satarupa22/MacromolecularLigandDB huggingface dataset:
Monobody 12D1 bound to KRAS(G12D) (PDB entry 8EZG)
Macromolecule: GTPase KRas
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.5.2
Sequence length: 168 residues
Sequence: MTEYKLVVVGADGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETSLLDILDTAGQEEYSAMRDQYMRTGEGFLLVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKSDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQGVDDAFYTLVREIRKHKE
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.52
R work: 0.171
R free: 0.2131
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 291
Crystal growth procedure: 2.8 M sodium acetate trihydrate
Matthews coefficient: 3.96
Solvent content (%): 68.94
Ligand: GUANOSINE-5'-DIPHOSPHATE (GDP)
Ligand formula: C10 H15 N5 O11 P2
Ligand molecular weight: 443.201
Ligand SMILES: c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
Ligand InChI: InChI=1S/C10H15N5O11P2/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(25-9)1-24-28(22,23)26-27(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1
Release date: 2023-07-19
Crystal structure of a mutated catalytic domain of Human MMP12 in complex with RXP470 (PDB entry 5CZM)
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): 1.303
R work: 0.1454
R free: 0.1739
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 9.5
Crystallization temperature (K): 293
Crystal growth procedure: Protein : MMP12h F67D K241A 850 micro-M + 10mM AHA
Drop : 1 micro-L protein + 0.35 micro-l inhibitor(1.5 milli-M, DMSO)
Precipitant : 20% PEG4K, 0.2 M TRIS pH9.5
Cryo protectant : 5% diethylene glycol, 0% ethylene glycol, 5% MPD + 5% glycerol, 5% 2,3-butanediol, 5mM NDSB 201, 25% PEG 6K, 100mM TRIS HCl, pH 8.0
Matthews coefficient: 2.23
Solvent content (%): 44.89
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: 2016-08-10
Structure of USP36 in complex with Ubiquitin-PA (PDB entry 8BS9)
Macromolecule: Ubiquitin carboxyl-terminal hydrolase 36
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.19.12
Sequence length: 346 residues
Sequence: GPARRQGSEHTYESCGDGVPAPQKVLFPTERLSLRWERVFRVGAGLHNLGNTCFLNATIQCLTYTPPLANYLLSKEHARSCHQGSFCMLCVMQNHIVQAFANSGNAIKPVSFIRDLKKIARHFRFGNQEDAHEFLRYTIDAMQKACLNGCAKLDRQTQATTLVHQIFGGYLRSRVKCSVCKSVSDTYDPYLDVALEIRQAANIVRALELFVKADVLSGENAYMCAKCKKKVPASKRFTIHRTSNVLTLSLKRFANFSGGKITKDVGYPEFLNIRPYMSQNNGDPVMYGLYAVLVHSGYSCHAGHYYCYVKASNGQWYQMNDSLVHSSNVKVVLNQQAYVLFYLRIP
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.9
R work: 0.171
R free: 0.2094
Average B factor: 40.43
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8
Crystallization temperature (K): 291
Crystal growth procedure: 0.3 M potassium formate, 14% (w/v) PEG 3350
Matthews coefficient: 2.68
Solvent content (%): 54.19
Ligand: ZINC ION (ZN)
Ligand formula: Zn
Ligand molecular weight: 65.409
Ligand SMILES: [Zn+2]
Ligand InChI: InChI=1S/Zn/q+2
Release date: 2023-07-12
Crystal structure of Tdp1 catalytic domain in complex with compound XZ578 (PDB entry 6N19)
Macromolecule: Tyrosyl-DNA phosphodiesterase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.4
