satarupa22/MacromolecularLigandDB huggingface dataset:
PCSK9 in complex with compound 16 (PDB entry 6U26)
Macromolecule: Proprotein convertase subtilisin/kexin type 9
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21
Sequence length: 707 residues
Sequence: QEDEDGDYEELVLALRSEEDGLAEAPEHGTTATFHRCAKDPWRLPGTYVVVLKEETHLSQSERTARRLQAQAARRGYLTKILHVFHGLLPGFLVKMSGDLLELALKLPHVDYIEEDSSVFAQSIPWNLERITPPRYRADEYQPPDGGSLVEVYLLDTSIQSDHREIEGRVMVTDFENVPEEDGTRFHRQASKCDSHGTHLAGVVSGRDAGVAKGASMRSLRVLNCQGKGTVSGTLIGLEFIRKSQLVQPVGPLVVLLPLAGGYSRVLNAACQRLARAGVVLVTAAGNFRDDACLYSPASAPEVITVGATNAQDQPVTLGTLGTNFGRCVDLFAPGEDIIGASSDCSTCFVSQSGTSQAAAHVAGIAAMMLSAEPELTLAELRQRLIHFSAKDVINEAWFPEDQRVLTPNLVAALPPSTHGAGWQLFCRTVWSAHSGPTRMATAIARCAPDEELLSCSSFSRSGKRRGERMEAQGGKLVCRAHNAFGGEGVYAIARCCLLPQANCSVHTAPPAEASMGTRVHCHQQGHVLTGCSSHWEVEDLGTHKPPVLRPRGQPNQCVGHREASIHASCCHAPGLECKVKEHGIPAPQEQVTVACEEGWTLTGCSALPGTSHVLGAYAVDNTCVVRSRDVSTTGSTSEEAVTAVAICCRSRHLAQASQELQKGNSADIQHSGGRSSLEGPRFEGKPIPNPLLGLDSTRTGHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.53
R work: 0.187
R free: 0.213
Average B factor: 28.77
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 295
Crystal growth procedure: 100 mM Tris (pH 7.8) 200 mM NaCl, 15% PEG 3350,
Matthews coefficient: 1.1
Solvent content (%): 54.68
Ligand: 4'-{[(1R)-6-{2-[2-({N~5~-[N,N'-bis(tert-butoxycarbonyl)carbamimidoyl]-N~2~-(tert-butoxycarbonyl)-L-ornithyl}amino)ethoxy]ethoxy}-1-methyl-1-{2-oxo-2-[(1,3-thiazol-2-yl)amino]ethyl}-1,2,3,4-tetrahydroisoquinolin-7-yl]oxy}-2'-fluoro[1,1'-biphenyl]-4-carboxylic acid (063)
Ligand formula: C53 H69 F N8 O13 S
Ligand molecular weight: 1077.224
Ligand SMILES: CC1(c2cc(c(cc2CCN1)OCCOCCNC(=O)C(CCCNC(=NC(=O)OC(C)(C)C)NC(=O)OC(C)(C)C)NC(=O)OC(C)(C)C)Oc3ccc(c(c3)F)c4ccc(cc4)C(=O)O)CC(=O)Nc5nccs5
Ligand InChI: InChI=1S/C53H69FN8O13S/c1-50(2,3)73-47(67)59-39(12-11-20-56-45(61-48(68)74-51(4,5)6)62-49(69)75-52(7,8)9)43(64)55-22-24-70-25-26-71-40-28-34-19-21-58-53(10,31-42(63)60-46-57-23-27-76-46)37(34)30-41(40)72-35-17-18-36(38(54)29-35)32-13-15-33(16-14-32)44(65)66/h13-18,23,27-30,39,58H,11-12,19-22,24-26,31H2,1-10H3,(H,55,64)(H,59,67)(H,65,66)(H,57,60,63)(H2,56,61,62,68,69)/t39-,53+/m0/s1
Release date: 2019-11-06
hALK in complex with 3-(3-chlorophenyl)-5-methyl-1H-pyrazole (PDB entry 7JYS)
Macromolecule: ALK tyrosine kinase receptor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 322 residues
Sequence: GAMGSTDYNPNYCFAGKTSSISDLKEVPRKNITLIRGLGHGAFGEVYEGQVSGMPNDPSPLQVAVKTLPEVCSEQDELDFLMEALIISKFNHQNIVRCIGVSLQSLPRFILLELMAGGDLKSFLRETRPRPSQPSSLAMLDLLHVARDIACGCQYLEENHFIHRDIAARNCLLTCPGPGRVAKIGDFGMARDIYRASYYRKGGCAMLPVKWMPPEAFMEGIFTSKTDTWSFGVLLWEIFSLGYMPYPSKSNQEVLEFVTSGGRMDPPKNCPGPVYRIMTQCWQHQPEDRPNFAIILERIEYCTQDPDVINTALPIEYGPLVE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.22
R work: 0.2141
R free: 0.2528
Average B factor: 55.83
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 8
