satarupa22/MacromolecularLigandDB huggingface dataset:
FKBP12 in complex with the BMP potentiator compound 9 at 1.55 A resolution (PDB entry 6YF0)
Macromolecule: Peptidyl-prolyl cis-trans isomerase FKBP1A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 5.2.1.8
Sequence length: 109 residues
Sequence: GPGVQVETISPGDGRTFPKRGQTCVVHYTGMLEDGKKFDSSRDRNKPFKFMLGKQEVIRGWEEGVAQMSVGQRAKLTISPDYAYGATGHPGIIPPHATLVFDVELLKLE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.55
R work: 0.2368
R free: 0.2571
Average B factor: 28.525
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.6
Crystallization temperature (K): 298
Crystal growth procedure: 2.2 M AmSO4, 0.2 M NaThiocyanate
Matthews coefficient: 3.17
Solvent content (%): 61.16
Ligand: 18-HYDROXYASCOMYCIN (818)
Ligand formula: C43 H69 N O13
Ligand molecular weight: 808.007
Ligand SMILES: CCC1C=C(C(C(CC(C2C(CC(C(O2)(C(=O)C(=O)N3CCCCC3C(=O)OC(C(C(CC1=O)O)C)C(=CC4CCC(C(C4)OC)O)C)O)C)OC)OC)C)O)C
Ligand InChI: InChI=1S/C43H69NO13/c1-10-29-18-23(2)37(48)24(3)19-35(54-8)39-36(55-9)20-26(5)43(52,57-39)40(49)41(50)44-16-12-11-13-30(44)42(51)56-38(27(6)32(46)22-33(29)47)25(4)17-28-14-15-31(45)34(21-28)53-7/h17-18,24,26-32,34-39,45-46,48,52H,10-16,19-22H2,1-9H3/b23-18+,25-17+/t24-,26-,27-,28+,29-,30+,31-,32+,34-,35+,36+,37-,38-,39-,43-/m1/s1
Release date: 2021-03-10
Sirtuin 2 protein with H3K18 myristoylated peptide (PDB entry 6L65)
Macromolecule: NAD-dependent protein deacetylase sirtuin-2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1.286
Sequence length: 307 residues
Sequence: SSLGSQKERLLDELTLEGVARYMQSERCRRVICLVGAGISTSAGIPDFRSPSTGLYDNLEKYHLPYPEAIFEISYFKKHPEPFFALAKELYPGQFKPTICHYFMRLLKDKGLLLRCYTQNIDTLERIAGLEQEDLVEAHGTFYTSHCVSASCRHEYPLSWMKEKIFSEVTPKCENCQSLVKPDIVFFGESLPARFFSCMQSDFLKVDLLLVMGTSLQVQPFASLISKAPLSTPRLLINKEKAGQSDPFLGMIMGLGGGMDFDSKKAYRDVAWLGECDQGCLALAELLGWKKELEDLVRREHASIDAQ
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.1769
R free: 0.2184
Average B factor: 20.5053
Crystallization method: EVAPORATION
Crystallization pH: 6.5
Crystallization temperature (K): 293.1
Crystal growth procedure: 0.1M MES, pH 6.5, 6%-20% (w/v) PEG 10000
Matthews coefficient: 2.21
Solvent content (%): 44.31
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: 2020-11-04
High salt structure of human protein kinase CK2alpha in complex with 3-aminopropyl-4,5,6,7-tetrabromobenzimidazol (PDB entry 5OWH)
Macromolecule: Casein kinase II subunit alpha
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 335 residues
Sequence: MSGPVPSRARVYTDVNTHRPREYWDYESHVVEWGNQDDYQLVRKLGRGKYSEVFEAINITNNEKVVVKILKPVKKKKIKREIKILENLRGGPNIITLADIVKDPVSRTPALVFEHVNNTDFKQLYQTLTDYDIRFYMYEILKALDYCHSMGIMHRDVKPHNVMIDHEHRKLRLIDWGLAEFYHPGQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRKEPFFHGHDNYDQLVRIAKVLGTEDLYDYIDKYNIELDPRFNDILGRHSRKRWERFVHSENQHLVSPEALDFLDKLLRYDHQSRLTAREAMEHPYFYTVVKDQARMG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.3
R work: 0.2192
R free: 0.2628
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293.15
Crystal growth procedure: 1 MIKROLITER OF A CK2ALPHA/INHIBITOR MIXTURE (COMPOSITION: 7 MG/ML CK2ALPHA ENZYME, 1 MILLIMOLAR         
INHIBITOR, 10 % DIMETHYL SULFOXIDE, 450 MM NACL, 22.5 MM TRIS/HCL, PH 8.5) WAS MIXED WITH 1 MIKROLITER RESERVOIR SOLUTION (COMPOSITION: 4.4 M sodium chloride, 0.1 M SODIUM Acetate, PH 5.5) FOLLOWED BY VAPOUR DIFFUSION EQUILIBRATION AGAINST MICROLITER OF THE RESERVOIR SOLUTION.
