satarupa22/MacromolecularLigandDB huggingface dataset:
Structure of Human Neurolysin (E475Q) in complex with neurotensin peptide products (PDB entry 5LUZ)
Macromolecule: Neurolysin, mitochondrial
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.24.16
Sequence length: 686 residues
Sequence: MGSSHHHHHHSSGLVPRGSSSYTVAGRNVLRWDLSPEQIKTRTEELIVQTKQVYDAVGMLGIEEVTYENCLQALADVEVKYIVERTMLDFPQHVSSDKEVRAASTEADKRLSRFDIEMSMRGDIFERIVHLQETCDLGKIKPEARRYLEKSIKMGKRNGLHLPEQVQNEIKSMKKRMSELCIDFNKNLNEDDTFLVFSKAELGALPDDFIDSLEKTDDDKYKITLKYPHYFPVMKKCCIPETRRRMEMAFNTRCKEENTIILQQLLPLRTKVAKLLGYSTHADFVLEMNTAKSTSRVTAFLDDLSQKLKPLGEAEREFILNLKKKECKDRGFEYDGKINAWDLYYYMTQTEELKYSIDQEFLKEYFPIEVVTEGLLNTYQELLGLSFEQMTDAHVWNKSVTLYTVKDKATGEVLGQFYLDLYPREGKYNHAACFGLQPGCLLPDGSRMMAVAALVVNFSQPVAGRPSLLRHDEVRTYFHQFGHVMHQICAQTDFARFSGTNVETDFVEVPSQMLENWVWDVDSLRRLSKHYKDGSPIADDLLEKLVASRLVNTGLLTLRQIVLSKVDQSLHTNTSLDAASEYAKYCSEILGVAATPGTNMPATFGHLAGGYDGQYYGYLWSEVFSMDMFYSCFKKEGIMNPEVGMKYRNLILKPGGSLDGMDMLHNFLKREPNQKAFLMSRGLHAP
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.7
R work: 0.21558
R free: 0.26786
Average B factor: 55.723
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 294
Crystal growth procedure: 0.1M Bis-Tris-propane, 11% PEG 3350, 10% glycerol, 0.2M potassium thiocyanate
Matthews coefficient: 2.7
Solvent content (%): 54.8
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: 2017-12-06
Crystal structure of human DDX1 helicase in complex with ADP (PDB entry 8TBX)
Macromolecule: ATP-dependent RNA helicase DDX1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.4.13
Sequence length: 470 residues
Sequence: GMAAFSEMGVMPEIAQAVEEMDWLLPTDIQAESIPLILGGGDVLMAAETGSGKTGAFSIPVIQIVYETLKDQQEGSGSGSGAPKALIVEPSRELAEQTLNNIKQFKKYIDNPKLRELLIIGGVAARDQLSVLENGVDIVVGTPGRLDDLVSTGKLNLSQVRFLVLDEADGLLSQGYSDFINRMHNQIPQVTSDGKRLQVIVCSATLHSFDVKKLSEKIMHFPTWVDLKGEDSVPDTVHHVVVPVNPKTDRLWERLGKSHIRTDDVHAKDNTRPGANSPEMWSEAIKILKGEYAVRAIKEHKMDQAIIFCRTKIDCDNLEQYFIQQGGGPDKKGHQFSCVCLHGDRKPHERKQNLERFKKGDVRFLICTDVAARGIDIHGVPYVINVTLPDEKQNYVHRIGRVGRAERMGLAISLVATEKEKVWYHVCSSRGKGCYNTRLKEDGGCTIWYNEMQLLSEIEEHLNCTISQVE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.71
R work: 0.20257
R free: 0.28647
Average B factor: 47.552
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 0.04M Potassium phosphate monobasic,16%w/v PEG 8K,20% v/v Glycerol
Matthews coefficient: 2.4
Solvent content (%): 48.68
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: 2023-07-26
Human ERK2 in complex with an irreversible inhibitor (PDB entry 4ZZO)
Macromolecule: MITOGEN-ACTIVATED PROTEIN KINASE 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.24
Sequence length: 350 residues
