satarupa22/MacromolecularLigandDB huggingface dataset:
Kinetic and Structural Changes in HsmtPheRS, Induced by Pathogenic Mutations in Human FARS2 (PDB entry 5MGV)
Macromolecule: Phenylalanine--tRNA ligase, mitochondrial
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 6.1.1.20
Sequence length: 405 residues
Sequence: PGSVVELLGKSYPQDDHSNLTRKVLTRVGRNLHNQQHHPLWLIKERVKEHFYKQYVGRFGTPLFSVYDNLSPVVTTWQNFDSLLIPADHPSRKKGDNYYLNRTHMLRAHTSAHQWDLLHAGLDAFLVVGDVYRRDQIDSQHYPIFHQLEAVRLFSKHELFAGIKDGESLQLFEQSSRSAHKQETHTMEAVKLVEFDLKQTLTRLMAHLFGDELEIRWVDCYFPFTHPSFEMEINFHGEWLEVLGCGVMEQQLVNSAGAQDRIGWAFGLGLERLAMILYYIPDIRLFWCEDERFLKQFCVSNINQKVKFQPLSKYPAVINDISFWLPSENYAENDFYDLVRTIGGDLVEKVDLIDKFVHPKTHKTSHCYRITYRHMERTLSQREVRHIHQALQEAAVQLLGVEGRF
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.05
R work: 0.2275
R free: 0.2711
Average B factor: 31.0362
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 292
Crystal growth procedure: 2 mM DTT, 100 mM bis-Tris propane pH 7 and 1.8 M sodium acetate pH 7
Matthews coefficient: 2.48
Solvent content (%): 50.37
Release date: 2017-05-03
PTP1B 1-284 F225Y-R199N in complex with TCS401 (PDB entry 7MNA)
Macromolecule: Tyrosine-protein phosphatase non-receptor type 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 289 residues
Sequence: GHMASMEMEKEFEQIDKSGSWAAIYQDIRHEASDFPCRVAKLPKNKNRNRYRDVSPFDHSRIKLHQEDNDYINASLIKMEEAQRSYILTQGPLPNTCGHFWEMVWEQKSRGVVMLNRVMEKGSLKCAQYWPQKEEKEMIFEDTNLKLTLISEDIKSYYTVRQLELENLTTQETREILHFHYTTWPDFGVPESPASFLNFLFKVNESGSLSPEHGPVVVHCSAGIGRSGTYCLADTCLLLMDKRKDPSSVDIKKVLLEMRKFRMGLIQTADQLRFSYLAVIEGAKFIMGD
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.47
R work: 0.1698
R free: 0.1941
Average B factor: 22.67
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 0.1 M Tris pH 7.4, 0.2 M MgCl2, 16% PEG
Matthews coefficient: 2.41
Solvent content (%): 48.99
Ligand: 2-(OXALYL-AMINO)-4,5,6,7-TETRAHYDRO-THIENO[2,3-C]PYRIDINE-3-CARBOXYLIC ACID (OTA)
Ligand formula: C10 H10 N2 O5 S
Ligand molecular weight: 270.262
Ligand SMILES: C1CNCc2c1c(c(s2)NC(=O)C(=O)O)C(=O)O
Ligand InChI: InChI=1S/C10H10N2O5S/c13-7(10(16)17)12-8-6(9(14)15)4-1-2-11-3-5(4)18-8/h11H,1-3H2,(H,12,13)(H,14,15)(H,16,17)
Release date: 2022-05-18
Crystal structure of PDGFRA in Complex with WQ-C-159 (PDB entry 5GRN)
Macromolecule: Platelet-derived growth factor receptor alpha
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 356 residues