Crystallization temperature (K): 293
Crystal growth procedure: 25 mM Tris pH 8.0, 150 mM NaCl, 0.5 mM EDTA, 0.25 mM TCEP
Matthews coefficient: 2.11
Solvent content (%): 41.81
Ligand: 3-(3-chlorophenyl)-5-methyl-1H-pyrazole (VTD)
Ligand formula: C10 H9 Cl N2
Ligand molecular weight: 192.645
Ligand SMILES: Cc1cc(n[nH]1)c2cccc(c2)Cl
Ligand InChI: InChI=1S/C10H9ClN2/c1-7-5-10(13-12-7)8-3-2-4-9(11)6-8/h2-6H,1H3,(H,12,13)
Release date: 2021-01-20
Crystal structure of MMP12 in complex with inhibitor BE4. (PDB entry 6ELA)
Macromolecule: Macrophage metalloelastase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.24.65
Sequence length: 159 residues
Sequence: MGPVWRKHYITYRINNYTPDMNREDVDYAIRKAFQVWSNVTPLKFSKINTGMADILVVFARGAHGDDHAFDGKGGILAHAFGPGSGIGGDAHFDEDEFWTTHSGGTNLFLTAVHEIGHSLGLGHSSDPKAVMFPTYAYVDINTFRLSADDIRGIQSLYG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.485
R work: 0.1714
R free: 0.2067
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 293
Crystal growth procedure: protein solution: hMMP12 at 314 micro-M + 10 milli-M acetohydroxamate +  1 milli-M BE4, 10% DMSO
precipitant:  38% PEG 4K, 0.16 M imidazole piperidine,15% Dioxane, pH 8.5.
Cryoprotectant: 40% CM15 (12.5 % diethylene glycol + 12.5 % ethylene glycol + 12.5 % MPD + 12.5 % glycerol + 12.5 % 1,2-propanediol + 12.5 % 1,4-dioxane + 12.5 mM NDSB 201), 25% PEG 6K, 100 milli-M TRIS HCl, pH 7.0
Matthews coefficient: 2.2
Solvent content (%): 44.13
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: 2018-05-16
non-phosphorylated AMP-activated protein kinase bound to pharmacological activator R734 (PDB entry 6C9H)
Macromolecule: 5'-AMP-activated protein kinase catalytic subunit alpha-1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 494 residues
Sequence: MGHHHHHHGSVKIGHYILGDTLGVGTFGKVKVGKHELTGHKVAVKILNRQKIRSLDVVGKIRREIQNLKLFRHPHIIKLYQVISTPSDIFMVMEYVSGGELFDYICKNGRLDEKESRRLFQQILSGVDYCHRHMVVHRDLKPENVLLDAHMNAKIADFGLSNMMSDGEFLRTSCGSPNYAAPEVISGRLYAGPEVDIWSSGVILYALLCGTLPFDDDHVPTLFKKICDGIFYTPQYLNPSVISLLKHMLQVDPMKRATIKDIREHEWFKQDLPKYLFPEDPSYSSTMIDDEALKEVCEKFECSEEEVLSCLYNRNHQDPLAVAYHLIIDNRRIMNEAKDFYLATSPPDSFLDDHHLTRPHPERVPFLVAETPRARHTLDELNPQKSKHQGVRKAKWHLGIRSQSRPNDIMAEVCRAIKQLDYEWKVVNPYYLRVRRKNPVTSTYSKMSLQLYQVDSRTYLLDFRSIDDELTPRPGSHTIEFFEMCANLIKILAQ
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.65
R work: 0.2133
R free: 0.2423
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 293
Crystal growth procedure: 0.2 M magnesium formate
Matthews coefficient: 3.81
Solvent content (%): 67.69
Ligand: 5-{[6-chloro-5-(1-methyl-1H-indol-5-yl)-1H-benzimidazol-2-yl]oxy}-N-hydroxy-2-methylbenzamide (R34)
Ligand formula: C24 H19 Cl N4 O3
Ligand molecular weight: 446.886
Ligand SMILES: Cc1ccc(cc1C(=O)NO)Oc2[nH]c3cc(c(cc3n2)c4ccc5c(c4)ccn5C)Cl
Ligand InChI: InChI=1S/C24H19ClN4O3/c1-13-3-5-16(10-17(13)23(30)28-31)32-24-26-20-11-18(19(25)12-21(20)27-24)14-4-6-22-15(9-14)7-8-29(22)2/h3-12,31H,1-2H3,(H,26,27)(H,28,30)