Sequence: PEMVRGQVFDVGPRYTNLSYIGEGAYGMVCSAYDNLNKVRVAIKKISPFEHQTYCQRTLREIKILLRFRHENIIGINDIIRAPTIEQMKDVYIVQDLMETDLYKLLKTQHLSNDHICYFLYQILRGLKYIHSANVLHRDLKPSNLLLNTTCDLKICDFGLARVADPDHDHTGFLTEYVATRWYRAPEIMLNSKGYTKSIDIWSVGCILAEMLSNRPIFPGKHYLDQLNHILGILGSPSQEDLNCIINLKARNYLLSLPHKNKVPWNRLFPNADSKALDLLDKMLTFNPHKRIEVEQALAHPYLEQYYDPSDEPIAEAPFKFDMELDDLPKEKLKELIFEETARFQPGYRS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.63
R work: 0.1846
R free: 0.2373
Average B factor: 25.58
Matthews coefficient: 2.38
Solvent content (%): 48.32
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: 2015-05-27
Human N-myristoyltransferase 1 (MNT1) with Myristoyl-CoA analogue X10 bound (PDB entry 5NPQ)
Macromolecule: Glycylpeptide N-tetradecanoyltransferase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1.97
Sequence length: 391 residues
Sequence: GPHMEEASKRSYQFWDTQPVPKLGEVVNTHGPVEPDKDNIRQEPYTLPQGFTWDALDLGDRGVLKELYTLLNENYVEDDDNMFRFDYSPEFLLWALRPPGWLPQWHCGVRVVSSRKLVGFISAIPANIHIYDTEKKMVEINFLCVHKKLRSKRVAPVLIREITRRVHLEGIFQAVYTAGVVLPKPVGTCRYWHRSLNPRKLIEVKFSHLSRNMTMQRTMKLYRLPETPKTAGLRPMETKDIPVVHQLLTRYLKQFHLTPVMSQEEVEHWFYPQENIIDTFVVENANGEVTDFLSFYTLPSTIMNHPTHKSLKAAYSFYNVHTQTPLLDLMSDALVLAKMKGFDVFNALDLMENKTFLEKLKFGIGDGNLQYYLYNWKCPSMGAEKVGLVLQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.372
R work: 0.1991
R free: 0.2606
Average B factor: 34.6127
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 4.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M NaCit pH 4.5, 5mM NiCl2, 2.5% glycerol and PEG 4K 18%
Protein concentration: 7.05 mg/ml
Matthews coefficient: 2.27
Solvent content (%): 45.89
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: 2018-05-30
Structure of the FK1 domain of the FKBP51 G64S variant in complex with SAFit1 (PDB entry 7R0L)
Macromolecule: Peptidyl-prolyl cis-trans isomerase FKBP5
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 5.2.1.8
Sequence length: 128 residues
Sequence: GAPATVTEQGEDITSKKDRGVLKIVKRVGNGEETPMIGDKVYVHYKGKLSNSKKFDSSHDRNEPFVFSLGKGQVIKAWDIGVATMKKGEIAHLLIKPEYAYGSAGSLPKIPSNATLFFEIELLDFKGE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.1
R work: 0.1431
R free: 0.1706
Average B factor: 15.762
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: 12% PEG3350, 0.2 M NH4-acetate and HEPES-NaOH pH 7.5
Matthews coefficient: 2.23
Solvent content (%): 44.92
Ligand: 2-[3-[(1~{R})-1-[(2~{S})-1-[(2~{S})-2-cyclohexyl-2-(3,4,5-trimethoxyphenyl)ethanoyl]piperidin-2-yl]carbonyloxy-3-(3,4-dimethoxyphenyl)propyl]phenoxy]ethanoic acid (GY1)
Ligand formula: C42 H53 N O11
Ligand molecular weight: 747.87
Ligand SMILES: COc1ccc(cc1OC)CCC(c2cccc(c2)OCC(=O)O)OC(=O)C3CCCCN3C(=O)C(c4cc(c(c(c4)OC)OC)OC)C5CCCCC5
Ligand InChI: InChI=1S/C42H53NO11/c1-48-34-20-18-27(22-35(34)49-2)17-19-33(29-14-11-15-31(23-29)53-26-38(44)45)54-42(47)32-16-9-10-21-43(32)41(46)39(28-12-7-6-8-13-28)30-24-36(50-3)40(52-5)37(25-30)51-4/h11,14-15,18,20,22-25,28,32-33,39H,6-10,12-13,16-17,19,21,26H2,1-5H3,(H,44,45)/t32-,33+,39-/m0/s1
Release date: 2022-11-16