Sequence: GAMDKQKPRYEIRWRVIESISPDGHEYIYVDPMQLPYDSRWEFPRDGLVLGRVLGSGAFGKVVEGTAYGLSRSQPVMKVAVKMLKPTARSSEKQALMSELKIMTHLGPHLNIVNLLGACTKSGPIYIITEYCFYGDLVNYLHKNRDSFLSHKKKSMLDSEVKNLLSDDNSEGLTLLDLLSFTYQVARGMEFLASKNCVHRDLAARNVLLAQGKIVKICDFGLARDIMHDSNYVSKGSTFLPVKWMAPESIFDNLYTTLSDVWSYGILLWEIFSLGGTPYPGMMVDSTFYNKIKSGYRMAKPDHATSEVYEIMVKCWNSEPEKRPSFYHLSEIVENLLPGQYKKSYEKIHLDFLKSD
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.77
R work: 0.157
R free: 0.1793
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.2M KCl, 20% PEG 3350, pH 7.0
Matthews coefficient: 1.61
Solvent content (%): 23.71
Ligand: N-[2-(dimethylamino)ethyl]-N-[[4-[[4-methyl-3-[(4-pyridin-3-ylpyrimidin-2-yl)amino]phenyl]carbamoyl]phenyl]methyl]pyridine-3-carboxamide (748)
Ligand formula: C34 H34 N8 O2
Ligand molecular weight: 586.686
Ligand SMILES: Cc1ccc(cc1Nc2nccc(n2)c3cccnc3)NC(=O)c4ccc(cc4)CN(CCN(C)C)C(=O)c5cccnc5
Ligand InChI: InChI=1S/C34H34N8O2/c1-24-8-13-29(20-31(24)40-34-37-17-14-30(39-34)27-6-4-15-35-21-27)38-32(43)26-11-9-25(10-12-26)23-42(19-18-41(2)3)33(44)28-7-5-16-36-22-28/h4-17,20-22H,18-19,23H2,1-3H3,(H,38,43)(H,37,39,40)
Release date: 2017-08-16
Crystal structure of the catalytic domain of human JARID1B in complex with 3D fragment 2-(2-oxo-2,3-dihydro-1H-indol-3-yl)acetonitrile (N10063a) (PDB entry 5FYZ)
Macromolecule: LYSINE-SPECIFIC DEMETHYLASE 5B
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11
Sequence length: 479 residues
Sequence: SMFLPPPECPVFEPSWEEFADPFAFIHKIRPIAEQTGICKVRPPPDWQPPFACDVDKLHFTPRIQRLNELEAQTRVKLGGGGARDYTLRTFGEMADAFKSDYFNMPVHMVPTELVEKEFWRLVSTIEEDVTVEYGADIASKEFGSGFPVRDGKIKLSPEEEEYLDSGWNLNNMPVMEQSVLAHITADICGMKLPWLYVGMCFSSFCWHIEDHWSYSINYLHWGEPKTWYGVPGYAAEQLENVMKKLAPELFVSQPDLLHQLVTIMNPNTLMTHEVPVYRTNQCAGEFVITFPRAYHSGFNQGFNFAEAVNFCTVDWLPLGRQCVEHYRLLHRYCVFSHDEMICKMASKADVLDVVVASTVQKDMAIMIEDEKALRETVRKLGVIDSERMDFELLPDDERQCVKCKTTCFMSAISCSCKPGLLVCLHHVKELCSCPPYKYKLRYRYTLDDLYPMMNALKLRAESYNEWALNVNEALEAKI
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.75
R work: 0.2015
R free: 0.2309
Crystallization pH: 7.5
Crystal growth procedure: 0.1M HEPES PH 7.5 -- 0.8M POTASSIUM PHOSPHATE DIBASIC -- 0.8M SODIUM PHOSPHATE MONOBASIC
Matthews coefficient: 2.11
Solvent content (%): 41.62
Ligand: ZINC ION (ZN)
Ligand formula: Zn
Ligand molecular weight: 65.409
Ligand SMILES: [Zn+2]
Ligand InChI: InChI=1S/Zn/q+2
Release date: 2016-03-23
TGF-BETA RECEPTOR TYPE 2 KINASE DOMAIN (E431A,R433A,E485A,K488A,R493A,R495A) (PDB entry 5E8V)
Macromolecule: TGF-beta receptor type-2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.30
Sequence length: 316 residues