Release date: 2018-11-28
Crystal Structure of human PARP-1 ART domain bound to inhibitor UTT83 (PDB entry 6NRI)
Macromolecule: Poly [ADP-ribose] polymerase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.4.2.30
Sequence length: 271 residues
Sequence: MGSSHHHHHHSSGLVPRGSHMTKSKLPKPVQDLIKMIFGSGSGSGGDPIDVNYEKLKTDIKVVDRDSEEAEIIRKYVKNTHATTHNAYDLEVIDIFKIEREGECQRYKPFKQLHNRRLLWHGSRTTNFAGILSQGLRIAPPEAPVTGYMFGKGIYFADMVSKSANYCHTSQGDPIGLILLGEVALGNMYELKHASHISKLPKGKHSVKGLGKTTPDPSANISLDGVDVPLGTGISSGVNDTSLLYNEYIVYDIAQVNLKYLLKLKFNFKTS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.2
R work: 0.1849
R free: 0.2375
Average B factor: 56.441
Crystallization method: EVAPORATION
Crystallization pH: 7.5
Crystallization temperature (K): 298
Crystal growth procedure: ~20% PEG 3350, 0.2 M ammonium sulfate or sodium citrate, 100 mM Hepes pH 7.5
Matthews coefficient: 2.54
Solvent content (%): 51.55
Ligand: (2Z)-2-{[4-(3-cyclopropyl-5,6-dihydro[1,2,4]triazolo[4,3-a]pyrazine-7(8H)-carbonyl)phenyl]methylidene}-3-oxo-2,3-dihydro-1-benzofuran-7-carboxamide (KYM)
Ligand formula: C25 H21 N5 O4
Ligand molecular weight: 455.465
Ligand SMILES: c1cc2c(c(c1)C(=O)N)OC(=Cc3ccc(cc3)C(=O)N4CCn5c(nnc5C6CC6)C4)C2=O
Ligand InChI: InChI=1S/C25H21N5O4/c26-23(32)18-3-1-2-17-21(31)19(34-22(17)18)12-14-4-6-16(7-5-14)25(33)29-10-11-30-20(13-29)27-28-24(30)15-8-9-15/h1-7,12,15H,8-11,13H2,(H2,26,32)/b19-12-
Release date: 2019-08-14
IRAK4 in complex with inhibitor (PDB entry 6THW)
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): 2.44
R work: 0.241
R free: 0.271
Average B factor: 82.72
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 298
Crystal growth procedure: AMS 0.1 M Hepes  & 
Protein Buffer:  25 mM HEPES pH 7.5, 1 mM EDTA, 1 mM TCEP, 5% Glycerol, 150 mM NaCl
Matthews coefficient: 2.5
Solvent content (%): 50.87
Ligand: 7-fluoranyl-4-(1-methylcyclopropyl)oxy-~{N}-[1-(1-methylpiperidin-4-yl)pyrazol-4-yl]-6-(2-methylpyrimidin-5-yl)pyrido[3,2-d]pyrimidin-2-amine (NBK)
Ligand formula: C25 H28 F N9 O
Ligand molecular weight: 489.548
Ligand SMILES: Cc1ncc(cn1)c2c(cc3c(n2)c(nc(n3)Nc4cnn(c4)C5CCN(CC5)C)OC6(CC6)C)F
Ligand InChI: InChI=1S/C25H28FN9O/c1-15-27-11-16(12-28-15)21-19(26)10-20-22(32-21)23(36-25(2)6-7-25)33-24(31-20)30-17-13-29-35(14-17)18-4-8-34(3)9-5-18/h10-14,18H,4-9H2,1-3H3,(H,30,31,33)
Release date: 2020-10-28
ARHGEF2 PanDDA analysis group deposition -- ARHGEF2 and RhoA in complex with Z104474512 (PDB entry 7G81)
Macromolecule: Transforming protein RhoA
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.5.2
Sequence length: 185 residues
Sequence: SMAAIRKKLVIVGDGACGKTCLLIVFSKDQFPEVYVPTVFENYVADIEVDGKQVELALWDTAGQEDYDRLRPLSYPDTDVILMCFSIDSPDSLENIPEKWTPEVKHFCPNVPIILVGNKKDLRNDEHTRRELAKMKQEPVKPEEGRDMANRIGAFGYMECSAKTKDGVREVFEMATRAALQARRG
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.51
R work: 0.1925
R free: 0.216
Average B factor: 26.55