Crystal structure of Jak3 complexed to N-[3-(6-Phenylamino-pyrazin-2-yl)-3H-benzoimidazol-5-yl]-acrylamide (PDB entry 4QPS)
Macromolecule: Tyrosine-protein kinase JAK3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 293 residues
Sequence: CQDPTIFEERHLKYISQLGKGNFGSVELCRYDPLGDNTGALVAVKQLQHSGPDQQRDFQREIQILKALHSDFIVKYRGVSYGPGRQSLRLVMEYLPSGCLRDFLQRHRARLDASRLLLYSSQICKGMEYLGSRRCVHRALAARNILVESEAHVKIADFGLAKLLPLDKDYYVVREPGQSPIFWYAPESLSDNIFSRQSDVWSFGVVLYELFTYCDKSCSPSAEFLRMMGSERDVPALSRLLELLEEGQRLPAPPACPAEVHELMKLCWAPSPQDRPSFSALGPQLDMLWSGSR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.2074
R free: 0.2509
Average B factor: 29.7
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 5.5
Crystallization temperature (K): 291
Crystal growth procedure: 25% PEG-3350, 0.2 M ammonium sulfate and 0.1 M BisTRIS pH 5.5, VAPOR DIFFUSION, temperature 291K
Matthews coefficient: 1.93
Solvent content (%): 36.43
Ligand: N-{1-[6-(phenylamino)pyrazin-2-yl]-1H-benzimidazol-6-yl}prop-2-enamide (37Q)
Ligand formula: C20 H16 N6 O
Ligand molecular weight: 356.381
Ligand SMILES: C=CC(=O)Nc1ccc2c(c1)n(cn2)c3cncc(n3)Nc4ccccc4
Ligand InChI: InChI=1S/C20H16N6O/c1-2-20(27)24-15-8-9-16-17(10-15)26(13-22-16)19-12-21-11-18(25-19)23-14-6-4-3-5-7-14/h2-13H,1H2,(H,23,25)(H,24,27)
Release date: 2015-01-14
Ternary complex of human DNA polymerase eta inserting rATP opposite an 8-Oxodeoxyguanosine Lesion (PDB entry 5EWG)
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): 1.75
R work: 0.1781
R free: 0.215
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6
Crystallization temperature (K): 291
Crystal growth procedure: NaMES (pH 6.0), polyethylene glycol monomethyl ether 2000, and calcium chloride
Matthews coefficient: 2.11
Solvent content (%): 41.7
Ligand: ADENOSINE-5'-TRIPHOSPHATE (ATP)
Ligand formula: C10 H16 N5 O13 P3
Ligand molecular weight: 507.181
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N
Ligand InChI: InChI=1S/C10H16N5O13P3/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(26-10)1-25-30(21,22)28-31(23,24)27-29(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H,23,24)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
Release date: 2016-01-13
A Structurally Dynamic N-terminal Region Drives Function of the Staphylococcal Peroxidase Inhibitor (SPIN) (PDB entry 6AZP)
Macromolecule: Myeloperoxidase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.11.2.2
Sequence length: 577 residues
Sequence: CPEQDKYRTITGMCNNRRSPTLGASNRAFVRWLPAEYEDGFSLPYGWTPGVKRNGFPVALARAVSNEIVRFPTDQLTPDQERSLMFMQWGQLLDHDLDFTPEPAARASFVTGVNCETSCVQQPPCFPLKIPPNDPRIKNQADCIPFFRSCPACPGSNITIRNQINALTSFVDASMVYGSEEPLARNLRNMSNQLGLLAVNQRFQDNGRALLPFDNLHDDPCLLTNRSARIPCFLAGDTRSSEMPELTSMHTLLLREHNRLATELKSLNPRWDGERLYQEARKIVGAMVQIITYRDYLPLVLGPTAMRKYLPTYRSYNDSVDPRIANVFTNAFRYGHTLIQPFMFRLDNRYQPMEPNPRVPLSRVFFASWRVVLEGGIDPILRGLMATPAKLNRQNQIAVDEIRERLFEQVMRIGLDLPALNMQRSRDHGLPGYNAWRRFCGLPQPETVGQLGTVLRNLKLARKLMEQYGTPNNIDIWMGGVSEPLKRKGRVGPLLACIIGTQFRKLRDGDRFWWENEGVFSMQQRQALAQISLPRIICDNTGITTVSKNNIFMSNSYPRDFVNCSTLPALNLASWRE
