodulin-dependent protein kinase kinase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.17
Sequence length: 298 residues
Sequence: GSSGSSGDCVQLNQYTLKDEIGKGSYGVVKLAYNENDNTYYAMKVLSKKKLIRQAGFPRRPPPRGTRPAPGGCIQPRGPIEQVYQEIAILKKLDHPNVVKLVEVLDDPNEDHLYMVFELVNQGPVMEVPTLKPLSEDQARFYFQDLIKGIEYLHYQKIIHRDIKPSNLLVGEDGHIKIADFGVSNEFKGSDALLSNTVGTPAFMAPESLSETRKIFSGKALDVWAMGVTLYCFVFGQCPFMDERIMCLHSKIKSQALEFPDQPDIAEDLKDLITRMLDKNPESRIVVPEIKLHPWVTR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.53
R work: 0.1675
R free: 0.2218
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M Na cocodylate pH 6.5, 0.2M Na acetate, 20% PEG 8000, 0.03M Glycyl-glycyl-glycine
Matthews coefficient: 3.25
Solvent content (%): 62.11
Ligand: 5-chloro-2-methoxy-4[(1Z)-3-(4-methoxyphenyl)-3-oxoprop-1-en-1-yl]aminobenzoic acid (91O)
Ligand formula: C18 H16 Cl N O5
Ligand molecular weight: 361.776
Ligand SMILES: COc1ccc(cc1)C(=O)C=CNc2cc(c(cc2Cl)C(=O)O)OC
Ligand InChI: InChI=1S/C18H16ClNO5/c1-24-12-5-3-11(4-6-12)16(21)7-8-20-15-10-17(25-2)13(18(22)23)9-14(15)19/h3-10,20H,1-2H3,(H,22,23)/b8-7-
Release date: 2018-12-05
Crystal structure of the bromodomain of human CREBBP in complex with UL04 (PDB entry 4TQN)
Macromolecule: CREB-binding protein
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1.48
Sequence length: 119 residues
Sequence: SMRKKIFKPEELRQALMPTLEALYRQDPESLPFRQPVDPQLLGIPDYFDIVKNPMDLSTIKRKLDTGQYQEPWQYVDDVWLMFNNAWLYNRKTSRVYKFCSKLAEVFEQEIDPVMQSLG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.7
R work: 0.1813
R free: 0.199
Average B factor: 23.261
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.1M  MES pH 6.5, 0.1M MgCl2, 20% PEG 6000, 10% EtGly
Matthews coefficient: 1.94
Solvent content (%): 36.63
Ligand: 3-[(5-acetyl-2-ethoxyphenyl)carbamoyl]benzoic acid (UL4)
Ligand formula: C18 H17 N O5
Ligand molecular weight: 327.331
Ligand SMILES: CCOc1ccc(cc1NC(=O)c2cccc(c2)C(=O)O)C(=O)C
Ligand InChI: InChI=1S/C18H17NO5/c1-3-24-16-8-7-12(11(2)20)10-15(16)19-17(21)13-5-4-6-14(9-13)18(22)23/h4-10H,3H2,1-2H3,(H,19,21)(H,22,23)
Release date: 2015-06-24
Thrombin Mutant A190S in complex with (S)-1-(D-phenylalanyl)-N-(4-carbamimidoylbenzyl)pyrrolidine-2-carboxamide (PDB entry 5MM6)
Macromolecule: Thrombin light chain
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.5
Sequence length: 36 residues
Sequence: TFGSGEADCGLRPLFEKKSLEDKTERELLESYIDGR
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.29
R work: 0.1234
R free: 0.1421
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 20 mM sodium dihydrogen phosphate ph 7.5, 350 mM NaCl, 27% PEG 8000
Matthews coefficient: 2.7
Solvent content (%): 53.7
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: 2017-12-20
BRAF in Complex with RAF709 (PDB entry 5VAM)
Macromolecule: Serine/threonine-protein kinase B-raf