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 293
Crystal growth procedure: 100 mM Tris, 2.6M sodium formate
Matthews coefficient: 2.54
Solvent content (%): 51.48
Ligand: 1-(2-ethoxyphenyl)piperazine (H04)
Ligand formula: C12 H18 N2 O
Ligand molecular weight: 206.284
Ligand SMILES: CCOc1ccccc1N2CCNCC2
Ligand InChI: InChI=1S/C12H18N2O/c1-2-15-12-6-4-3-5-11(12)14-9-7-13-8-10-14/h3-6,13H,2,7-10H2,1H3
Release date: 2023-07-12
Crystal structure of human Casein Kinase I delta in complex with a photoswitchable 2-Azoimidazole-based Inhibitor (compound 3) (PDB entry 6HMP)
Macromolecule: Casein kinase I isoform delta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 314 residues
Sequence: MGSSHHHHHHSSGLVPRGSHMELRVGNRYRLGRKIGSGSFGDIYLGTDIAAGEEVAIKLECVKTKHPQLHIESKIYKMMQGGVGIPTIRWCGAEGDYNVMVMELLGPSLEDLFNFCSRKFSLKTVLLLADQMISRIEYIHSKNFIHRDVKPDNFLMGLGKKGNLVYIIDFGLAKKYRDARTHQHIPYRENKNLTGTARYASINTHLGIEQSRRDDLESLGYVLMYFNLGSLPWQGLKAATKRQKYERISEKKMSTPIEVLCKGYPSEFATYLNFCRSLRFDDKPDYSYLRQLFRNLFHRQGFSYDYVFDWNMLK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.039
R work: 0.1853
R free: 0.219
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.2 M Ammonium citrate tribasic pH 7.0
20 % w/v Polyethylene glycol 3,350
Matthews coefficient: 2.1
Solvent content (%): 41.52
Ligand: 3-(2,5-dimethoxyphenyl)-~{N}-[4-[5-(4-fluorophenyl)-2-[(~{E})-(4-fluorophenyl)diazenyl]-3-methyl-imidazol-4-yl]pyridin-2-yl]propanamide (GEW)
Ligand formula: C32 H28 F2 N6 O3
Ligand molecular weight: 582.6
Ligand SMILES: Cn1c(c(nc1N=Nc2ccc(cc2)F)c3ccc(cc3)F)c4ccnc(c4)NC(=O)CCc5cc(ccc5OC)OC
Ligand InChI: InChI=1S/C32H28F2N6O3/c1-40-31(30(20-4-7-23(33)8-5-20)37-32(40)39-38-25-11-9-24(34)10-12-25)22-16-17-35-28(19-22)36-29(41)15-6-21-18-26(42-2)13-14-27(21)43-3/h4-5,7-14,16-19H,6,15H2,1-3H3,(H,35,36,41)/b39-38+
Release date: 2019-09-11
Inhibitor of MDM2-p53 Interaction (PDB entry 7BIR)
Macromolecule: E3 ubiquitin-protein ligase Mdm2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2.27
Sequence length: 98 residues
Sequence: GPLGSSQIPASEQETLVRPKPLLLKLLKSVGAQKDTYTMKEVLFYLGQYIMTKRLYDAAQQHIVYCSNDLLGDLFGVPSFSVKEHRKIYTMIYRNLVV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.02
R work: 0.219
R free: 0.243
Average B factor: 45.868
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 277
Crystal growth procedure: 2M (NH4)2SO4
5% PEG 400
.1M pH=6.5 Na MES/HCl
Matthews coefficient: 3.34
Solvent content (%): 63.12
Ligand: SULFATE ION (SO4)
Ligand formula: O4 S
Ligand molecular weight: 96.063
Ligand SMILES: [O-]S(=O)(=O)[O-]
Ligand InChI: InChI=1S/H2O4S/c1-5(2,3)4/h(H2,1,2,3,4)/p-2
Release date: 2021-04-07
Crystal Structure of p38alpha in Complex with Lipid Pocket Ligand 9h (PDB entry 5N65)
Macromolecule: Mitogen-activated protein kinase 14
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.24
Sequence length: 360 residues
