satarupa22/MacromolecularLigandDB huggingface dataset:
Factor XIa in complex with the inhibitor (2E)-N-[(1S)-1-[5-chloro-4-(4-hydroxy-2-oxo-1,2-dihydroquinolin-6-yl)-1H-imidazol-2-yl]-3-(4-methylpiperazin-1-yl)-3-oxopropyl]-3-[5-chloro-2-(1H-tetrazol-1-yl)phenyl]prop-2-enamide (PDB entry 4Y8Z)
Macromolecule: Coagulation factor XIa
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.27
Sequence length: 244 residues
Sequence: IVGGTASVRGEWPWQVTLHTTSPTQRHLCGGSIIGNQWILTAAHCFYGVESPKILRVYSGILNQSEIKEDTSFFGVQEIIIHDQYKMAESGYDIALLKLETTVGYGDSQRPICLPSKGDRNVIYTDCWVTGWGYRKLRDKIQNTLQKAKIPLVTNEECQKRYRGHKITHKMICAGYREGGKDACKGDSGGPLSCKHNEVWHLVGITSWGEGCAQRERPGVYTNVVEYVDWILEKTQAVHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.2
R work: 0.2391
R free: 0.2608
Average B factor: 40.85
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 4.6
Crystallization temperature (K): 277
Crystal growth procedure: 100 mM sodium acetate, pH 4.6, 26% w/v MEPEG2000, 200 mM ammonium sulfate (crystals were grown at pH4.6 and transferred to pH 7 prior to soaking with compound)
Matthews coefficient: 3.59
Solvent content (%): 65.73
Ligand: (2E)-N-[(1S)-1-[5-chloro-4-(4-hydroxy-2-oxo-1,2-dihydroquinolin-6-yl)-1H-imidazol-2-yl]-3-(4-methylpiperazin-1-yl)-3-oxopropyl]-3-[5-chloro-2-(1H-tetrazol-1-yl)phenyl]prop-2-enamide (4CE)
Ligand formula: C30 H28 Cl2 N10 O4
Ligand molecular weight: 663.514
Ligand SMILES: CN1CCN(CC1)C(=O)CC(c2[nH]c(c(n2)c3ccc4c(c3)C(=CC(=O)N4)O)Cl)NC(=O)C=Cc5cc(ccc5n6cnnn6)Cl
Ligand InChI: InChI=1S/C30H28Cl2N10O4/c1-40-8-10-41(11-9-40)27(46)14-22(35-25(44)7-3-17-12-19(31)4-6-23(17)42-16-33-38-39-42)30-36-28(29(32)37-30)18-2-5-21-20(13-18)24(43)15-26(45)34-21/h2-7,12-13,15-16,22H,8-11,14H2,1H3,(H,35,44)(H,36,37)(H2,34,43,45)/b7-3+/t22-/m0/s1
Release date: 2015-05-27
Crystal structure of a monomeric human FGF9 in complex with the ectodomain of human FGFR1c (PDB entry 5W59)
Macromolecule: Fibroblast growth factor 9
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 175 residues
Sequence: MDHLGQSEAGGLPRGPAVTDLDHLKGILRRRQLYCRTGFHLEIFPNGTIQGTRKDHSRFGILEFISIAVGLVSIRGVDSGLYLGMNEKGELYGSEKLTQECVFREQFEENWYNTYSSNLYKHVDTGRRYYVALNKDGTPREGTRTKRHQKFTHFLPRPVDPAKVPELYKDAASQS
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.498
R work: 0.1709
R free: 0.2211
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8
Crystallization temperature (K): 291
Crystal growth procedure: 100 mM Tris, pH 8.0, 8% w/v PEG20000, 0.3 M sodium chloride, 40 mM L-proline
Matthews coefficient: 2.76
Solvent content (%): 55.37
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: 2017-08-16
Crystal structure of the human bromodomain of CREBBP bound to the inhibitor XDM-CBP (PDB entry 5NU3)