Matthews coefficient: 2.13
Solvent content (%): 42.32
Ligand: 3-[4,5,6,7-tetrakis(bromanyl)benzimidazol-1-yl]propan-1-amine (B0K)
Ligand formula: C10 H9 Br4 N3
Ligand molecular weight: 490.815
Ligand SMILES: c1nc2c(n1CCCN)c(c(c(c2Br)Br)Br)Br
Ligand InChI: InChI=1S/C10H9Br4N3/c11-5-6(12)8(14)10-9(7(5)13)16-4-17(10)3-1-2-15/h4H,1-3,15H2
Release date: 2018-07-25
PanDDA analysis group deposition -- Crystal structure of PTP1B in complex with compound_FMOPL000484a (PDB entry 5QDX)
Macromolecule: Tyrosine-protein phosphatase non-receptor type 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 321 residues
Sequence: MEMEKEFEQIDKSGSWAAIYQDIRHEASDFPSRVAKLPKNKNRNRYRDVSPFDHSRIKLHQEDNDYINASLIKMEEAQRSYILTQGPLPNTVGHFWEMVWEQKSRGVVMLNRVMEKGSLKCAQYWPQKEEKEMIFEDTNLKLTLISEDIKSYYTVRQLELENLTTQETREILHFHYTTWPDFGVPESPASFLNFLFKVRESGSLSPEHGPVVVHCSAGIGRSGTFCLADTCLLLMDKRKDPSSVDIKKVLLEMRKFRMGLIQTADQLRFSYLAVIEGAKFIMGDSSVQDQWKELSHEDLEPPPEHIPPPPRPPKRILEPHN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.062
R work: 0.2379
R free: 0.2734
Average B factor: 37.8978
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: well solution: 0.3 M magnesium acetate, 0.1 M HEPES pH 7.5, 0.1% beta-mercaptoethanol, 13-14% PEG 8000, 2% ethanol
Matthews coefficient: 3.35
Solvent content (%): 63.32
Ligand: {N}-[(2~{S})-1-diazanyl-3-(4-hydroxyphenyl)-1-oxidanylidene-propan-2-yl]ethanamide (JGM)
Ligand formula: C11 H15 N3 O3
Ligand molecular weight: 237.255
Ligand SMILES: CC(=O)NC(Cc1ccc(cc1)O)C(=O)NN
Ligand InChI: InChI=1S/C11H15N3O3/c1-7(15)13-10(11(17)14-12)6-8-2-4-9(16)5-3-8/h2-5,10,16H,6,12H2,1H3,(H,13,15)(H,14,17)/t10-/m0/s1
Release date: 2018-10-10
Human MMP12 catalytic domain in complex with AP280 (PDB entry 6RD0)
Macromolecule: Macrophage metalloelastase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.24.65
Sequence length: 159 residues
Sequence: MGPVWRKHYITYRINNYTPDMNREDVDYAIRKAFQVWSNVTPLKFSKINTGMADILVVFARGAHGDDHAFDGKGGILAHAFGPGSGIGGDAHFDEDEFWTTHSGGTNLFLTAVHEIGHSLGLGHSSDPKAVMFPTYKYVDINTFRLSADDIRGIQSLYG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.9
R work: 0.16676
R free: 0.20885
Average B factor: 27.782
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8
Crystallization temperature (K): 293
Crystal growth procedure: 25% PEH 6000, 0.1 M Tris-HCl
Matthews coefficient: 2.31
Solvent content (%): 46.81
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: 2020-02-19
Crystal structure of sarin surrogate NIMP inhibited recombinant human bile salt activated lipase (PDB entry 6H18)
Macromolecule: Bile salt-activated lipase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.1.13
Sequence length: 547 residues
Sequence: HHHHHHHHENLYFQSKLGAVYTEGGFVEGVNKKLGLLGDSVDIFKGIPFAAPTKALENPQPHPGWQGTLKAKNFKKRCLQATITQDSTYGDEDCLYLNIWVPQGRKQVSRDLPVMIWIYGGAFLMGSGHGANFLNNYLYDGEEIATRGNVIVVTFNYRVGPLGFLSTGDANLPGNYGLRDQHMAIAWVKRNIAAFGGDPDNITLFGESAGGASVSLQTLSPYNKGLIRRAISQSGVALSPWVIQKNPLFWAKKVAEKVGCPVGDAARMAQCLKVTDPRALTLAYKVPLAGLEYPMLHYVGFVPVIDGDFIPDDPINLYANAADIDYIAGTNNMDGHIFASIDMPAINKGNKKVTEEDFYKLVSEFTITKGLRGAKTTFDVYTESWAQDPSQENKKKTVVDFETDVLFLVPTEIALAQHRANAKSAKTYAYLFSHPSRMPVYPKWVGADHADDIQYVFGKPFATPTGYRPQDRTVSKAMIAYWTNFAKTGDPNMGDSAVPTHWEPYTTENSGYLEITKKMGSSSMKRSLRTNFLRYWTLTYLALPTVT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.85