Sequence: MSQERPTFYRQELNKTIWEVPERYQNLSPVGSGAYGSVCAAFDTKTGLRVAVKKLSRPFQSIIHAKRTYRELRLLKHMKHENVIGLLDVFTPARSLEEFNDVYLVTHLMGADLNNIVKCQKLTDDHVQFLIYQILRGLKYIHSADIIHRDLKPSNLAVNEDCELKILDFGLARHTDDEMTGYVATRWYRAPEIMLNWMHYNQTVDIWSVGCIMAELLTGRTLFPGTDHIDQLKLILRLVGTPGAELLKKISSESARNYIQSLTQMPKMNFANVFIGANPLAVDLLEKMLVLDSDKRITAAQALAHAYFAQYHDPDDEPVADPYDQSFESRDLLIDEWKSLTYDEVISFVPPPLDQEEMES
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.0
R work: 0.1921
R free: 0.2163
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293.15
Crystal growth procedure: 100 mM MES pH 5.6-6.2
20-30 % PEG4000
50 mM BOG
Matthews coefficient: 2.17
Solvent content (%): 43.42
Ligand: 2-phenyl-~{N}4-(2-thiophen-2-ylethyl)quinazoline-4,7-diamine (8OT)
Ligand formula: C20 H18 N4 S
Ligand molecular weight: 346.449
Ligand SMILES: c1ccc(cc1)c2nc3cc(ccc3c(n2)NCCc4cccs4)N
Ligand InChI: InChI=1S/C20H18N4S/c21-15-8-9-17-18(13-15)23-19(14-5-2-1-3-6-14)24-20(17)22-11-10-16-7-4-12-25-16/h1-9,12-13H,10-11,21H2,(H,22,23,24)
Release date: 2017-09-20
Crystal structure of the bromodomain of human CREBBP in complex with a benzoxazepine compound (PDB entry 5J0D)
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): 1.05
R work: 0.17828
R free: 0.19736
Average B factor: 19.092
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 25% PEG3350, 0.2 M MgCl2, 0.1M BisTris pH 7.5
Matthews coefficient: 2.22
Solvent content (%): 44.59
Ligand: 7-(3,5-dimethoxyphenyl)-N-[(3S)-1-methylpiperidin-3-yl]-4-propanoyl-2,3,4,5-tetrahydro-1,4-benzoxazepine-9-carboxamide (6F9)
Ligand formula: C27 H35 N3 O5
Ligand molecular weight: 481.584
Ligand SMILES: CCC(=O)N1CCOc2c(cc(cc2C(=O)NC3CCCN(C3)C)c4cc(cc(c4)OC)OC)C1
Ligand InChI: InChI=1S/C27H35N3O5/c1-5-25(31)30-9-10-35-26-20(16-30)11-18(19-12-22(33-3)15-23(13-19)34-4)14-24(26)27(32)28-21-7-6-8-29(2)17-21/h11-15,21H,5-10,16-17H2,1-4H3,(H,28,32)/t21-/m0/s1
Release date: 2016-10-05
APOBEC3F Chimeric Catalytic Domain in Complex with DNA(dC9) (PDB entry 5ZVA)
Macromolecule: APEBEC3F/ssDNA-C9
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.5.4
Sequence length: 209 residues
Sequence: MAHHHHHHVDDDDKMLVPRGSENLYFQGSAMDPPTFTFNFNNEPWVRGRHETYLCFTMEVVKHHSPVSWKRGVFRNQVDPETHCHAERCFLSWFCDDILSPNTNYEVTWYTSWSPCPECAGEVAEFLARHSNVNLTIFTARLYYFWDTDYQEGLRSLSQEGASVEIMGYKDFKYCWENFVYNDDEPFKPWKGLKYNFLFLDSKLQEILE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.3
R work: 0.161
R free: 0.208
Average B factor: 50.96
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 291
Crystal growth procedure: 0.05M sodium cacodylate, pH 6.5, and 30%(v/v) 2-methyl-2,4-pentanediol(MPD)
Matthews coefficient: 2.42
Solvent content (%): 53.92
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: 2018-11-21
MR in complex with dexamethasone (PDB entry 4UDA)
Macromolecule: MINERALOCORTICOID RECEPTOR
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 251 residues