Sequence: GHMHNTELLPIELDTLVGKGRFAEVYKAKLKQNTSEQFETVAVKIFPYEEYASWKTEKDIFSDINLKHENILQFLTAEERKTELGKQYWLITAFHAKGNLQEYLTRHVISWEDLRKLGSSLARGIAHLHSDHTPCGRPKMPIVHRDLKSSNILVKNDLTCCLCDFGLSLRLDPTLSVDDLANSGQVGTARYMAPEVLASAMNLENVESFKQTDVYSMALVLWEMTSRCNAVGEVKDYEPPFGSKVREHPCVASMADNVLADAGRPEIPSFWLNHQGIQMVCETLTECWDHDPEARLTAQCVAERFSELEHLDRLSG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.69
R work: 0.1926
R free: 0.2194
Average B factor: 31.25
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 277
Crystal growth procedure: 100 mm TRIS-HCl, PH 8.5, 150 mm MgCl2, 24%(w/v) PEG4000, 20%(v/v) glcyerol
Matthews coefficient: 2.53
Solvent content (%): 51.44
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: 2016-05-11
The ATAD2 bromodomain in complex with compound UZH-DU32 (PDB entry 6EPW)
Macromolecule: ATPase family AAA domain-containing protein 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.1.3
Sequence length: 130 residues
Sequence: SMQEEDTFRELRIFLRNVTHRLAIDKRFRVFTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLRDIDLICSNALEYNPDRDPGDRLIRHRACALRDTAYAIIKEELDEDFEQLCEEIQESR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.924
R work: 0.2227
R free: 0.2429
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 2M ammonium sulfate, 0.1M Bis-Tris pH 5.5
Matthews coefficient: 4.08
Solvent content (%): 69.86
Ligand: (2~{R})-~{N}-[5-[3,5-bis(oxidanyl)phenyl]-4-ethanoyl-1,3-thiazol-2-yl]-2-carbamimidamido-propanamide (BQ8)
Ligand formula: C15 H17 N5 O4 S
Ligand molecular weight: 363.392
Ligand SMILES: CC(C(=O)Nc1nc(c(s1)c2cc(cc(c2)O)O)C(=O)C)NC(=N)N
Ligand InChI: InChI=1S/C15H17N5O4S/c1-6(18-14(16)17)13(24)20-15-19-11(7(2)21)12(25-15)8-3-9(22)5-10(23)4-8/h3-6,22-23H,1-2H3,(H4,16,17,18)(H,19,20,24)/t6-/m1/s1
Release date: 2018-10-31
Crystal structure of a transition-state mimic of the GSK-3/Axin complex bound to a beta-catenin S45D peptide (PDB entry 8VMF)
Macromolecule: Glycogen synthase kinase-3 beta
Type: Protein, polypeptide(L)
Source organism: Mus musculus
EC number: 2.7.11.26
Sequence length: 364 residues
Sequence: MKVSRDKDGSKVTTVVATPGQGPDRPQEVSYTDTKVIGNGSFGVVYQAKLCDSGELVAIKKVLQDKRFKNRELQIMRKLDHCNIVRLRYFFYSSGEKKDEVYLNLVLDYVPETVYRVARHYSRAKQTLPVIYVKLYMYQLFRSLAYIHSFGICHRDIKPQNLLLDPDTAVLKLCDFGSAKQLVRGEPNVSYICSRYYRAPELIFGATDYTSSIDVWSAGCVLAELLLGQPIFPGDSGVDQLVEIIKVLGTPTREQIREMNPNYTEFKFPQIKAHPWTKVFRPRTPPEAIALCSRLLEYTPTARLTPLEACAHSFFDELRDPNVKLPNGRDTPALFNFTTQELSSNPPLATILIPPHARHHHHHH
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.5
R work: 0.2091
R free: 0.2506
Average B factor: 68.34
Crystallization method: MICRODIALYSIS
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 10% PEG35000, 20 mM Tris, pH 7.5, 300 mM sodium chloride, 5% glycerol, 10 mM magnesium chloride, 5 mM DTT, 200 uM ADP, 200 uM aluminum nitrate, 1.2 mM sodium fluoride