Sequence length: 461 residues
Sequence: SGEGQDIWDMLDKGNPFQFYLTRVSGVKPKYNSGALHIKDILSPLFGTLVSSAQFNYCFDVDWLVKQYPPEFRKKPILLVHGDKREAKAHLHAQAKPYENISLCQAKLDIAFGTHHTKMMLLLYEEGLRVVIHTSNLIHADWHQKTQGIWLSPLYPRIADGTHKSGESPTHFKADLISYLMAYNAPSLKEWIDVIHKHDLSETNVYLIGSTPGRFQGSQKDNWGHFRLKKLLKDHASSMPNAESWPVVGQFSSVGSLGADESKWLCSEFKESMLTLGKESKTPGKSSVPLYLIYPSVENVRTSLEGYPAGGSLPYSIQTAEKQNWLHSYFHKWSAETSGRSNAMPHIKTYMRPSPDFSKIAWFLVTSANLSKAAWGALEKNGTQLMIRSYELGVLFLPSAFGLDSFKVKQKFFAGSQEPMATFPVPYDLPPELYGSKDRPWIWNIPYVKAPDTHGNMWVPS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.501
R work: 0.1797
R free: 0.205
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 291
Crystal growth procedure: 0.1M MOPS/HEPES-Na pH 7.5, 10% (w/v) PEG 8000, 20% (v/v) ethylene glycol, 0.03 M sodium fluoride, 0.03 M sodium bromide, 0.03 M sodium iodide
Matthews coefficient: 2.43
Solvent content (%): 49.45
Ligand: 4-[(4-carboxybutanoyl)amino]benzene-1,2-dicarboxylic acid (K8V)
Ligand formula: C13 H13 N O7
Ligand molecular weight: 295.245
Ligand SMILES: c1cc(c(cc1NC(=O)CCCC(=O)O)C(=O)O)C(=O)O
Ligand InChI: InChI=1S/C13H13NO7/c15-10(2-1-3-11(16)17)14-7-4-5-8(12(18)19)9(6-7)13(20)21/h4-6H,1-3H2,(H,14,15)(H,16,17)(H,18,19)(H,20,21)
Release date: 2019-07-03
Human Carbonic Anhydrase II in complex with Methyl 2-(benzenesulfonyl)-4-chloro-5-sulfamoylbenzoate (PDB entry 7Q0E)
Macromolecule: Carbonic anhydrase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 258 residues
Sequence: HHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHAFNVEFDDSQDKAVLKGGPLDGTYRLIQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDFGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTKGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLLECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.3
R work: 0.1261
R free: 0.1691
Average B factor: 12.855
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: Crystallization buffer: 0.1M sodium bicine (pH 9.0), 0.2 M ammonium sulfate and 2M sodium malonate (pH 7.0)
Matthews coefficient: 2.09
Solvent content (%): 41.2
Ligand: ZINC ION (ZN)
Ligand formula: Zn
Ligand molecular weight: 65.409
Ligand SMILES: [Zn+2]
Ligand InChI: InChI=1S/Zn/q+2
Release date: 2022-01-12
AKR1B1 at 3.45 MGy radiation dose. (PDB entry 6F8O)
Macromolecule: Aldose reductase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.1.1.21
Sequence length: 316 residues
Sequence: MASRILLNNGAKMPILGLGTWKSPPGQVTEAVKVAIDVGYRHIDCAHVYQNENEVGVAIQEKLREQVVKREELFIVSKLWCTYHEKGLVKGACQKTLSDLKLDYLDLYLIHWPTGFKPGKEFFPLDESGNVVPSDTNILDTWAAMEELVDEGLVKAIGISNFNHLQVEMILNKPGLKYKPAVNQIECHPYLTQEKLIQYCQSKGIVVTAYSPLGSPDRPWAKPEDPSLLEDPRIKAIAAKHNKTTAQVLIRFPMQRNLVVIPKSVTPERIAENFKVFDFELSSQDMTTLLSYNRNWRVCALLSCTSHKDYPFHEEF
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.17
R work: 0.1185
R free: 0.163
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5
Crystallization temperature (K): 298
Crystal growth procedure: PEG 6000, AmCitrate
Matthews coefficient: 2.17
Solvent content (%): 43.28
Ligand: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE (NAP)
Ligand formula: C21 H28 N7 O17 P3