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.291
R work: 0.179
R free: 0.2291
Average B factor: 42.0145
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7
Crystallization temperature (K): 298
Crystal growth procedure: 20% w/v PEG3350, 0.2 M ammonium citrate, pH 7.0
Matthews coefficient: 2.88
Solvent content (%): 57.33
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: 2017-12-27
The co-crystal structure of DYRK2 with a small molecule inhibitor 5 (PDB entry 7DH3)
Macromolecule: Dual specificity tyrosine-phosphorylation-regulated kinase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.12.1
Sequence length: 326 residues
Sequence: VPHDHVAYRYEVLKVIGKGSFGQVVKAYDHKVHQHVALKMVRNEKRFHRQAAEEIRILEHLRKQDKDNTMNVIHMLENFTFRNHICMTFELLSMNLYELIKKNKFQGFSLPLVRKFAHSILQCLDALHKNRIIHCDLKPENILLKQQGRSGIKVIDFGSSCYEHQRVYTYIQSRFYRAPEVILGARYGMPIDMWSLGCILAELLTGYPLLPGEDEGDQLACMIELLGMPSQKLLDASKRAKNFVSSKGYPRYCTVTTLSDGSVVLNGGRSRRGKLRGPPESREWGNALKGCDDPLFLDFLKQCLEWDPAVRMTPGQALRHPWLRRR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.33
R work: 0.1938
R free: 0.2172
Average B factor: 56.1622
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 0.36 M-0.5 M sodium citrate tribasic dehydrate, 0.01 M sodium borate, pH 7.5-9.5
Matthews coefficient: 3.62
Solvent content (%): 66.06
Ligand: 2,7-dimethoxy-9-piperidin-4-ylsulfanyl-acridine (H7C)
Ligand formula: C20 H22 N2 O2 S
Ligand molecular weight: 354.466
Ligand SMILES: COc1ccc2c(c1)c(c3cc(ccc3n2)OC)SC4CCNCC4
Ligand InChI: InChI=1S/C20H22N2O2S/c1-23-13-3-5-18-16(11-13)20(25-15-7-9-21-10-8-15)17-12-14(24-2)4-6-19(17)22-18/h3-6,11-12,15,21H,7-10H2,1-2H3
Release date: 2021-11-17
PanDDA analysis group deposition of models with modelled events (e.g. bound ligands) -- Crystal Structure of HAO1 in complex with Z2856434894 (PDB entry 5QIE)
Macromolecule: Hydroxyacid oxidase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.1.3.15
Sequence length: 369 residues
Sequence: SMLPRLICINDYEQHAKSVLPKSIYDYYRSGANDEETLADNIAAFSRWKLYPRMLRNVAETDLSTSVLGQRVSMPICVGATAMQRMAHVDGELATVRACQSLGTGMMLSSWATSSIEEVAEAGPEALRWLQLYIYKDREVTKKLVRQAEKMGYKAIFVTVDTPYLGNRLDDVRNRFKLPPQLRMKNFETSTLSFSPEENFGDDSGLAAYVAKAIDPSISWEDIKWLRRLTSLPIVAKGILRGDDAREAVKHGLNGILVSNHGARQLDGVPATIDVLPEIVEAVEGKVEVFLDGGVRKGTDVLKALALGAKAVFVGRPIVWGLAFQGEKGVQDVLEILKEEFRLAMALSGCQNVKVIDKTLVRKNPLAVS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.34
R work: 0.1648
R free: 0.1927
Average B factor: 17.532
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.75
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M MIB pH 5.75 - 7.0, 27.5-35% PEG1000
Matthews coefficient: 2.35
Solvent content (%): 47.64
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: 2018-07-18