Matthews coefficient: 2.92
Solvent content (%): 57.89
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: 2024-08-28
MTH1 in complex with TH001969 (PDB entry 8A07)
Macromolecule: 7,8-dihydro-8-oxoguanine triphosphatase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.1.55
Sequence length: 159 residues
Sequence: GSHMGASRLYTLVLVLQPQRVLLGMKKRGFGAGRWNGFGGKVQEGETIEDGARRELQEESGLTVDALHKVGQIVFEFVGEPELMDVHVFCTDSIQGTPVESDEMRPCWFQLDQIPFKDMWPDDSYWFPLLLQKKKFHGYFKFQGQDTILDYTLREVDTV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.19
R work: 0.23556
R free: 0.29185
Average B factor: 26.168
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 292
Crystal growth procedure: 0.2 M lithium sulfate, 0.1 M sodium acetate trihydrate pH 3.5, 32 % PEG6000
Matthews coefficient: 2.2
Solvent content (%): 44.09
Ligand: 1~{H}-quinazoline-2,4-dione (L3N)
Ligand formula: C8 H6 N2 O2
Ligand molecular weight: 162.145
Ligand SMILES: c1ccc2c(c1)C(=O)NC(=O)N2
Ligand InChI: InChI=1S/C8H6N2O2/c11-7-5-3-1-2-4-6(5)9-8(12)10-7/h1-4H,(H2,9,10,11,12)
Release date: 2023-09-13
Crystal structure of the human N-acetyl-alpha-glucosaminidase (PDB entry 4XWH)
Macromolecule: Alpha-N-acetylglucosaminidase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.2.1.50
Sequence length: 720 residues
Sequence: DEAREAAAVRALVARLLGPGPAADFSVSVERALAAKPGLDTYSLGGGGAARVRVRGSTGVAAAAGLHRYLRDFCGCHVAWSGSQLRLPRPLPAVPGELTEATPNRYRYYQNVCTQSYSFVWWDWARWEREIDWMALNGINLALAWSGQEAIWQRVYLALGLTQAEINEFFTGPAFLAWGRMGNLHTWDGPLPPSWHIKQLYLQHRVLDQMRSFGMTPVLPAFAGHVPEAVTRVFPQVNVTKMGSWGHFNCSYSCSFLLAPEDPIFPIIGSLFLRELIKEFGTDHIYGADTFNEMQPPSSEPSYLAAATTAVYEAMTAVDTEAVWLLQGWLFQHQPQFWGPAQIRAVLGAVPRGRLLVLDLFAESQPVYTRTASFQGQPFIWCMLHNFGGNHGLFGALEAVNGGPEAARLFPNSTMVGTGMAPEGISQNEVVYSLMAELGWRKDPVPDLAAWVTSFAARRYGVSHPDAGAAWRLLLRSVYNCSGEACRGHNRSPLVRRPSLQMNTSIWYNRSDVFEAWRLLLTSAPSLATSPAFRYDLLDLTRQAVQELVSLYYEEARSAYLSKELASLLRAGGVLAYELLPALDEVLASDSRFLLGSWLEQARAAAVSEAEADFYEQNSRYQLTLWGPEGNILDYANKQLAGLVANYYTPRWRLFLEALVDSVAQGIPFQQHQFDKNVFQLEQAFVLSKQRYPSQPRGDTVDLAKKIFLKYYPRWVAGSW
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.32
R work: 0.16591
R free: 0.18579
Average B factor: 53.533
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 291
Crystal growth procedure: 1.0 M lithium sulfate, 0.01 M nickel chloride, 0.1 M Tris
Matthews coefficient: 5.94
Solvent content (%): 79.3
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: 2016-02-03
Structure of DYRK1A in complex with compound 56 (PDB entry 7AKB)