Ligand molecular weight: 743.405
Ligand SMILES: c1cc(c[n+](c1)C2C(C(C(O2)COP(=O)([O-])OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)OP(=O)(O)O)O)O)O)C(=O)N
Ligand InChI: InChI=1S/C21H28N7O17P3/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(44-46(33,34)35)14(30)11(43-21)6-41-48(38,39)45-47(36,37)40-5-10-13(29)15(31)20(42-10)27-3-1-2-9(4-27)18(23)32/h1-4,7-8,10-11,13-16,20-21,29-31H,5-6H2,(H7-,22,23,24,25,32,33,34,35,36,37,38,39)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
Release date: 2019-03-13
Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with dCTP (PDB entry 6CTQ)
Macromolecule: DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*(2DA))-3')
Type: DNA, polydeoxyribonucleotide
Source organism: Homo sapiens
Sequence length: 10 residues
Sequence: GCTGATGCGA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.87
R work: 0.1751
R free: 0.2283
Average B factor: 29.7868
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 16-18% PEG 3350
Matthews coefficient: 2.3
Solvent content (%): 46.5
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: 2018-06-20
BTK-inhibitor co-structure (PDB entry 5FBO)
Macromolecule: Tyrosine-protein kinase BTK
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 271 residues
Sequence: GLGYGSWEIDPKDLTFLKELGTGQFGVVKYGKWRGQYDVAIKMIKEGSMSEDEFIEEAKVMMNLSHEKLVQLYGVCTKQRPIFIITEYMANGCLLNYLREMRHRFQTQQLLEMCKDVCEAMEYLESKQFLHRDLAARNCLVNDQGVVKVSDFGLSRYVLDDEYTSSVGSKFPVRWSPPEVLMYSKFSSKSDIWAFGVLMWEIYSLGKMPYERFTNSETAEHIAQGLRLYRPHLASEKVYTIMYSCWHEKADERPTFKILLSNILDVMDEES
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.894
R work: 0.211
R free: 0.236
Average B factor: 44.3
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 277
Crystal growth procedure: 5.5 v/v PEG 10000, 0.1M Ammonium Acetate, 0.1M Bis-Tris Cl pH 6.5, 2.5 mM(S)-4-(8-amino-3-(1-(4-(dimethylamino)butanoyl)pyrrolidin-2-yl)imidazo[1,5-a]pyrazin-1-yl)-N-(thiazol-2-yl)benzamide
Matthews coefficient: 2.28
Solvent content (%): 46.08
Ligand: 4-[8-azanyl-3-[(3~{R},6~{S})-1-cyclopropylcarbonyl-6-methyl-piperidin-3-yl]imidazo[1,5-a]pyrazin-1-yl]-3-fluoranyl-~{N}-[4-(trifluoromethyl)pyridin-2-yl]benzamide (5WH)
Ligand formula: C29 H27 F4 N7 O2
Ligand molecular weight: 581.564
Ligand SMILES: CC1CCC(CN1C(=O)C2CC2)c3nc(c4n3ccnc4N)c5ccc(cc5F)C(=O)Nc6cc(ccn6)C(F)(F)F
Ligand InChI: InChI=1S/C29H27F4N7O2/c1-15-2-3-18(14-40(15)28(42)16-4-5-16)26-38-23(24-25(34)36-10-11-39(24)26)20-7-6-17(12-21(20)30)27(41)37-22-13-19(8-9-35-22)29(31,32)33/h6-13,15-16,18H,2-5,14H2,1H3,(H2,34,36)(H,35,37,41)/t15-,18+/m0/s1
Release date: 2016-03-23
Synthesis and evaluation of heterocyclic catechol mimics as inhibitors of catechol-O-methyltransferase (COMT): Structure with Cmpd18 (1-(biphenyl-3-yl)-3-hydroxypyridin-4(1H)-one) (PDB entry 4XUC)
Macromolecule: Catechol O-methyltransferase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1.6
Sequence length: 218 residues
Sequence: NLLAGDTKEQRILNHVLQHAEPGNAQSVLEAIDTYCEQKEWAMNVGDKKGKIVDAVIQEHQPSVLLELGAYCGYSAVRMARLLSPGARLITIEINPDCAAITQRMVDFAGVKDKVTLVVGASQDIIPQLKKKYDVDTLDMVFLDHWKDRYLPDTLLLEECGLLRKGTVLLADNVICPGAPDFLAHVRGSSCFECTHYQSFLEYREVVDGLEKAIYKGP