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 281 residues
Sequence: GSDSSDDWEIPDGQITVGQRIGSGSFGTVYKGKWHGDVAVKMLNVTAPTPQQLQAFKNEVGVLRKTRHVNILLFMGYSTKPQLAIVTQWCEGSSLYHHLHIIETKFEMIKLIDIARQTAQGMDYLHAKSIIHRDLKSNNIFLHEDLTVKIGDFGLATVKSRWSGSHQFEQLSGSILWMAPEVIRMQDKNPYSFQSDVYAFGIVLYELMTGQLPYSNINNRDQIIFMVGRGYLSPDLSKVRSNCPKAMKRLMAECLKKKRDERPLFPQILASIELLARSLPK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.1
R work: 0.192
R free: 0.223
Average B factor: 35.45
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8.4
Crystallization temperature (K): 291
Crystal growth procedure: 100 mM Tris ph 8.4, 12% PEG8000, and 50mM NaCl
Matthews coefficient: 3.19
Solvent content (%): 61.4
Ligand: N-{2-methyl-5'-(morpholin-4-yl)-6'-[(oxan-4-yl)oxy][3,3'-bipyridin]-5-yl}-3-(trifluoromethyl)benzamide (92J)
Ligand formula: C28 H29 F3 N4 O4
Ligand molecular weight: 542.549
Ligand SMILES: Cc1c(cc(cn1)NC(=O)c2cccc(c2)C(F)(F)F)c3cc(c(nc3)OC4CCOCC4)N5CCOCC5
Ligand InChI: InChI=1S/C28H29F3N4O4/c1-18-24(15-22(17-32-18)34-26(36)19-3-2-4-21(13-19)28(29,30)31)20-14-25(35-7-11-38-12-8-35)27(33-16-20)39-23-5-9-37-10-6-23/h2-4,13-17,23H,5-12H2,1H3,(H,34,36)
Release date: 2017-06-28
[1,2,4]Triazolo[1,5-a]pyrimidine Phosphodiesterase 2 Inhibitors (PDB entry 6ZND)
Macromolecule: cGMP-dependent 3',5'-cyclic phosphodiesterase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.4.17
Sequence length: 353 residues
Sequence: MGSDDEYTKLLHDGIQPVAAIDSNFASFTYTPRSLPEDDTSMAILSMLQDMNFINNYKIDCPTLARFCLMVKKGYRDPPYHNWMHAFSVSHFCYLLYKNLELTNYLEDIEIFALFISCMCHDLDHRGTNNSFQVASKSVLAALYSSEGSVMERHHFAQAIAILNTHGCNIFDHFSRKDYQRMLDLMRDIILATDLAHHLRIFKDLQKMAEVGYDRNNKQHHRLLLCLLMTSCDLSDQTKGWKTTRKIAELIYKEFFSQGDLEKAMGNRPMEMMDREKAYIPELQISFMEHIAMPIYKLLQDLFPKAAELYERVASNREHWTKVSHKFTIRGLPSNNSLDFLDEEYERHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.35
R work: 0.2146
R free: 0.2906
Average B factor: 25.992
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8
Crystallization temperature (K): 293
Crystal growth procedure: 0.2 M MgCl2, 0.1 M Tris-HCl pH 8.0 and 20 % PEG 3350
Matthews coefficient: 1.98
Solvent content (%): 37.76
Ligand: [(3~{S})-3-([1,2,4]triazolo[1,5-a]pyrimidin-7-yl)piperidin-1-yl]-(3,4,5-trimethoxyphenyl)methanone (QMZ)
Ligand formula: C20 H23 N5 O4
Ligand molecular weight: 397.428
Ligand SMILES: COc1cc(cc(c1OC)OC)C(=O)N2CCCC(C2)c3ccnc4n3ncn4
Ligand InChI: InChI=1S/C20H23N5O4/c1-27-16-9-14(10-17(28-2)18(16)29-3)19(26)24-8-4-5-13(11-24)15-6-7-21-20-22-12-23-25(15)20/h6-7,9-10,12-13H,4-5,8,11H2,1-3H3/t13-/m0/s1
Release date: 2020-07-22
Human SIRT2 in complex with myristoyl thiourea inhibitor, No.13 (PDB entry 7BOS)
Macromolecule: NAD-dependent protein deacetylase sirtuin-2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1.286
Sequence length: 293 residues