Macromolecule: Dual specificity tyrosine-phosphorylation-regulated kinase 1A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.12.1
Sequence length: 359 residues
Sequence: MGSSHHHHHHSSGLVPRGSHMIVKNGEKWMDRYEIDSLIGKGSFGQVVKAYDRVEQEWVAIKIIKNKKAFLNQAQIEVRLLELMNKHDTEMKYYIVHLKRHFMFRNHLCLVFEMLSYNLYDLLRNTNFRGVSLNLTRKFAQQMCTALLFLATPELSIIHCDLKPENILLCNPKRSAIKIVDFGSSCQLGQRIYQYIQSRFYRSPEVLLGMPYDLAIDMWSLGCILVEMHTGEPLFSGANEVDQMNKIVEVLGIPPAHILDQAPKARKFFEKLPDGTWNLKKTKDGKREYKPPGTRKLHNILGVETGGPGGRRAGESGHTVADYLKFKDLILRMLDYDPKTRIQPYYALQHSFFKKTADE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.8
R work: 0.1938
R free: 0.2478
Average B factor: 48.273
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 7% PEG 8k, 0.15M Ca acetate, 16% ethylene glycol, 0.1M MES buffer pH 6.5
Matthews coefficient: 2.31
Solvent content (%): 46.65
Ligand: 4-[3-[2-(6-bromanylpyridin-2-yl)oxyethyl]-2-methyl-imidazo[4,5-b]pyridin-5-yl]pyridine-2,6-diamine (RJZ)
Ligand formula: C19 H18 Br N7 O
Ligand molecular weight: 440.297
Ligand SMILES: Cc1nc2ccc(nc2n1CCOc3cccc(n3)Br)c4cc(nc(c4)N)N
Ligand InChI: InChI=1S/C19H18BrN7O/c1-11-23-14-6-5-13(12-9-16(21)26-17(22)10-12)24-19(14)27(11)7-8-28-18-4-2-3-15(20)25-18/h2-6,9-10H,7-8H2,1H3,(H4,21,22,26)
Release date: 2021-05-26
PanDDA analysis group deposition -- Crystal Structure of ATAD2 in complex with PC581 (PDB entry 5QXK)
Macromolecule: ATPase family AAA domain-containing protein 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.1.3
Sequence length: 130 residues
Sequence: SMQEEDTFRELRIFLRNVTHRLAIDKRFRVFTKPVDPDEVPDYRTVIKEPMDLSSVISKIDLHKYLTVKDYLRDIDLICSNALEYNPDRDPGDRLIRHRACALRDTAYAIIKEELDEDFEQLCEEIQESR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.72
R work: 0.159
R free: 0.1836
Average B factor: 23.767
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 277
Crystal growth procedure: 1.6M Ammonium Sulfate, 0.1M bis-tris pH 5.5
Matthews coefficient: 4.2
Solvent content (%): 70.7
Ligand: (3aS,8S,9aS)-2-acetyl-10-methyl-2,3,6,8,9,9a-hexahydro-3a,8-epiminocyclohepta[1,2-c:4,5-c']dipyrrol-4(1H)-one (RGM)
Ligand formula: C14 H17 N3 O2
Ligand molecular weight: 259.304
Ligand SMILES: CC(=O)N1CC2CC3c4c[nH]cc4C(=O)C2(C1)N3C
Ligand InChI: InChI=1S/C14H17N3O2/c1-8(18)17-6-9-3-12-10-4-15-5-11(10)13(19)14(9,7-17)16(12)2/h4-5,9,12,15H,3,6-7H2,1-2H3/t9-,12-,14+/m0/s1
Release date: 2020-04-08
Crystal structure of S39D HDAC8 in complex with a largazole analogue. (PDB entry 4RN1)
Macromolecule: Histone deacetylase 8
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.5.1.98
Sequence length: 389 residues