R work: 0.1981
R free: 0.2357
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: PEG 8000, cacodylate, Zinc Acetate
Matthews coefficient: 2.49
Solvent content (%): 50.56
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: 2019-03-27
Crystal structure of human ATAD2 bromodomain in complex with N-(4-chloro-3-(N,N-dimethylsulfamoyl)phenyl)-2-(2,5-dioxo-3',4'-dihydro-2'H-spiro[imidazolidine-4,1'-naphthalen]-1-yl)acetamide (PDB entry 6S56)
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): 2.01
R work: 0.22036
R free: 0.2763
Average B factor: 40.602
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 278
Crystal growth procedure: 0.1M trisHCl pH 7.0-8.0, 1.2-1.5M ammonium sulphate and 20-25% PEG3350
Matthews coefficient: 3.99
Solvent content (%): 69.15
Ligand: 1,2-ETHANEDIOL (EDO)
Ligand formula: C2 H6 O2
Ligand molecular weight: 62.068
Ligand SMILES: C(CO)O
Ligand InChI: InChI=1S/C2H6O2/c3-1-2-4/h3-4H,1-2H2
Release date: 2019-08-21
Crystal structure of calcium-activated EndoU (PDB entry 9FTW)
Macromolecule: Uridylate-specific endoribonuclease
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.6.1
Sequence length: 410 residues
Sequence: MRACISLVLAVLCGLAWAGKIESCASRCNEKFNRDAACQCDRRCLWHGNCCEDYEHLCTEDHKESEPLPQLEEETEEALASNLYSAPTSCQGRCYEAFDKHHQCHCNARCQEFGNCCKDFESLCSDHEVSHSSDAITKEEIQSISEKIYRADTNKAQKEDIVLNSQNCISPSETRNQVDRCPKPLFTYVNEKLFSKPTYAAFINLLNNYQRATGHGEHFSAQELAEQDAFLREIMKTAVMKELYSFLHHQNRYGSEQEFVDDLKNMWFGLYSRGNEEGDSSGFEHVFSGEVKKGKVTGFHNWIRFYLEEKEGLVDYYSHIYDGPWDSYPDVLAMQFNWDGYYKEVGSAFIGSSPEFEFALYSLCFIARPGKVCQLSLGGYPLAVRTYTWDKSTYGNGKKYIATAYIVSST
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.65
R work: 0.1881
R free: 0.2159
Average B factor: 25.4
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.1M Na Acetate
0.1 M HEPES pH 7.5
22 % PEG 4000
Matthews coefficient: 2.13
Solvent content (%): 42.31
Ligand: ACETATE ION (ACT)
Ligand formula: C2 H3 O2
Ligand molecular weight: 59.044
Ligand SMILES: CC(=O)[O-]
Ligand InChI: InChI=1S/C2H4O2/c1-2(3)4/h1H3,(H,3,4)/p-1
Release date: 2024-08-14
Protein Tyrosine Phosphatase 1B YAYA (Y152A, Y153A) mutant in complex with TCS401, closed state (PDB entry 5KA3)
Macromolecule: Tyrosine-protein phosphatase non-receptor type 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 306 residues
Sequence: GHMASMEMEKEFEQIDKSGSWAAIYQDIRHEASDFPCRVAKLPKNKNRNRYRDVSPFDHSRIKLHQEDNDYINASLIKMEEAQRSYILTQGPLPNTCGHFWEMVWEQKSRGVVMLNRVMEKGSLKCAQYWPQKEEKEMIFEDTNLKLTLISEDIKSAATVRQLELENLTTQETREILHFHYTTWPDFGVPESPASFLNFLFKVRESGSLSPEHGPVVVHCSAGIGRSGTFCLADTCLLLMDKRKDPSSVDIKKVLLEMRKFRMGLIQTADQLRFSYLAVIEGAKFIMGDSSVQDQWKELSHEDLEP
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.141
R work: 0.2005
R free: 0.2367
Average B factor: 39.2286