Sequence: GSQKERLLDELTLEGVARYMQSERCRRVICLVGAGISTSAGIPDFRSPSTGLYDNLEKYHLPYPEAIFEISYFKKHPEPFFALAKELYPGQFKPTICHYFMRLLKDKGLLLRCYTQNIDTLERIAGLEQEDLVEAHGTFYTSHCVSASCRHEYPLSWMKEKIFSEVTPKCEDCQSLVKPDIVFFGESLPARFFSCMQSDFLKVDLLLVMGTSLQVQPFASLISKAPLSTPRLLINKEKAGGGGMDFDSKKAYRDVAWLGECDQGCLALAELLGWKKELEDLVRREHASIDAQS
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.7
R work: 0.2226
R free: 0.2626
Average B factor: 32.799
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M HEPES pH 7.0, 30% v/v Jeffamine ED-2001
Matthews coefficient: 2.07
Solvent content (%): 40.7
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: 2021-03-24
Structure of DYRK1A in complex with compound 25 (PDB entry 7AJ8)
Macromolecule: Dual specificity tyrosine-phosphorylation-regulated kinase 1A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.12.1
Sequence length: 359 residues
Sequence: MGSSHHHHHHSSGLVPRGSHMIVKNGEKWMDRYEIDSLIGKGSFGQVVKAYDRVEQEWVAIKIIKNKKAFLNQAQIEVRLLELMNKHDTEMKYYIVHLKRHFMFRNHLCLVFEMLSYNLYDLLRNTNFRGVSLNLTRKFAQQMCTALLFLATPELSIIHCDLKPENILLCNPKRSAIKIVDFGSSCQLGQRIYQYIQSRFYRSPEVLLGMPYDLAIDMWSLGCILVEMHTGEPLFSGANEVDQMNKIVEVLGIPPAHILDQAPKARKFFEKLPDGTWNLKKTKDGKREYKPPGTRKLHNILGVETGGPGGRRAGESGHTVADYLKFKDLILRMLDYDPKTRIQPYYALQHSFFKKTADE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.0
R work: 0.1727
R free: 0.2104
Average B factor: 36.722
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 12% PEG3350, 0.1M MES buffer pH6.5, 0.2M MgCl2
Matthews coefficient: 2.48
Solvent content (%): 50.31
Ligand: CHLORIDE ION (CL)
Ligand formula: Cl
Ligand molecular weight: 35.453
Ligand SMILES: [Cl-]
Ligand InChI: InChI=1S/ClH/h1H/p-1
Release date: 2021-05-26
human PDE10A in complex with 3-(2-Chloro-5-phenyl-3H-imidazol-4-yl)-1-(3-trifluoromethoxy-phenyl)-1H-pyridazin-4-one at 2.30A (PDB entry 5EDG)
Macromolecule: cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.4.17
Sequence length: 315 residues
Sequence: AQGLMQFTLPVRLCREIELFHFDIGPFENMWPGIFVYMVHRSCGTSCFELEKLCRFIMSVKKNYRRVPYHNWKHAVTVAHCMYAILQNNHTLFTDLERKGLLIACLCHDLDHRGFSNSYLQKFDHPLAALYSTSTMEQHHFSQTVSILQLEGHNIFSTLSSSEYEQVLEIIRKAIIATDLALYFGNRKQLEEMYQTGSLNLNNQSHRDRVIGLMMTACDLCSVTKLWPVTKLTANDIYAEFWAEGDEMKKLGIQPIPMMDRDKKDEVPQGQLGFYNAVAIPCYTTLTQILPPTEPLLKACRDNLSQWEKVIRGEE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.3
R work: 0.2124
R free: 0.2614
Average B factor: 40.211
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 295
Crystal growth procedure: 0.1 M HEPES/NaOH pH 7.5, 30% PEG550MME, 50mM MgCl2
Matthews coefficient: 2.84
Solvent content (%): 56.76
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: 2016-03-09
Crystal structure of UTX complexed with 5-hydroxy-4-keto-1-methyl-picolinate (PDB entry 6FUL)
Macromolecule: Lysine-specific demethylase 6A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11
Sequence length: 531 residues