BTK complex with compound 13 (PDB entry 6BLN)
Macromolecule: Tyrosine-protein kinase BTK
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 287 residues
Sequence: MGSWEIDPKDLTFLKELGTGQFGVVKYGKWRGQYDVAIKMIKEGSMSEDEFIEEAKVMMNLSHEKLVQLYGVCTKQRPIFIITEYMANGCLLNYLREMRHRFQTQQLLEMCKDVCEAMEYLESKQFLHRDLAARNCLVNDQGVVKVSDFGLSRYVLDDEYTSSVGSKFPVRWSPPEVLMYSKFSSKSDIWAFGVLMWEIYSLGKMPYERFTNSETAEHIAQGLRLYRPHLASEKVYTIMYSCWHEKADERPTFKILLSNILDVMDENLYFQGEEYMPTEHHHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.3
R work: 0.156
R free: 0.1764
Average B factor: 23.8356
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 277
Crystal growth procedure: PEG 10000, Li2SO4, pH 7.0
Matthews coefficient: 2.07
Solvent content (%): 40.68
Ligand: N-(3-{5-[(1,5-dimethyl-1H-pyrazol-3-yl)amino]-6-oxo-1,6-dihydropyridazin-3-yl}-2,6-difluorophenyl)-4,5,6,7-tetrahydro-1-benzothiophene-2-carboxamide (DY4)
Ligand formula: C24 H22 F2 N6 O2 S
Ligand molecular weight: 496.532
Ligand SMILES: Cc1cc(nn1C)NC2=CC(=NNC2=O)c3ccc(c(c3F)NC(=O)c4cc5c(s4)CCCC5)F
Ligand InChI: InChI=1S/C24H22F2N6O2S/c1-12-9-20(31-32(12)2)27-17-11-16(29-30-23(17)33)14-7-8-15(25)22(21(14)26)28-24(34)19-10-13-5-3-4-6-18(13)35-19/h7-11H,3-6H2,1-2H3,(H,28,34)(H,30,33)(H,27,29,31)
Release date: 2018-11-07
Y271G DNA polymerase beta substrate complex with templating cytosine and incoming r8-oxo-GTP (PDB entry 6UOK)
Macromolecule: DNA (5'-D(*CP*CP*GP*AP*CP*CP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')
Type: DNA, polydeoxyribonucleotide
Source organism: synthetic construct
Sequence length: 16 residues
Sequence: CCGACCGCGCATCAGC
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.55
R work: 0.2243
R free: 0.2787
Average B factor: 43.09
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8
Crystallization temperature (K): 291
Crystal growth procedure: 19% PEG3350, 0.05M Imidazole (pH 8.0), 0.35 Sodium Acetate
Matthews coefficient: 2.36
Solvent content (%): 47.92
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: 2020-01-08
Crystal structure of human NEIL1(R242, Y244R) bound to duplex DNA containing 2'-fluoro-2'-deoxy-5,6-dihydrouridine (PDB entry 6LWP)
Macromolecule: Endonuclease 8-like 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.2.2
Sequence length: 295 residues
Sequence: MPEGPELHLASQFVNEACRALVFGGCVEKSSVSRNPEVPFESSAYRISASARGKELRLILSPLPGAQPQQEPLALVFRFGMSGSFQLVPREELPRHAHLRFYTAPPGPRLALCFVDIRRFGRWDLGGKWQPGRGPCVLQEYQQFRENVLRNLADKAFDRPICEALLDQRFFNGIGNYLRAEILYRLKIPPFEKARSVLEALQQHRPSPELTLSQKIRTKLQNPDLLELCHSVPKEVVQLGGRGRGSESGEEDFAAFRAWLRCYGMPGMSSLQDRHGRTIWFQGDPGPLAPKGRKS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.64
R work: 0.2034
R free: 0.2319
Average B factor: 81.84
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 277.15
Crystal growth procedure: 0.1 M cacodylic acid (pH 6.5), 0.1 M NaCl, 0.05 M MgCl2 and 18% (w/v) PEG 8000