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): 1.75
R work: 0.168
R free: 0.1998
Average B factor: 19.4934
Crystallization method: EVAPORATION
Crystallization pH: 6.5
Crystallization temperature (K): 277
Crystal growth procedure: LiSO4, PEG 3350, ethylene glycol
Matthews coefficient: 2.5
Solvent content (%): 50.77
Ligand: ~{N}-[[2,8-bis(oxidanyl)naphthalen-1-yl]methyl]-4-ethanoyl-3-ethyl-5-methyl-1~{H}-pyrrole-2-carboxamide (99E)
Ligand formula: C21 H22 N2 O4
Ligand molecular weight: 366.41
Ligand SMILES: CCc1c(c([nH]c1C(=O)NCc2c(ccc3c2c(ccc3)O)O)C)C(=O)C
Ligand InChI: InChI=1S/C21H22N2O4/c1-4-14-18(12(3)24)11(2)23-20(14)21(27)22-10-15-16(25)9-8-13-6-5-7-17(26)19(13)15/h5-9,23,25-26H,4,10H2,1-3H3,(H,22,27)
Release date: 2017-08-16
STRUCTURE OF HLA-B*07:02 IN COMPLEX WITH DOT1L(998-1006) PEPTIDE (PDB entry 7S7E)
Macromolecule: Beta-2-microglobulin
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 100 residues
Sequence: MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDWSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.04
R work: 0.172
R free: 0.235
Average B factor: 35.045
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8
Crystallization temperature (K): 290
Crystal growth procedure: 18-24% PEG4000, 0.1 SODIUM CITRATE, 20% ISOPROPANOL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE
Matthews coefficient: 2.83
Solvent content (%): 56.59
Ligand: SODIUM ION ()
Ligand formula: Na
Ligand molecular weight: 22.99
Ligand SMILES: [Na+]
Ligand InChI: InChI=1S/Na/q+1
Release date: 2022-11-02
Human Pancreatic Alpha-Amylase in complex with the mechanism based inactivator glucosyl epi-cyclophellitol (PDB entry 5EMY)
Macromolecule: Pancreatic alpha-amylase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.2.1.1
Sequence length: 496 residues
Sequence: QYSPNTQQGRTSIVHLFEWRWVDIALECERYLAPKGFGGVQVSPPNENVAIYNPFRPWWERYQPVSYKLCTRSGNEDEFRNMVTRCNNVGVRIYVDAVINHMCGNAVSAGTSSTCGSYFNPGSRDFPAVPYSGWDFNDGKCKTGSGDIENYNDATQVRDCRLTGLLDLALEKDYVRSKIAEYMNHLIDIGVAGFRLDASKHMWPGDIKAILDKLHNLNSNWFPAGSKPFIYQEVIDLGGEPIKSSDYFGNGRVTEFKYGAKLGTVIRKWNGEKMSYLKNWGEGWGFVPSDRALVFVDNHDNQRGHGAGGASILTFWDARLYKMAVGFMLAHPYGFTRVMSSYRWPRQFQNGNDVNDWVGPPNNNGVIKEVTINPDTTCGNDWVCEHRWRQIRNMVIFRNVVDGQPFTNWYDNGSNQVAFGRGNRGFIVFNNDDWSFSLTLQTGLPAGTYCDVISGDKINGNCTGIKIYVSDDGKAHFSISNSAEDPFIAIHAESKL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.231
R work: 0.1189
R free: 0.1421
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: 100 mM sodium cacodylate, 58% MPD, obtained crystals were soaked in 100mM glucosyl epi-cyclophellitol solution and incubated for up to two weeks to allow complex formation.