Sequence: GPGYQDPNSQIIPSMSVSIYPSSAEVLKACRNLGKNGLSNSSILLDKCPPPRPPSSPYPPLPKDKLNPPTPSIYLENKRDAFFPPLHQFCTNPNNPVTVIRGLAGALKLDLGLFSTKTLVEANNEHMVEVRTQLLQPADENWDPTGTKKIWHCESNRSHTTIAKYAQYQASSFQESLREENEKRSHHKDHSDSESTSSDNSGRRRKGPFKTIKFGTNIDLSDDKKWKLQLHELTKLPAFVRVVSAGNLLSHVGHTILGMNTVQLYMKVPGSRTPGHQENNNFCSVNINIGPGDCEWFVVPEGYWGVLNDFCEKNNLNFLMGSWWPNLEDLYEANVPVYRFIQRPGDLVWINAGTVHWVQAIGWCNNIAWNVGPLTACQYKLAVERYEWNKLQSVKSIVPMVHLSWNMARNIKVSDPKLFEMIKYCLLRTLKQCQTLREALIAAGKEIIWHGRTKEEPAHYCSICEVEVFDLLFVTNESNSRKTYIVHCQDCARKTSGNLENFVVLEQYKMEDLMQVYDQFTLAPPLPSASS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.649
R work: 0.1764
R free: 0.2079
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.1 M Tris-HCl (pH 8.5), Li2 SO4 (0.15-0.25 M), PEG 3350 (20-25% w/v)
Matthews coefficient: 2.53
Solvent content (%): 51.45
Ligand: 1-methyl-5-oxidanyl-4-oxidanylidene-pyridine-2-carboxylic acid (E7Z)
Ligand formula: C7 H7 N O4
Ligand molecular weight: 169.135
Ligand SMILES: CN1C=C(C(=O)C=C1C(=O)O)O
Ligand InChI: InChI=1S/C7H7NO4/c1-8-3-6(10)5(9)2-4(8)7(11)12/h2-3,10H,1H3,(H,11,12)
Release date: 2018-10-10
Crystal structure of human MMP-7 in complex with inhibitor (PDB entry 7WXX)
Macromolecule: Matrilysin
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.24.23
Sequence length: 175 residues
Sequence: MGYSLFPNSPKWTSKVVTYRIVSYTRDLPHITVDRLVSKALNMWGKEIPLHFRKVVWGTADIMIGFARGAHGDSYPFDGPGNTLAHAFAPGTGLGGDAHFDEDERWTDGSSLGINFLYAATHQLGHSLGMGHSSDPNAVMYPTYGNGDPQNFKLSQDDIKGIQKLYGKRSNSRKK
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.5
R work: 0.17018
R free: 0.20343
Average B factor: 25.12
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 6
Crystallization temperature (K): 293
Crystal growth procedure: 20% w/v Polyethylene glycol 6000, 100mM MES pH6.0, 200mM Lithium chloride
Matthews coefficient: 2.29
Solvent content (%): 46.35
Ligand: CALCIUM ION (CA)
Ligand formula: Ca
Ligand molecular weight: 40.078
Ligand SMILES: [Ca+2]
Ligand InChI: InChI=1S/Ca/q+2
Release date: 2022-10-05
Human PrimPol misinserting dATP opposite the 8-oxoguanine lesion (3'-end base of the primer strand is 2',3'-dideoxy-terminated). (PDB entry 7JKL)
Macromolecule: DNA-directed primase/polymerase protein
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7
Sequence length: 354 residues
Sequence: MNRKWEAKLKQIEERASHYERKPLSSVYRPRLSKPEEPPSIWRLFHRQAQAFNFVKSCKEDVHVFALECKVGDGQRIYLVTTYAEFWFYYKSRKNLLHCYEVIPENAVCKLYFDLEFNKPANPGADGKKMVALLIEYVCKALQELYGVNCSAEDVLNLDSSTDEKFSRHLIFQLHDVAFKDNIHVGNFLRKILQPALDLLGSEDDDSAPETTGHGFPHFSEAPARQGFSFNKMFTEKATEESWTSNSKKLERLGSAEQSSPDLSFLVVKNNMGEKHLFVDLGVYTRNRNFRLYKSSKIGKRVALEVTEDNKFFPIQSKDVSDEYQYFLSSLVSNVRFSDTLRILTCEPSQNKQK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.384
R work: 0.2197
R free: 0.277
Average B factor: 82.6032
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: 225- 250 mM CaCl2, 16 -19% PEG 3350
Matthews coefficient: 2.33
Solvent content (%): 47.17