Matthews coefficient: 2.82
Solvent content (%): 56.32
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: 2021-06-09
Co-crystal structure of KRIT1 with a 1-hydroxy 2-naphthaldehyde derivative (6-(furan-2-yl)-2-hydroxy-1-naphthaldehyde). (PDB entry 8SU8)
Macromolecule: Krev interaction trapped protein 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 318 residues
Sequence: YEKVRIYRMDGSYRSVELKHGNNTTVQQIMEGMRLSQETQQYFTIWICSENLSLQLKPYHKPLQHVRDWPEILAELTNLDPQRETPQLFLRRDVRLPLEVEKQIEDPLAILILFDEARYNLLKGFYTAPDAKLITLASLLLQIVYGNYESKKHKQGFLNEENLKSIVPVTKLKSKAPHWTNRILHEYKNLSTSEGVSKEMHHLQRMFLQNCWEIPTYGAAFFTGQIFTKASPSNHKVIPVYVGVNIKGLHLLNMETKALLISLKYGCFMWQLGDTDTCFQIHSMENKMSFIVHTKQAGLVVKLLMKLNGQLMPTERNS
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.01
R work: 0.2043
R free: 0.2381
Average B factor: 46.73
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 293
Crystal growth procedure: 20% PEG 3350, 100 mM Tris, pH 8.5, 100 mM KCl
Matthews coefficient: 2.32
Solvent content (%): 47.06
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
CRYSTAL STRUCTURE OF CATHEPSIN K WITH N-DESMETHYL THALASSOSPIRAMIDE C (PDB entry 6HGY)
Macromolecule: Cathepsin K
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.22.38
Sequence length: 215 residues
Sequence: APDSVDYRKKGYVTPVKNQGQCGSCWAFSSVGALEGQLKKKTGKLLNLSPQNLVDCVSENDGCGGGYMTNAFQYVQKNRGIDSEDAYPYVGQEESCMYNPTGKAAKCRGYREIPEGNEKALKRAVARVGPVSVAIDASLTSFQFYSKGVYYDESCNSDNLNHAVLAVGYGIQKGNKHWIIKNSWGENWGNKGYILMARNKNNACGIANLASFPKM
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.2
R work: 0.25006
R free: 0.30996
Average B factor: 40.45
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 277
Crystal growth procedure: 0.05M MES pH 6.0, 0.1M Na-Oxalate, 0.1M CaCl2
Matthews coefficient: 1.9
Solvent content (%): 35.33
Ligand: THALASSOSPIRAMIDE C (G4B)
Ligand formula: C43 H61 N5 O9
Ligand molecular weight: 791.973
Ligand SMILES: CCCCCCC=CCC(=O)NC(Cc1ccc(cc1)O)C(=O)NC(C(C)C)C(=O)NC2CCC(=O)NC(C(=O)NC(C(=O)OC2)Cc3ccc(cc3)O)C(C)C
Ligand InChI: InChI=1S/C43H61N5O9/c1-6-7-8-9-10-11-12-13-36(51)45-34(24-29-14-19-32(49)20-15-29)40(53)48-39(28(4)5)41(54)44-31-18-23-37(52)47-38(27(2)3)42(55)46-35(43(56)57-26-31)25-30-16-21-33(50)22-17-30/h11-12,14-17,19-22,27-28,31,34-35,38-39,49-50H,6-10,13,18,23-26H2,1-5H3,(H,44,54)(H,45,51)(H,46,55)(H,47,52)(H,48,53)/b12-11-/t31-,34+,35+,38+,39+/m1/s1
Release date: 2019-06-26
Crystal Structure of JAK1 in complex with compound 25 (PDB entry 6BBU)
Macromolecule: Tyrosine-protein kinase JAK1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 316 residues
Sequence: GSIMRDINKLEEQNPDIVSEKKPATEVDPTHFEKRFLKRIRDLGEGHFGKVELCRYDPEGDNTGEQVAVKSLKPESGGNHIADLKKEIEILRNLYHENIVKYKGICTEDGGNGIKLIMEFLPSGSLKEYLPKNKNKINLKQQLKYAVQICKGMDYLGSRQYVHRDLAARNVLVESEHQVKIGDFGLTKAIETDKEYYTVKDDRDSPVFWYAPECLMQSKFYIASDVWSFGVTLHELLTYCDSDSSPMALFLKMIGPTHGQMTVTRLVNTLKEGKRLPCPPNCPDEVYQLMRKCWEFQPSNRTSFQNLIEGFEALLK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.08