Matthews coefficient: 2.08
Solvent content (%): 40.98
Ligand: (1R,2R,3S,5R,6S)-2,3,5-trihydroxy-6-(hydroxymethyl)cyclohexyl alpha-D-glucopyranoside (5QP)
Ligand formula: C13 H24 O10
Ligand molecular weight: 340.324
Ligand SMILES: C1C(C(C(C(C1O)O)OC2C(C(C(C(O2)CO)O)O)O)CO)O
Ligand InChI: InChI=1S/C13H24O10/c14-2-4-5(16)1-6(17)8(18)12(4)23-13-11(21)10(20)9(19)7(3-15)22-13/h4-21H,1-3H2/t4-,5+,6-,7+,8+,9+,10-,11+,12+,13+/m0/s1
Release date: 2016-07-06
Crystal structure of Sirt2 in complex with selective inhibitor A29 (PDB entry 5YQM)
Macromolecule: NAD-dependent protein deacetylase sirtuin-2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.5.1
Sequence length: 306 residues
Sequence: GASGSERLLDELTLEGVARYMQSERCRRVICLVGAGISTSAGIPDFRSPSTGLYDNLEKYHLPYPEAIFEISYFKKHPEPFFALAKELYPGQFKPTICHYFMRLLKDKGLLLRCYTQNIDTLERIAGLEQEDLVEAHGTFYTSHCVSASCRHEYPLSWMKEKIFSEVTPKCEDCQSLVKPDIVFFGESLPARFFSCMQSDFLKVDLLLVMGTSLQVQPFASLISKAPLSTPRLLINKEKAGQSDPFLGMIMGLGGGMDFDSKKAYRDVAWLGECDQGCLALAELLGWKKELEDLVRREHASIDAQS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.735
R work: 0.1826
R free: 0.2196
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M HEPES PH6.8, 25%-30% PEG 3350
Matthews coefficient: 2.14
Solvent content (%): 42.49
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: 2018-10-17
Crystal Structure of human mARC1 (PDB entry 6FW2)
Macromolecule: Mitochondrial amidoxime-reducing component 1,Endolysin,Mitochondrial amidoxime-reducing component 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1
Sequence length: 459 residues
Sequence: MRGSMQQVGTVAQLWIYPVKSCKGVPVSEAECTAMGLRSGNLRDRFWLVINQEGNMVTARQEPRLVLISLTCDGDTLTLSAMNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNCNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRCALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDAYTKDLLLPIKTPTTNAVHKCRVHGLEIEGRDCGEAAAQWITSFLKSQPYRLVHFEPHMRPRRPHQIADLFRPKDQIAYSDTSPFLILSEASLADLNSRLEKKVKATNFRPNIVISGCDVYAEDSWDELLIGDVELKRVMACSRCILTTVDPDTGVMSRKEPLETLKSYRQCDPSERKLYGKSPLFGQYFVLENPGTIKVGDPVYLLGQGTVDHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.78
R work: 0.1694
R free: 0.2082
Average B factor: 29.685
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 291
Crystal growth procedure: Bis-TRIS propane, Na2MoO4, PEG3350
Matthews coefficient: 2.45
Solvent content (%): 49.9
Ligand: PHOSPHONIC ACIDMONO-(2-AMINO-5,6-DIMERCAPTO-4-OXO-3,7,8A,9,10,10A-HEXAHYDRO-4H-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-7-YLMETHYL)ESTER (MTE)
Ligand formula: C10 H14 N5 O6 P S2
Ligand molecular weight: 395.352
Ligand SMILES: C(C1C(=C(C2C(O1)NC3=C(N2)C(=O)NC(=N3)N)S)S)OP(=O)(O)O
Ligand InChI: InChI=1S/C10H14N5O6PS2/c11-10-14-7-4(8(16)15-10)12-3-6(24)5(23)2(21-9(3)13-7)1-20-22(17,18)19/h2-3,9,12,23-24H,1H2,(H2,17,18,19)(H4,11,13,14,15,16)/t2-,3+,9-/m1/s1
Release date: 2018-10-31
STRUCTURE OF THE CATALYTIC SUBUNIT OF PROTEIN KINASE CK2 (CK2ALPHA') IN COMPLEX WITH THE NON-HYDROLYZABLE GTP ANALOGUE GMPPNP (PDB entry 8QF1)