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.1736
R free: 0.2156
Average B factor: 20.192
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 298
Crystal growth procedure: 0.1M MES, pH 6.5, 0.1M NaOAc, 30% PEG 2000MME; MA000417 (PEGsII), drop b10 :100uM ligand, 11mg/ml protein
Matthews coefficient: 2.53
Solvent content (%): 51.41
Ligand: 1-(biphenyl-3-yl)-3-hydroxypyridin-4(1H)-one (43G)
Ligand formula: C17 H13 N O2
Ligand molecular weight: 263.291
Ligand SMILES: c1ccc(cc1)c2cccc(c2)N3C=CC(=O)C(=C3)O
Ligand InChI: InChI=1S/C17H13NO2/c19-16-9-10-18(12-17(16)20)15-8-4-7-14(11-15)13-5-2-1-3-6-13/h1-12,20H
Release date: 2015-04-15
Joint X-ray/neutron structure of Human Carbonic Anhydrase II in complex with Methazolamide (PDB entry 5C8I)
Macromolecule: Carbonic anhydrase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 260 residues
Sequence: MSHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHAFNVEFDDSQDKAVLKGGPLDGTYRLIQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDFGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTKGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLLECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION, NEUTRON DIFFRACTION
Refinement resolution (Å): 1.56, 2.2
R work: 0.204
R free: 0.221
Average B factor: 21.3
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.8
Crystallization temperature (K): 298
Crystal growth procedure: 1.6M Na-citrate, 50 mM Tris
Matthews coefficient: 2.16
Solvent content (%): 43.03
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: 2016-07-20
Apo form crystal structure of human Lipocalin PGDS . (PDB entry 5WY9)
Macromolecule: Prostaglandin-H2 D-isomerase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 5.3.99.2
Sequence length: 176 residues
Sequence: MAPEAQVSVQPNFQQDKFLGRWFSAGLASNSSWLREKKAALSMCKSVVAPATDGGLNLTSTFLRKNQCETRTMLLQPAGSLGSYSYRSPHWGSTYSVSVVETDYDQYALLYSQGSKGPGEDFRMATLYSRTQTPRAELKEKFTAFCKAQGFTEDTIVFLPQTDKCMTEQAHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.45
R work: 0.17625
R free: 0.2109
Average B factor: 20.528
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277.15
Crystal growth procedure: 0.05M Potassium thiocyanate, 30%PEG MME 2000
Matthews coefficient: 1.88
Solvent content (%): 34.75
Ligand: 2-(2-METHOXYETHOXY)ETHANOL (PG0)
Ligand formula: C5 H12 O3
Ligand molecular weight: 120.147
Ligand SMILES: COCCOCCO
Ligand InChI: InChI=1S/C5H12O3/c1-7-4-5-8-3-2-6/h6H,2-5H2,1H3
Release date: 2017-01-25
Rapid optimisation of fragments and hits to lead compounds from screening of crude reaction mixtures (PDB entry 6TMQ)
Macromolecule: [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.2
Sequence length: 394 residues
Sequence: GSAPKYIEHFSKFSPSPLSMKQFLDFGSSNACEKTSFTFLRQELPVRLANIMKEINLLPDRVLSTPSVQLVQSWYVQSLLDIMEFLDKDPEDHRTLSQFTDALVTIRNRHNDVVPTMAQGVLEYKDTYGDDPVSNQNIQYFLDRFYLSRISIRMLINQHTLIFDGSTNPAHPKHIGSIDPNCNVSEVVKDAYDMAKLLCDKYYMASPDLEIQEINAANSKQPIHMVYVPSHLYHMLFELFKNAMRATVESHESSLILPPIKVMVALGEEDLSIKMSDRGGGVPLRKIERLFSYMYSTAPTPQPGTGGTPLAGFGYGLPISRLYAKYFQGDLQLFSMEGFGTDAVIYLKALSTDSVERLPVYNKSAWRHYQTIQEAGDWCVPSTEPKNTSTYRVS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.112