Sequence: GTPSPVMVLENIEPEIVYAGYDSSKPDTAENLLSTLNRLAGKQMIQVVKWAKVLPGFKNLPLEDQITLIQYSWMSLSSFALSWRSYKHTNSQFLYFAPDLVFNEEKMHQSAMYELCQGMHQISLQFVRLQLTFEEYTIMKVLLLLSTIPKDGLKSQAAFEEMRTNYIKELRKMVTKSPNNSGQSWQRFYQLTKLLDSMHDLVSDLLEFCFYTFRESHALKVEFPAMLVEIISDQLPKVESGNAKPLYFHRK
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.03
R work: 0.1847
R free: 0.2401
Average B factor: 30.86
Crystallization pH: 7.5
Crystal growth procedure: 30% PEG4000, 0.1M NACL, 0.2M PIPES PH 7.5
Matthews coefficient: 2.29
Solvent content (%): 46
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: 2015-11-25
Human DNA polymerase eta-DNA-dT-ended primer binary complex (PDB entry 8E8A)
Macromolecule: DNA polymerase eta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 435 residues
Sequence: GPHMATGQDRVVALVDMDCFFVQVEQRQNPHLRNKPCAVVQYKSWKGGGIIAVSYEARAFGVTRSMWADDAKKLCPDLLLAQVRESRGKANLTKYREASVEVMEIMSRFAVIERASIDEAYVDLTSAVQERLQKLQGQPISADLLPSTYIEGLPQGPTTAEETVQKEGMRKQGLFQWLDSLQIDNLTSPDLQLTVGAVIVEEMRAAIERETGFQCSAGISHNKVLAKLACGLNKPNRQTLVSHGSVPQLFSQMPIRKIRSLGGKLGASVIEILGIEYMGELTQFTESQLQSHFGEKNGSWLYAMCRGIEHDPVKPRQLPKTIGCSKNFPGKTALATREQVQWWLLQLAQELEERLTKDRNDNDRVATQLVVSIRVQGDKRLSSLRRCCALTRYDAHKMSHDAFTVIKNCNTSGIQTEWSPPLTMLFLCATKFSAS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.2056
R free: 0.2266
Average B factor: 36.8759
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7
Crystallization temperature (K): 298
Crystal growth procedure: PEG 2000MME, 0.1 M MES
Matthews coefficient: 2.09
Solvent content (%): 41.23
Release date: 2023-02-01
Crystal Structure of the R422Q missense variant of human PGM1 (PDB entry 6UO6)
Macromolecule: Phosphoglucomutase-1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 5.4.2.2
Sequence length: 585 residues
Sequence: MHHHHHHSSGVDLGTENLYFQSNMVKIVTVKTQAYQDQKPGTSGLRKRVKVFQSSANYAENFIQSIISTVEPAQRQEATLVVGGDGRFYMKEAIQLIARIAAANGIGRLVIGQNGILSTPAVSCIIRKIKAIGGIILTASHNPGGPNGDFGIKFNISNGGPAPEAITDKIFQISKTIEEYAVCPDLKVDLGVLGKQQFDLENKFKPFTVEIVDSVEAYATMLRSIFDFSALKELLSGPNRLKIRIDAMHGVVGPYVKKILCEELGAPANSAVNCVPLEDFGGHHPDPNLTYAADLVETMKSGEHDFGAAFDGDGDRNMILGKHGFFVNPSDSVAVIAANIFSIPYFQQTGVRGFARSMPTSGALDRVASATKIALYETPTGWKFFGNLMDASKLSLCGEESFGTGSDHIREKDGLWAVLAWLSILATRKQSVEDILKDHWQKYGQNFFTRYDYEEVEAEGANKMMKDLEALMFDRSFVGKQFSANDKVYTVEKADNFEYSDPVDGSISRNQGLRLIFTDGSRIVFRLSGTGSAGATIRLYIDSYEKDVAKINQDPQVMLAPLISIALKVSQLQERTGRTAPTVIT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.15
R work: 0.1752
R free: 0.213
Average B factor: 45.04
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8
Crystallization temperature (K): 293
Crystal growth procedure: 1.7-1.95 ammonium sulfate, 0.1 M Tris HCl, pH 8.0
Matthews coefficient: 2.85
Solvent content (%): 56.91
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: 2020-03-04
Crystal structure of CREBBP bromodomain complexd with DT29 (PDB entry 6FQO)
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): 1.35
R work: 0.1709
R free: 0.1941
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 0.15 M KSCN, 20% PEG3350, 10% EG