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: MGSSHHHHHHSQDPMPGPAAGSRARVYAEVNSLRSREYWDYEAHVPSWGNQDDYQLVRKLGRGKYSEVFEAINITNNERVVVKILKPVKKKKIKREVKILENLRGGTNIIKLIDTVKDPVSKTPALVFEYINNTDFKQLYQILTDFDIRFYMYELLKALDYCHSKGIMHRDVKPHNVMIDHQQKKLRLIDWGLAEFYHPAQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRREPFFHGQDNYDQLVRIAKVLGTEELYGYLKKYHIDLDPHFNDILGQHSRKRWENFIHSENRHLVSPEALDLLDKLLRYDHQQRLTAKEAMEHPYFYPVVKEQSQPSADNAVLSSGLTAAR
Oligomeric state: Homo 2-mer
Stoichiometry: A2
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.32
R work: 0.2139
R free: 0.2324
Average B factor: 23.67
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 10 MIKROLITER CK2ALPHA' SOLUTION AFTER PROTEIN PURIFICATION (5 MG/ML CK2ALPHA' IN 500 MM NACL, 25 MM TRIS/HCl, PH 8.5) WERE MIXED WITH 5 MIKROLITER RESERVOIR SOLUTION [810 MM LICL, 28% (W/V) PEG 6000, 100 MM TRIS/HCL, PH 8.5]. AFTER EQUILIBRATION (SITTING DROP PLATES; VAPOUR DIFFUSION), CRYSTALLIZATION WAS INITIATED BY MICROSEEDING. THE CRYSTALS WERE OPTIMIZED BY MACROSEEDING. THE GTP-ANALOGUE GMPPNP WAS COMBINED WITH THESE CRYSTALS BY SOAKING. A 20 MM GMPPNP SOLUTION IN 60 MM MGCL2 WAS PREPARED. FOR SOAKING, 3 MICROLITER OF THE CRYSTAL MOTHER LIQUOR WAS REMOVED AND REPLACED BY 3 MICROLITER OF 20 MM GMPPNP, 60 MM MGCL2. ALL STEPS WERE PERFORMED AT A TEMPERATURE OF 293 K.
Matthews coefficient: 2.19
Solvent content (%): 43.87
Ligand: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER (GNP)
Ligand formula: C10 H17 N6 O13 P3
Ligand molecular weight: 522.196
Ligand SMILES: c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(NP(=O)(O)O)O)O)O)N=C(NC2=O)N
Ligand InChI: InChI=1S/C10H17N6O13P3/c11-10-13-7-4(8(19)14-10)12-2-16(7)9-6(18)5(17)3(28-9)1-27-32(25,26)29-31(23,24)15-30(20,21)22/h2-3,5-6,9,17-18H,1H2,(H,25,26)(H3,11,13,14,19)(H4,15,20,21,22,23,24)/t3-,5-,6-,9-/m1/s1
Release date: 2023-12-06
PanDDA analysis group deposition -- Crystal Structure of Kalirin/Rac1 in complex with MolPort-004-412-710 (PDB entry 5QQF)
Macromolecule: Ras-related C3 botulinum toxin substrate 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 178 residues
Sequence: SMQAIKCVVVGDGAVGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPVNLGLWDTAGQEDYDRLRPLSYPQTDVFLICFSLVSPASFENVRAKWYPEVRHHCPNTPIILVGTKLDLRDDKDTIEKLKEKKLTPITYPQGLAMAKEIGAVKYLECSALTQRGLKTVFDEAIRAVL
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.26
R work: 0.1977
R free: 0.2699
Average B factor: 52.975
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 293.15
Crystal growth procedure: 0.1M bis-tris pH 5.5 24% PEG 3350
Matthews coefficient: 2.34
Solvent content (%): 47.47
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: 2019-12-18
Crystal structure of the N-terminal domain single mutant (S92A) of the human mitochondrial calcium uniporter fused with T4 lysozyme (PDB entry 5BZ6)