R work: 0.1758
R free: 0.2343
Average B factor: 45.574
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.8
Crystallization temperature (K): 277
Crystal growth procedure: 0.1 M Sodium acetate pH 5.8
0.125 M Magnesium chloride
Matthews coefficient: 3.3
Solvent content (%): 62.75
Ligand: N-(2-AMINOETHYL)-2-{3-CHLORO-4-[(4-ISOPROPYLBENZYL)OXY]PHENYL} ACETAMIDE (TF3)
Ligand formula: C20 H25 Cl N2 O2
Ligand molecular weight: 360.878
Ligand SMILES: CC(C)c1ccc(cc1)COc2ccc(cc2Cl)CC(=O)NCCN
Ligand InChI: InChI=1S/C20H25ClN2O2/c1-14(2)17-6-3-15(4-7-17)13-25-19-8-5-16(11-18(19)21)12-20(24)23-10-9-22/h3-8,11,14H,9-10,12-13,22H2,1-2H3,(H,23,24)
Release date: 2020-10-14
IRAK4 IN COMPLEX WITH inhibitor (PDB entry 6F3D)
Macromolecule: Interleukin-1 receptor-associated kinase 4
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 295 residues
Sequence: RFHSFSFYELKNVTNNFDERPISVGGNKMGEGGFGVVYKGYVNNTTVAVKKLAAMVDITTEELKQQFDQEIKVMAKCQHENLVELLGFSSDGDDLCLVYVYMPNGSLLDRLSCLDGTPPLSWHMRCKIAQGAANGINFLHENHHIHRDIKSANILLDEAFTAKISDFGLARASEKFAQTVMTSRIVGTTAYMAPEALRGEITPKSDIYSFGVVLLEIITGLPAVDEHREPQLLLDIKEEIEDEEKTIEDYIDKKMNDADSTSVEAMYSVASQCLHEKKNKRPDIKKVQQLLQEMT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.38
R work: 0.1975
R free: 0.2271
Average B factor: 63.65
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 293
Crystal growth procedure: 50 mM Hepes pH 7.5, 0.02% octylglucoside, 10% glycerol, 0.3 M NaCl, 1 mM TCEP
Matthews coefficient: 3.02
Solvent content (%): 59.31
Ligand: 4-[4-[[4-(dimethylamino)cyclohexyl]amino]-7~{H}-pyrrolo[2,3-d]pyrimidin-5-yl]cyclohexane-1-carboxamide (CJT)
Ligand formula: C21 H32 N6 O
Ligand molecular weight: 384.518
Ligand SMILES: CN(C)C1CCC(CC1)Nc2c3c(c[nH]c3ncn2)C4CCC(CC4)C(=O)N
Ligand InChI: InChI=1S/C21H32N6O/c1-27(2)16-9-7-15(8-10-16)26-21-18-17(11-23-20(18)24-12-25-21)13-3-5-14(6-4-13)19(22)28/h11-16H,3-10H2,1-2H3,(H2,22,28)(H2,23,24,25,26)/t13-,14-,15-,16-
Release date: 2018-05-23
Structure of DYRK1A in complex with compound 32 (PDB entry 7AJM)
Macromolecule: Dual specificity tyrosine-phosphorylation-regulated kinase 1A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.12.1
Sequence length: 355 residues
Sequence: MGSSHHHHHHSSGLVPRGSHMIVKNGEKWMDRYEIDSLIGKGSFGQVVKAYDRVEQEWVAIKIIKNKKAFLNQAQIEVRLLELMNKHDTEMKYYIVHLKRHFMFRNHLCLVFEMLSYNLYDLLRNTNFRGVSLNLTRKFAQQMCTALLFLATPELSIIHCDLKPENILLCNPKRSAIKIVDFGSSCQLGQRIYQYIQSRFYRSPEVLLGMPYDLAIDMWSLGCILVEMHTGEPLFSGANEVDQMNKIVEVLGIPPAHILDQAPKARKFFEKLPDGTWNLKKTKDGKREYKPPGTRKLHNILGVETGGPGGRRAGESGHTVADYLKFKDLILRMLDYDPKTRIQPYYALQHSFFAA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.4
R work: 0.1616
R free: 0.2101
Average B factor: 29.405
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: 2.3
Solvent content (%): 46.63
Ligand: ~{N}-[6-azanyl-4-(1-benzofuran-5-yl)pyridin-2-yl]-2-(methylamino)ethanamide (RKW)
Ligand formula: C16 H16 N4 O2
Ligand molecular weight: 296.324
Ligand SMILES: CNCC(=O)Nc1cc(cc(n1)N)c2ccc3c(c2)cco3