Ligand: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE (DTP)
Ligand formula: C10 H16 N5 O12 P3
Ligand molecular weight: 491.182
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3CC(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)N
Ligand InChI: InChI=1S/C10H16N5O12P3/c11-9-8-10(13-3-12-9)15(4-14-8)7-1-5(16)6(25-7)2-24-29(20,21)27-30(22,23)26-28(17,18)19/h3-7,16H,1-2H2,(H,20,21)(H,22,23)(H2,11,12,13)(H2,17,18,19)/t5-,6+,7+/m0/s1
Release date: 2021-06-30
Gcase in complex with small molecule inhibitor 1 (PDB entry 9FAL)
Macromolecule: Lysosomal acid glucosylceramidase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.2.1.45
Sequence length: 546 residues
Sequence: MEFSSPSREECPKPLSRVSIMAGSLTGLLLLQAVSWASGARPCIPKSFGYSSVVCVCNATYCDSFDPPTFPALGTFSRYESTRSGRRMELSMGPIQANHTGTGLLLTLQPEQKFQKVKGFGGAMTDAAALNILALSPPAQNLLLKSYFSEEGIGYNIIRVPMASCDFSIRTYTYADTPDDFQLHNFSLPEEDTKLKIPLIHRALQLAQRPVSLLASPWTSPTWLKTNGAVNGKGSLKGQPGDIYHQTWARYFVKFLDAYAEHKLQFWAVTAENEPSAGLLSGYPFQCLGFTPEHQRDFIARDLGPTLANSTHHNVRLLMLDDQRLLLPHWAKVVLTDPEAAKYVHGIAVHWYLDFLAPAKATLGETHRLFPNTMLFASEACVGSKFWEQSVRLGSWDRGMQYSHSIITNLLYHVVGWTDWNLALNPEGGPNWVRNFVDSPIIVDITKDTFYKQPMFYHLGHFSKFIPEGSQRVGLVASQKNDLDAVALMHPDGSAVVVVLNRSSKDVPLTIKDPAVGFLETISPGYSIHTYLWRRQHHHHHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.39
R work: 0.1541
R free: 0.18266
Average B factor: 22.405
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M KSCN
25% PEG 3350
Matthews coefficient: 2.15
Solvent content (%): 42.72
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: 2024-07-03
Crystal structure of an inhibitor-bound Syk (PDB entry 4XG4)
Macromolecule: Tyrosine-protein kinase SYK
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 290 residues
Sequence: EEIRPKEVYLDRKLLTLEDKELGSGNFGTVKKGYYQMKKVVKTVAVKILKNEANDPALKDELLAEANVMQQLDNPYIVRMIGICEAESWMLVMEMAELGPLNKYLQQNRHVKDKNIIELVHQVSMGMKYLEESNFVHRDLAARNVLLVTQHYAKISDFGLSKALRADENYYKAQTHGKWPVKWYAPECINYYKFSSKSDVWSFGVLMWEAFSYGQKPYRGMKGSEVTAMLEKGERMGCPAGCPREMYDLMNLCWTYDVENRPGFAAVELRLRNYYYDVVNLEHHHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.3
R work: 0.19352
R free: 0.22843
Average B factor: 45.297
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 278
Crystal growth procedure: 10~20%(v/v) PEG3350, 100 mM Tris-HCl
Matthews coefficient: 2.08
Solvent content (%): 40.91
Ligand: (3R)-1-{[1-(5-fluoro-2-{[4-(2-hydroxyethoxy)-3,5-dimethylphenyl]amino}pyrimidin-4-yl)-4-methyl-1H-pyrrol-3-yl]methyl}pyrrolidin-3-ol (X4G)
Ligand formula: C24 H30 F N5 O3
Ligand molecular weight: 455.525
Ligand SMILES: Cc1cc(cc(c1OCCO)C)Nc2ncc(c(n2)n3cc(c(c3)CN4CCC(C4)O)C)F
Ligand InChI: InChI=1S/C24H30FN5O3/c1-15-8-19(9-16(2)22(15)33-7-6-31)27-24-26-10-21(25)23(28-24)30-11-17(3)18(13-30)12-29-5-4-20(32)14-29/h8-11,13,20,31-32H,4-7,12,14H2,1-3H3,(H,26,27,28)/t20-/m1/s1
Release date: 2015-12-30