Macromolecule: Lysozyme,Calcium uniporter protein, mitochondrial
Type: Protein, polypeptide(L)
Source organism: Tequatrovirus T4
EC number: 3.2.1.17
Sequence length: 262 residues
Sequence: MNIFEMLRIDEGLRLKIYKNTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDAYGSVTVVYQNGLPVISVRLPARRERCQFTLKPISDSVGVFLRQLQEEDRGIDRVAIYSPDGVRVAASTGIDLLLLDDFKLVINDLTYHVRPPKRLEHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.75
R work: 0.164
R free: 0.234
Average B factor: 34.21
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 25% PEG 3350, 0.1M Bis-Tris-HCl (pH 6.5), 0.2M ammonium sulfate
Matthews coefficient: 2.98
Solvent content (%): 58.68
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: 2015-09-16
MavC-UBE2N-Ub complex (PDB entry 7BXG)
Macromolecule: MavC
Type: Protein, polypeptide(L)
Source organism: Legionella pneumophila subsp. pneumophila str. Philadelphia 1
Sequence length: 386 residues
Sequence: SMTTSKLEKTGLHVHEKIKHMVKNYGTMITGIPAEILGQNEAEISVGYVKKMGNMKENIAEVVRKSEMTQPTNSCGKASNEVCDLLLGTEGASEFEKSSYQVLSGDGSNLKGSLPNKNLLVRVEMDRFNAPQKYQKIKREEFNPETAEKNKIYLLEDQLVYLDIFGKVIDLGQTSDTCHRLFNAITTPFYQNYILYDEYIDPEESAEEAAMFEMGEIVKAKMKNIDCWTATHSFTIFVPESDSEDTRTLYPYQAYWTSHTLQQWFSGDKDEKLSRLGIDGYIEKLALLGTTTDSKIRSSIYGELFSPPGKEHVFCTGMNEKFSPLRVKFKVTEVNPEIALQNLEEVQEFIDTNYPGENAKDQCELYKIKAQEAMTKQLEMRLLIEP
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.705
R work: 0.1929
R free: 0.2432
Average B factor: 42.6374
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M sodium malonate, pH 7.0, 12% PEG3350
Matthews coefficient: 2.73
Solvent content (%): 54.96
Release date: 2020-05-20
Crystal Structure of CK2alpha with N-(3-(((2-chloro-[1,1'-biphenyl]-4-yl)methyl)amino)propyl)methanesulfonamide bound (PDB entry 5MO5)
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): 2.04
R work: 0.1957
R free: 0.2127
Average B factor: 55.59
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: 2.23
Solvent content (%): 44.74
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: 2017-05-24
BACE1 in complex with a macrocyclic inhibitor (PDB entry 6NV7)
Macromolecule: Beta-secretase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.23.46
Sequence length: 390 residues
Sequence: GSFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHPFLHRYYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTVRANIAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTHVPNLFSLQLCGAGFPLNQSEVLASVGGSMIIGGIDHSLYTGSLWYTPIRREWYYEVIIVRVEINGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVKSIKAASSTEKFPDGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRITILPQQYLRPVEDVATSQDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSACHVHDEFRTAAVEGPFVTLDMEDCGYNI
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.132
R work: 0.1897
R free: 0.2168
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 295
Crystal growth procedure: 0.2 M MgSO4
0.1 M sodium citrate
12-14 % PEG4000
Matthews coefficient: 3.19