Ligand InChI: InChI=1S/C16H16N4O2/c1-18-9-16(21)20-15-8-12(7-14(17)19-15)10-2-3-13-11(6-10)4-5-22-13/h2-8,18H,9H2,1H3,(H3,17,19,20,21)
Release date: 2021-05-26
Structure of human DNA polymerase beta N279A complexed with 8OA in the template base paired with incoming non-hydrolyzable GTP (PDB entry 6PKZ)
Macromolecule: DNA polymerase beta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 335 residues
Sequence: MSKRKAPQETLNGGITDMLTELANFEKNVSQAIHKYNAYRKAASVIAKYPHKIKSGAEAKKLPGVGTKIAEKIDEFLATGKLRKLEKIRQDDTSSSINFLTRVSGIGPSAARKFVDEGIKTLEDLRKNEDKLNHHQRIGLKYFGDFEKRIPREEMLQMQDIVLNEVKKVDSEYIATVCGSFRRGAESSGDMDVLLTHPSFTSESTKQPKLLHQVVEQLQKVHFITDTLSKGETKFMGVCQLPSKNDEKEYPHRRIDIRLIPKDQYYCGVLYFTGSDIFAKNMRAHALEKGFTINEYTIRPLGVTGVAGEPLPVDSEKDIFDYIQWKYREPKDRSE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.74
R work: 0.175
R free: 0.249
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 298
Crystal growth procedure: 14-23% PEG3400, 350 MM SODIUM ACETATE
 IN 50 MM IMIDAZOLE, PH 7.5, VAPOR DIFFUSION, SITTING DROP,
 TEMPERATURE 295K
Matthews coefficient: 2.36
Solvent content (%): 47.82
Ligand: SODIUM ION ()
Ligand formula: Na
Ligand molecular weight: 22.99
Ligand SMILES: [Na+]
Ligand InChI: InChI=1S/Na/q+1
Release date: 2020-07-01
PDE2 complexed with 2-[6-fluoro-8-methylsulfonyl-9-[(1R)-1-[4-(trifluoromethyl)phenyl]ethyl]-1,2,3,4-tetrahydrocarbazol-1-yl]acetic acid (PDB entry 6BLF)
Macromolecule: cGMP-dependent 3',5'-cyclic phosphodiesterase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.4.17
Sequence length: 373 residues
Sequence: MHHHHHHENLYFQGELSTSLYKKAGFDDDDKSDDEYTKLLHDGIQPVAAIDSNFASFTYTPRSLPEDDTSMAILSMLQDMNFINNYKIDCPTLARFCLMVKKGYRDPPYHNWMHAFSVSHFCYLLYKNLELTNYLEDIEIFALFISCMCHDLDHRGTNNSFQVASKSVLAALYSSEGSVMERHHFAQAIAILNTHGCNIFDHFSRKDYQRMLDLMRDIILATDLAHHLRIFKDLQKMAEVGYDRNNKQHHRLLLCLLMTSCDLSDQTKGWKTTRKIAELIYKEFFSQGDLEKAMGNRPMEMMDREKAYIPELQISFMEHIAMPIYKLLQDLFPKAAELYERVASNREHWTKVSHKFTIRGLPSNNSLDFLDEE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.11
R work: 0.185
R free: 0.228
Average B factor: 36.44
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M HEPES pH 7.5, 15% PEG 8000, 2% Ethylene Glycol, 10 mM TCEP
Matthews coefficient: 2.06
Solvent content (%): 40.18
Ligand: [(1S)-6-fluoro-8-(methylsulfonyl)-9-{(1R)-1-[4-(trifluoromethyl)phenyl]ethyl}-2,3,4,9-tetrahydro-1H-carbazol-1-yl]acetic acid (DY1)
Ligand formula: C24 H23 F4 N O4 S
Ligand molecular weight: 497.502
Ligand SMILES: CC(c1ccc(cc1)C(F)(F)F)n2c3c(cc(cc3S(=O)(=O)C)F)c4c2C(CCC4)CC(=O)O
Ligand InChI: InChI=1S/C24H23F4NO4S/c1-13(14-6-8-16(9-7-14)24(26,27)28)29-22-15(10-21(30)31)4-3-5-18(22)19-11-17(25)12-20(23(19)29)34(2,32)33/h6-9,11-13,15H,3-5,10H2,1-2H3,(H,30,31)/t13-,15+/m1/s1
Release date: 2018-11-14
Crystal structure of the human METTL3-METTL14 complex with compound UOZ120 (PDB entry 7OEM)
Macromolecule: N6-adenosine-methyltransferase catalytic subunit
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1.348
Sequence length: 246 residues