Sequence: MEEPEEPADSGQSLVPVYIYSPEYVSMCDSLAKIPKRADMVHSLIEAYALHKQMRIVKPKVASMEEMATFHTDAYLQHLQKVSQEGDDDHPDSIEYGLGYDCPATEGIFDYAAAIGGATITAAQCLIDGMCKVAINWSGGWHHAKKDEASGFCYLNDAVLGILRLRRKFERILYVDLDLHHGDGVEDAFSFTSKVMTVSLHKFSPGFFPGTGDVSDVGLGKGRYYSVNVPIQDGIQDEKYYQICESVLKEVYQAFNPKAVVLQLGADTIAGDPMCSFNMTPVGIGKCLKYILQWQLATLILGGGGYNLANTARCWTYLTGVILGKTLSSEIPDHEFFTAYGPDYVLEITPSCRPDRNEPHRIQQILNYIKGNLKHVVIEGRGSHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.18
R work: 0.1819
R free: 0.2125
Average B factor: 36.08
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.3
Crystallization temperature (K): 277
Crystal growth procedure: 0.1 M Imidazole (pH=7.0), 4 mM tris(2-carboxyethyl)phosphine (TCEP), 13% PEG 3350, pH 7.3, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Matthews coefficient: 2.5
Solvent content (%): 50.71
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: 2015-04-08
Crystal structure of human Btk SH2 domain bound to rF10 repebody (PDB entry 6HTF)
Macromolecule: Tyrosine-protein kinase BTK
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 117 residues
Sequence: GAMGEAEDSIEMYEWYSKHMTRSQAEQLLKQEGKEGGFIVRDSSKAGKYTVSVFAKSTGDPQGVIRHYVVCSTPQSQYYLAEKHLFSTIPELINYHQHNSAGLISRLKYPVSQQNKN
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.102
R work: 0.2105
R free: 0.256
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 291
Crystal growth procedure: Morpheus B12 BUFFER 0.09M Halogens 0,1M Buffer 3 pH 8.5 50% precipitant 4
Matthews coefficient: 2
Solvent content (%): 43.62
Release date: 2020-05-20
Crystal structure of human GSK3B in complex with G12 (PDB entry 7U2Z)
Macromolecule: Glycogen synthase kinase-3 beta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.26
Sequence length: 348 residues
Sequence: SKVTTVVATPGQGPDRPQEVSYTDTKVIGNGSFGVVYQAKLCDSGELVAIKKVLQDKRFKNRELQIMRKLDHCNIVRLRYFFYSSGEKKDEVYLNLVLDYVPETVYRVARHYSRAKQTLPVIYVKLYMYQLFRSLAYIHSFGICHRDIKPQNLLLDPDTAVLKLCDFGSAKQLVRGEPNVSYICSRYYRAPELIFGATDYTSSIDVWSAGCVLAELLLGQPIFPGDSGVDQLVEIIKVLGTPTREQIREMNPNYTEFKFPQIKAHPWTKVFRPRTPPEAIALCSRLLEYTPTARLTPLEACAHSFFDELRDPNVKLPNGRDTPALFNFTTQELSSNPPLATILIPPHA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.21
R work: 0.247
R free: 0.2662
Average B factor: 54.117
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.4
Crystallization temperature (K): 293
Crystal growth procedure: PEG3350, Sodium Chloride, Hepes
Matthews coefficient: 3.96
Solvent content (%): 68.95
Ligand: (3R)-1-[3-(2-fluorophenyl)propanoyl]-N-(pyridin-2-yl)pyrrolidine-3-carboxamide (L7C)
Ligand formula: C19 H20 F N3 O2