Solvent content (%): 61.4
Ligand: (E)-N-(2-methylpropylidene)-N~2~-{[(4S)-17-[(methylsulfonyl)(propyl)amino]-2-oxo-3-azatricyclo[13.3.1.1~6,10~]icosa-1(19),6(20),7,9,15,17-hexaen-4-yl]methyl}-D-threoninamide (L3J)
Ligand formula: C32 H46 N4 O5 S
Ligand molecular weight: 598.796
Ligand SMILES: CCCN(c1cc2cc(c1)C(=O)NC(Cc3cccc(c3)CCCC2)CNC(C(C)O)C(=O)N=CC(C)C)S(=O)(=O)C
Ligand InChI: InChI=1S/C32H46N4O5S/c1-6-14-36(42(5,40)41)29-18-26-11-8-7-10-24-12-9-13-25(15-24)17-28(35-31(38)27(16-26)19-29)21-33-30(23(4)37)32(39)34-20-22(2)3/h9,12-13,15-16,18-20,22-23,28,30,33,37H,6-8,10-11,14,17,21H2,1-5H3,(H,35,38)/b34-20+/t23-,28-,30+/m0/s1
Release date: 2019-10-09
Crystal structure of haspin in complex with ZW282 (compound 2a) (PDB entry 7OPS)
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): 2.38
R work: 0.1765
R free: 0.2285
Average B factor: 38.815
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277.15
Crystal growth procedure: 60% MPD, 0.1M SPG 6.5
Matthews coefficient: 3.05
Solvent content (%): 59.61
Ligand: 2-methylsulfanyl-10-nitro-pyrido[3,4-g]quinazoline (07C)
Ligand formula: C12 H8 N4 O2 S
Ligand molecular weight: 272.283
Ligand SMILES: CSc1ncc2cc3cnccc3c(c2n1)[N+](=O)[O-]
Ligand InChI: InChI=1S/C12H8N4O2S/c1-19-12-14-6-8-4-7-5-13-3-2-9(7)11(16(17)18)10(8)15-12/h2-6H,1H3
Release date: 2021-07-21
Structure of human dihydroorotate dehydrogenase in complex with 275-10-COOMe (PDB entry 5ZF4)
Macromolecule: Dihydroorotate dehydrogenase (quinone), mitochondrial
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.3.5.2
Sequence length: 390 residues
Sequence: MGHHHHHHHHHHSSGHIDDDDKHMATGDERFYAEHLMPTLQGLLDPESAHRLAVRFTSLGLLPRARFQDSDMLEVRVLGHKFRNPVGIAAGFDKHGEAVDGLYKMGFGFVEIGSVTPKPQEGNPRPRVFRLPEDQAVINRYGFNSHGLSVVEHRLRARQQKQAKLTEDGLPLGVNLGKNKTSVDAAEDYAEGVRVLGPLADYLVVNVSSPNTAGLRSLQGKAELRRLLTKVLQERDGLRRVHRPAVLVKIAPDLTSQDKEDIASVVKELGIDGLIVTNTTVSRPAGLQGALRSETGGLSGKPLRDLSTQTIREMYALTQGRVPIIGVGGVSSGQDALEKIRAGASLVQLYTALTFWGPPVVGKVKRELEALLKEQGFGGVTDAIGADHRR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.66
R work: 0.16752
R free: 0.18075
Average B factor: 20.814
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 4.9
Crystallization temperature (K): 293
Crystal growth procedure: 100MM SODIUM ACETATE, 1.8-1.9M AMMONIUM SULPHATE, 40MM C11DAO, 20.8MM DDAO, 2MM DIHYDROOROTATE
Matthews coefficient: 3.41
Solvent content (%): 63.9
Ligand: FLAVIN MONONUCLEOTIDE (FMN)
Ligand formula: C17 H21 N4 O9 P
Ligand molecular weight: 456.344
Ligand SMILES: Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)CC(C(C(COP(=O)(O)O)O)O)O
Ligand InChI: InChI=1S/C17H21N4O9P/c1-7-3-9-10(4-8(7)2)21(15-13(18-9)16(25)20-17(26)19-15)5-11(22)14(24)12(23)6-30-31(27,28)29/h3-4,11-12,14,22-24H,5-6H2,1-2H3,(H,20,25,26)(H2,27,28,29)/t11-,12+,14-/m0/s1
Release date: 2018-09-26
GABARAP-L1 ATG4B LIR Complex (PDB entry 5LXH)