Sequence: MGHHHHHHSSGRENLYFQGALTQSVGGDSSADRLFPPQWICCDIRYLDVSILGKFAVVMADPPWDIHMELPYGTLTDDEMRRLNIPVLQDDGFLFLWVTGRAMELGRECLNLWGYERVDEIIWVKTNQLQRIIRTGRTGHWLNHGKEHCLVGVKGNPQGFNQGLDCDVIVAEVRSTSHKPDEIYGMIERLSPGTRKIELFGRPHNVQPNWITLGNQLDGIHLLDPDVVARFKQRYPDGIISKPKNL
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.2
R work: 0.2066
R free: 0.2576
Average B factor: 46.55
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 295
Crystal growth procedure: 20% PEG 3350, 400mM Mg acetate
Matthews coefficient: 2.17
Solvent content (%): 43.2
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: 2021-10-20
RepoMan-PP1g (protein phosphatase 1, gamma isoform) holoenzyme complex (PDB entry 5INB)
Macromolecule: Serine/threonine-protein phosphatase PP1-gamma catalytic subunit
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.16
Sequence length: 305 residues
Sequence: GHMLNIDSIIQRLLEVRGSKPGKNVQLQENEIRGLCLKSREIFLSQPILLELEAPLKICGDIHGQYYDLLRLFEYGGFPPESNYLFLGDYVDRGKQSLETICLLLAYKIKYPENFFLLRGNHECASINRIYGFYDECKRRYNIKLWKTFTDCFNCLPIAAIVDEKIFCCHGGLSPDLQSMEQIRRIMRPTDVPDQGLLCDLLWSDPDKDVLGWGENDRGVSFTFGAEVVAKFLHKHDLDLICRAHQVVEDGYEFFAKRQLVTLFSAPNYCGEFDNAGAMMSVDETLMCSFQILKPAEKKKPNATR
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.3
R work: 0.1324
R free: 0.1534
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 4.3
Crystallization temperature (K): 277
Crystal growth procedure: 1 M Sodium Malonate
Matthews coefficient: 2.9
Solvent content (%): 57.52
Ligand: MALONATE ION (MLI)
Ligand formula: C3 H2 O4
Ligand molecular weight: 102.046
Ligand SMILES: C(C(=O)[O-])C(=O)[O-]
Ligand InChI: InChI=1S/C3H4O4/c4-2(5)1-3(6)7/h1H2,(H,4,5)(H,6,7)/p-2
Release date: 2016-10-05
BACE-1 in complex with compound #3 (PDB entry 6UVP)
Macromolecule: Beta-secretase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.23.46
Sequence length: 442 residues
Sequence: MAGVLPAHGTQHGIRLPLRSGLGGAPLGLRLPRETDEEPEEPGRRGSFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHPFLHRYYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTVRANIAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTHVPNLFSLQLCGAGFPLNQSEVLASVGGSMIIGGIDHSLYTGSLWYTPIRREWYYEVIIVRVEINGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVKSIKAASSTEKFPDGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRITILPQQYLRPVEDVATSQDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSACHVHDEFRTAAVEGPFVTLDMEDCGYNIPQTDEST
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.56
R work: 0.1378
R free: 0.1819
Average B factor: 18.445
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 277
Crystal growth procedure: 100mM Sodium Cacodylate pH 7.4, 12% PEG 8K, 200mM Ammonium Sulfate
Matthews coefficient: 2.62
Solvent content (%): 53.14
Ligand: N-{(1S,2S)-2-[(4aS,7aR)-2-amino-4a,5-dihydro-4H-furo[3,4-d][1,3]thiazin-7a(7H)-yl]cyclopropyl}-5-fluoropyridine-2-carboxamide (QJJ)
Ligand formula: C15 H17 F N4 O2 S
Ligand molecular weight: 336.384
Ligand SMILES: c1cc(ncc1F)C(=O)NC2CC2C34COCC3CSC(=N4)N
Ligand InChI: InChI=1S/C15H17FN4O2S/c16-9-1-2-11(18-4-9)13(21)19-12-3-10(12)15-7-22-5-8(15)6-23-14(17)20-15/h1-2,4,8,10,12H,3,5-7H2,(H2,17,20)(H,19,21)/t8-,10-,12-,15-/m0/s1
Release date: 2019-12-11