Ligand molecular weight: 341.379
Ligand SMILES: c1ccc(c(c1)CCC(=O)N2CCC(C2)C(=O)Nc3ccccn3)F
Ligand InChI: InChI=1S/C19H20FN3O2/c20-16-6-2-1-5-14(16)8-9-18(24)23-12-10-15(13-23)19(25)22-17-7-3-4-11-21-17/h1-7,11,15H,8-10,12-13H2,(H,21,22,25)/t15-/m1/s1
Release date: 2022-04-27
Protein Tyrosine Phosphatase 1B (1-301), T177A mutant, vanadate bound state (PDB entry 6PGT)
Macromolecule: Tyrosine-protein phosphatase non-receptor type 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 298 residues
Sequence: EMEKEFEQIDKSGSWAAIYQDIRHEASDFPCRVAKLPKNKNRNRYRDVSPFDHSRIKLHQEDNDYINASLIKMEEAQRSYILTQGPLPNTCGHFWEMVWEQKSRGVVMLNRVMEKGSLKCAQYWPQKEEKEMIFEDTNLKLTLISEDIKSYYTVRQLELENLTTQETREILHFHYATWPDFGVPESPASFLNFLFKVRESGSLSPEHGPVVVHCSAGIGRSGTFCLADTCLLLMDKRKDPSSVDIKKVLLEMRKFRMGLIQTADQLRFSYLAVIEGAKFIMGDSSVQDQWKELSHEDL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.2
R work: 0.1882
R free: 0.2301
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 0.1M Hepes,  0.2 M magnesium acetate and 15-20% polyethylene glycol 8000
Matthews coefficient: 3.35
Solvent content (%): 63.24
Ligand: VANADATE ION (VO4)
Ligand formula: O4 V
Ligand molecular weight: 114.939
Ligand SMILES: [O-][V](=O)([O-])[O-]
Ligand InChI: InChI=1S/4O.V/q;3*-1;
Release date: 2019-08-07
PanDDA analysis group deposition -- Crystal Structure of JMJD1B in complex with FM001810a (PDB entry 5RAC)
Macromolecule: Lysine-specific demethylase 3B
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11
Sequence length: 372 residues
Sequence: MHHHHHHSSGVDLGTENLYFQSMTSHSWLCDGRLLCLHDPSNKNNWKIFRECWKQGQPVLVSGVHKKLKSELWKPEAFSQEFGDQDVDLVNCRNCAIISDVKVRDFWDGFEIICKRLRSEDGQPMVLKLKDWPPGEDFRDMMPTRFEDLMENLPLPEYTKRDGRLNLASRLPSYFVRPDLGPKMYNAYGLITAEDRRVGTTNLHLDVSDAVNVMVYVGIPIGEGAHDEEVLKTIDEGDADEVTKERIHDHKEKPGALWHIYAAKDAEKIRELLRKVGEEQGQENPPDHDPIHDQSWYLDQTLRKRLYEEYGVQGWAIVQFLGDAVFIPAGAPHQVHNLYSCIKVAEDFVSPEHVKHCFRLTQEFRHLSNTHT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.73
R work: 0.1866
R free: 0.2203
Average B factor: 36.323
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.1M bis-tris pH 5.5 21% PEG3350  0.3M magnesium chloride
Matthews coefficient: 2.8
Solvent content (%): 56.06
Ligand: 4-[(3,4-dihydroisoquinolin-2(1H)-yl)methyl]phenol (O3M)
Ligand formula: C16 H17 N O
Ligand molecular weight: 239.312
Ligand SMILES: c1ccc2c(c1)CCN(C2)Cc3ccc(cc3)O
Ligand InChI: InChI=1S/C16H17NO/c18-16-7-5-13(6-8-16)11-17-10-9-14-3-1-2-4-15(14)12-17/h1-8,18H,9-12H2
Release date: 2020-04-22
BACE crystal structure with bicyclic aminothiazine inhibitor (PDB entry 4ZSP)