R work: 0.1829
R free: 0.2135
Average B factor: 44.45
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 281
Crystal growth procedure: 250mM NaCl, 5mM TCEP, 10 mM ATP, 10 mM MgCl2, 30% PEG1500, 8% MPD, 0.1M Tris pH 9.0
Matthews coefficient: 2.05
Solvent content (%): 40.15
Ligand: N-{cis-3-[methyl(7H-pyrrolo[2,3-d]pyrimidin-4-yl)amino]cyclobutyl}propane-1-sulfonamide (D7D)
Ligand formula: C14 H21 N5 O2 S
Ligand molecular weight: 323.414
Ligand SMILES: CCCS(=O)(=O)NC1CC(C1)N(C)c2c3cc[nH]c3ncn2
Ligand InChI: InChI=1S/C14H21N5O2S/c1-3-6-22(20,21)18-10-7-11(8-10)19(2)14-12-4-5-15-13(12)16-9-17-14/h4-5,9-11,18H,3,6-8H2,1-2H3,(H,15,16,17)/t10-,11+
Release date: 2018-01-17
Structure of MLK4 kinase domain with ATPgammaS (PDB entry 4UYA)
Macromolecule: MITOGEN-ACTIVATED PROTEIN KINASE KINASE KINASE MLK4
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.25
Sequence length: 340 residues
Sequence: MGHHHHHHGGGENLYFQGSPVHVAFERLELKELIGAGGFGQVYRATWQGQEVAVKAARQDPEQDAAAAAESVRREARLFAMLRHPNIIELRGVCLQQPHLCLVLEFARGGALNRALAGRRIPPHVLVNWAVQIARGMLYLHEEAFVPILHRDLKSSNILLLEKIEHDDICNKTLKITDFGLAREWHRTTKMATAGAYAWMAPEVIKSSLFSKGSDIWSYGVLLWELLTGEVPYRGIDGLAVAYGVAVNKLTLPIPSTCPEPFAKLMKECWQQDPHIRPSFALILEQLTAIEGAVMTEMPQESFHSMQDDWKLEIQQMFDELRTKEKELRSREEELTRAAL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.8
R work: 0.2011
R free: 0.2606
Average B factor: 82.07
Matthews coefficient: 2.37
Solvent content (%): 47.71
Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER (AGS)
Ligand formula: C10 H16 N5 O12 P3 S
Ligand molecular weight: 523.247
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=S)(O)O)O)O)N
Ligand InChI: InChI=1S/C10H16N5O12P3S/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(25-10)1-24-28(18,19)26-29(20,21)27-30(22,23)31/h2-4,6-7,10,16-17H,1H2,(H,18,19)(H,20,21)(H2,11,12,13)(H2,22,23,31)/t4-,6-,7-,10-/m1/s1
Release date: 2015-09-30
Crystal structure of human APOBEC3B N-terminal Domain (PDB entry 5TKM)
Macromolecule: DNA dC->dU-editing enzyme APOBEC-3B
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.5.4
Sequence length: 198 residues
Sequence: GPGGSGGMNPQIRNPMERMDRDTFYDNFENEPILSGRSYTWLCYEVKIKRGRSNLLWDTGVFRGQVYFKPQYHAEMCFLSWFCGNQLPADKCFQITWFVSWTPCPDCVAKLAEFLSEHPNVTLTISAARLYYYSERDYRRALCRLSQAGARVKIMDYEEFAYCWENFVDNEGQQFMPWYKFDENYAFLHRTLKEILRH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.9
R work: 0.1877
R free: 0.2027
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.6
Crystallization temperature (K): 291
Crystal growth procedure: 0.01 M Iron (III) chloride hexahydrate, 0.1 M sodium citrate dehydrate pH 5.6, 10% v/v Jeffamine M-600
Matthews coefficient: 2.23
Solvent content (%): 44.77
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: 2017-06-14