Matthews coefficient: 1.97
Solvent content (%): 37.58
Ligand: ~{N}-[3-(2,5-dimethyl-3-oxidanylidene-1,2-oxazol-4-yl)-5-(5-ethanoyl-2-ethoxy-phenyl)phenyl]furan-2-carboxamide (E2T)
Ligand formula: C26 H24 N2 O6
Ligand molecular weight: 460.479
Ligand SMILES: CCOc1ccc(cc1c2cc(cc(c2)NC(=O)c3ccco3)C4=C(ON(C4=O)C)C)C(=O)C
Ligand InChI: InChI=1S/C26H24N2O6/c1-5-32-22-9-8-17(15(2)29)14-21(22)18-11-19(24-16(3)34-28(4)26(24)31)13-20(12-18)27-25(30)23-7-6-10-33-23/h6-14H,5H2,1-4H3,(H,27,30)
Release date: 2018-08-29
Crystal structure of constitutively active PARP-2 (PDB entry 5DSY)
Macromolecule: Poly [ADP-ribose] polymerase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.4.2.30
Sequence length: 280 residues
Sequence: MGSSHHHHHHSSGLVPRGSHPESQLDLRVQELIKLICNVQAMEEKTELQSPEHPLDQHYRNLHCALRPLDHESYEFKVISQYLQSTHAPTHSDYTMTLLDLFEVEKDGEKEAFREDLHNRMLLWHGSRMSNWVGILSHGLRIAPPEAPITGYMFGKGIYFADMSSKSANYCFASRLKNTGLLLLSEVALGQCNELLEANPKAEGLLQGKHSTKGLGKMAPSSAHFVTLNGSTVPLGPASDTGILNPDGYTLNYNEYIVYNPNQVRMRYLLKVQFNFLQLW
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.7
R work: 0.1926
R free: 0.248
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8
Crystallization temperature (K): 298
Crystal growth procedure: 2.55-2.65 M NaCl and 0.1 M Tris
Matthews coefficient: 2.63
Solvent content (%): 53.28
Ligand: 2-[4-[(2S,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]carbonylpiperazin-1-yl]-N-(1-oxidanylidene-2,3-dihydroisoindol-4-yl)ethanamide (UHB)
Ligand formula: C24 H27 N9 O6
Ligand molecular weight: 537.528
Ligand SMILES: c1cc2c(c(c1)NC(=O)CN3CCN(CC3)C(=O)C4C(C(C(O4)n5cnc6c5ncnc6N)O)O)CNC2=O
Ligand InChI: InChI=1S/C24H25N9O6/c25-20-16-21(28-10-27-20)33(11-29-16)24-18(36)17(35)19(39-24)23(38)32-6-4-31(5-7-32)9-15(34)30-14-3-1-2-12-13(14)8-26-22(12)37/h1-3,8,10-11,17-19,24,35-36H,4-7,9H2,(H,26,37)(H2,25,27,28)/b30-14-/t17-,18+,19-,24+/m0/s1
Release date: 2016-07-27
Structure of Cyclophilin A in complex with Benzamide. (PDB entry 4N1N)
Macromolecule: Peptidyl-prolyl cis-trans isomerase A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 5.2.1.8
Sequence length: 165 residues
Sequence: MVNPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGFGYKGSCFHRIIPGFMCQGGDFTRHNGTGGKSIYGEKFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKTEWLDGKHVVFGKVKEGMNIVEAMERFGSRNGKTSKKITIADCGQLE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.5
R work: 0.1664
R free: 0.21283
Average B factor: 26.028
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8
Crystallization temperature (K): 277
Crystal growth procedure: Tris, PEG8000, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Matthews coefficient: 2.79
Solvent content (%): 55.97
Ligand: BENZAMIDE (UNU)
Ligand formula: C7 H7 N O
Ligand molecular weight: 121.137
Ligand SMILES: c1ccc(cc1)C(=O)N
Ligand InChI: InChI=1S/C7H7NO/c8-7(9)6-4-2-1-3-5-6/h1-5H,(H2,8,9)
Release date: 2015-08-12