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): 1.91
R work: 0.18874
R free: 0.24269
Average B factor: 32.621
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.4
Crystallization temperature (K): 277
Crystal growth procedure: PEG8000, sodium cacodylate, ammonium sulfate
Matthews coefficient: 2.66
Solvent content (%): 53.77
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: 2015-06-10
Linked KDM5A JMJ Domain Bound to the Covalent Inhibitor N69 i.e. [2-((3-acrylamidophenyl)(2-(piperidin-1-yl)ethoxy)methyl)thieno[3,2-b]pyridine-7-carboxylic acid] (PDB entry 6DQ9)
Macromolecule: Linked KDM5A Jmj Domain
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11
Sequence length: 330 residues
Sequence: HNMAGVGPGGYAAEFVPPPECPVFEPSWEEFTDPLSFIGRIRPLAEKTGICKIRPPKDWQPPFACEVKSFRFTPRVQRLNELEAMTRVRPREAFGFEQAVREYTLQSFGEMADNFKSDYFNMPVHMVPTELVEKEFWRLVSSIEEDVIVEYGADISSKDFGSGFPVKDGRRKILPEEEEYALSGWNLNNMPVLEQSVLAHINVDISGMKVPWLYVGMCFSSFCWHIEDHWSYSINYLHWGEPKTWYGVPSHAAEQLEEVMRELAPELFESQPDLLHQLVTIMNPNVLMEHGVPVYRTNQCAGEFVVTFPRAYHSGFNQGYNFAEAVNFCT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.748
R work: 0.1735
R free: 0.1983
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 289
Crystal growth procedure: 1.2-1.35 M (NH4)2SO4, 0.1 M Tris-HCl (pH 8.6-9.2) 0-20% glycerol 25 mM (Na/K) dibasic/monobasic phosphate
Matthews coefficient: 2.24
Solvent content (%): 45.13
Ligand: 2-{(R)-[3-(acryloylamino)phenyl][2-(piperidin-1-yl)ethoxy]methyl}thieno[3,2-b]pyridine-7-carboxylic acid (H74)
Ligand formula: C25 H27 N3 O4 S
Ligand molecular weight: 465.565
Ligand SMILES: C=CC(=O)Nc1cccc(c1)C(c2cc3c(s2)c(ccn3)C(=O)O)OCCN4CCCCC4
Ligand InChI: InChI=1S/C25H27N3O4S/c1-2-22(29)27-18-8-6-7-17(15-18)23(32-14-13-28-11-4-3-5-12-28)21-16-20-24(33-21)19(25(30)31)9-10-26-20/h2,6-10,15-16,23H,1,3-5,11-14H2,(H,27,29)(H,30,31)/t23-/m1/s1
Release date: 2018-11-21
DNA Polymerase Lambda, TTPaS:At Mn2+ Product State Ternary Complex, 60 min (PDB entry 7M4L)
Macromolecule: DNA (5'-D(*CP*AP*GP*TP*AP*CP*(YQS))-3')
Type: DNA, polydeoxyribonucleotide
Source organism: Homo sapiens
Sequence length: 7 residues
Sequence: CAGTACX
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.701
R work: 0.1894
R free: 0.2153
Average B factor: 45.6853
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 80-95mM BICINE pH 8.3, 0.3M Na-K Tartrate, 18-22.5% PolyPure PEG
Matthews coefficient: 2.82
Solvent content (%): 56.44
Ligand: MANGANESE (II) ION (MN)
Ligand formula: Mn
Ligand molecular weight: 54.938
Ligand SMILES: [Mn+2]
Ligand InChI: InChI=1S/Mn/q+2
Release date: 2022-07-06