Macromolecule: Gamma-aminobutyric acid receptor-associated protein-like 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 123 residues
Sequence: GPTMGSMKFQYKEDHPFEYRKKEGEKIRKKYPDRVPVIVEKAPKARVPDLDKRKYLVPSDLTVGQFYFLIRKRIHLRPEDALFFFVNNTIPPTSATMGQLYEDNHEEDYFLYVAYSDESVYGK
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.58
R work: 0.2053
R free: 0.2375
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.17 M AMSO4, 40 % PEG 4000, 15 % glycerol
Matthews coefficient: 2.24
Solvent content (%): 45.16
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: 2017-02-08
Crystal structure of Ser/Thr kinase Pim1 in complex with 10-DEBC derivatives (PDB entry 6L11)
Macromolecule: Serine/threonine-protein kinase pim-1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 289 residues
Sequence: GPHMKEKEPLESQYQVGPLLGSGGFGSVYSGIRVSDNLPVAIKHVEKDRISDWGELPNGTRVPMEVVLLKKVSSGFSGVIRLLDWFERPDSFVLILERPEPVQDLFDFITERGALQEELARSFFWQVLEAVRHCHNCGVLHRDIKDENILIDLNRGELKLIDFGSGALLKDTVYTDFDGTRVYSPPEWIRYHRYHGRSAAVWSLGILLYDMVCGDIPFEHDEEIIRGQVFFRQRVSSECQHLIRWCLALRPSDRPTFEEIQNHPWMQDVLLPQETAEIHLHSLSPGPSK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.05
R work: 0.213
R free: 0.2398
Average B factor: 42.265
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8
Crystallization temperature (K): 291
Crystal growth procedure: 0.4M potassium sodium tartrate tetrahydrate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Matthews coefficient: 3.54
Solvent content (%): 65.21
Ligand: 5-(2-chloranylphenoxazin-10-yl)-~{N},~{N}-diethyl-pentan-1-amine (E2C)
Ligand formula: C21 H27 Cl N2 O
Ligand molecular weight: 358.905
Ligand SMILES: CCN(CC)CCCCCN1c2ccccc2Oc3c1cc(cc3)Cl
Ligand InChI: InChI=1S/C21H27ClN2O/c1-3-23(4-2)14-8-5-9-15-24-18-10-6-7-11-20(18)25-21-13-12-17(22)16-19(21)24/h6-7,10-13,16H,3-5,8-9,14-15H2,1-2H3
Release date: 2020-05-27
crystal structure of the human TGT catalytic subunit QTRT1 (PDB entry 6H42)
Macromolecule: Queuine tRNA-ribosyltransferase catalytic subunit 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.4.2.29
Sequence length: 393 residues
Sequence: ESAPRIMRLVAECSRSRARAGELWLPHGTVATPVFMPVGTQATMKGITTEQLDALGCRICLGNTYHLGLRPGPELIQKANGLHGFMNWPHNLLTDSGGFQMVSLVSLSEVTEEGVRFRSPYDGNETLLSPEKSVQIQNALGSDIIMQLDDVVSSTVTGPRVEEAMYRSIRWLDRCIAAHQRPDKQNLFAIIQGGLDADLRATCLEEMTKRDVPGFAIGGLSGGESKSQFWRMVALSTSRLPKDKPRYLMGVGYATDLVVCVALGCDMFDCVFPTRTARFGSALVPTGNLQLRKKVFEKDFGPIDPECTCPTCQKHSRAFLHALLHSDNTAALHHLTVHNIAYQLQLMSAVRTSIVEKRFPDFVRDFMGAMYGDPTLCPTWATDALASVGITLG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.45
R work: 0.2024
R free: 0.2313
Average B factor: 67.1975
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 273
Crystal growth procedure: 100 mM Tris pH 7.8
200 mM KBr
200 mM KSCN
3 % (w/v) PGA-LM
5 % PEG 4000
Matthews coefficient: 2.64
Solvent content (%): 53.46
Ligand: POTASSIUM ION (K)
Ligand formula: K
Ligand molecular weight: 39.098
Ligand SMILES: [K+]
Ligand InChI: InChI=1S/K/q+1
Release date: 2018-09-05