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 0.1 HEPES, pH 7.8, 0.2 M MgCl2, 20.5% PEG8000
Matthews coefficient: 3.45
Solvent content (%): 64.37
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: 2017-03-08
CDK8/CYCC IN COMPLEX WITH 8-{3-Chloro-5-[4-(1-methyl-1H-pyrazol-4-yl)-phenyl]-pyridin- 4-yl}-2,8-diaza-spiro[4.5]decan-1-one (PDB entry 5BNJ)
Macromolecule: Cyclin-dependent kinase 8
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.22
Sequence length: 405 residues
Sequence: DKMDYDFKVKLSSERERVEDLFEYEGCKVGRGTYGHVYKAKRKDGKDDKDYALKQIEGTGISMSACREIALLRELKHPNVISLQKVFLSHADRKVWLLFDYAEHDLWHIIKFHRASKANKKPVQLPRGMVKSLLYQILDGIHYLHANWVLHRDLKPANILVMGEGPERGRVKIADMGFARLFNSPLKPLADLDPVVVTFWYRAPELLLGARHYTKAIDIWAIGCIFAELLTSEPIFHCRQEDIKTSNPYHHDQLDRIFNVMGFPADKDWEDIKKMPEHSTLMKDFRRNTYTNCSLIKYMEKHKVKPDSKAFHLLQKLLTMDPIKRITSEQAMQDPYFLEDPLPTSDVFAGCQIPYPKREFLTEEEPDDKGDKKNQQQQQGNNHTNGTGHPGNQDSSHTQGPPLKK
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.64
R work: 0.2261
R free: 0.2734
Average B factor: 46.604
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 6.9
Crystallization temperature (K): 293
Crystal growth procedure: 20% PEG3350, 0.2 M sodium formate, pH 6.9,
Matthews coefficient: 3.08
Solvent content (%): 60.09
Ligand: 8-{3-chloro-5-[4-(1-methyl-1H-pyrazol-4-yl)phenyl]pyridin-4-yl}-2,8-diazaspiro[4.5]decan-1-one (4TV)
Ligand formula: C23 H24 Cl N5 O
Ligand molecular weight: 421.923
Ligand SMILES: Cn1cc(cn1)c2ccc(cc2)c3cncc(c3N4CCC5(CCNC5=O)CC4)Cl
Ligand InChI: InChI=1S/C23H24ClN5O/c1-28-15-18(12-27-28)16-2-4-17(5-3-16)19-13-25-14-20(24)21(19)29-10-7-23(8-11-29)6-9-26-22(23)30/h2-5,12-15H,6-11H2,1H3,(H,26,30)
Release date: 2015-10-14
Crystal structure of TNKS2 in complex with 2-[4-(morpholin-4-yl)phenyl]-3,4-dihydroquinazolin-4-one (PDB entry 5NT4)
Macromolecule: Tankyrase-2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.4.2.30
Sequence length: 191 residues
Sequence: MHHHHHHSSGVDLGTENLYFQSMLNTSGSGTILIDLSPDDKEFQSVEEEMQSTVREHRDGGHAGGIFNRYNILKIQKVCNKKLWERYTHRRKEVSEENHNHANERMLFHGSPFVNAIIHKGFDERHAYIGGMFGAGIYFAENSSKSNQYVYGIGGGTGCPVHKDRSCYICHRQLLFCRVTLGKSFLQFSAM
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.9
R work: 0.17324
R free: 0.20412
Average B factor: 31.597
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.2 M LISO4, 0.1 M TRIS HCL, 24% PEG3350
Matthews coefficient: 2.39
Solvent content (%): 48.64
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: 2018-03-07
Structure of human galactokinase 1 bound with azepan-1-yl(2,6-difluorophenyl)methanone (PDB entry 7OZX)
Macromolecule: Galactokinase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.1.6
Sequence length: 399 residues
Sequence: MAHHHHHHAALRQPQVAELLAEARRAFREEFGAEPELAVSAPGRVNLIGEHTDYNQGLVLPMALELMTVLVGSPRKDGLVSLLTTSEGADEPQRLQFPLPTAQRSLEPGTPRWANYVKGVIQYYPAAPLPGFSAVVVSSVPLGGGLSSSASLEVATYTFLQQLCPDSGTIAARAQVCQQAEHSFAGMPCGIMDQFISLMGQKGHALLIDCRSLETSLVPLSDPKLAVLITNSNVRHSLASSEYPVRRRQCEEVARALGAASLREVQLEELEAARDLVSKEGFRRARHVVGEIRRTAQAAAALRRGDYRAFGRLMVESHRSLRDDYEVSCPELDQLVEAALAVPGVYGSRMTGGGFGGCTVTLLEASAAPHAMRHIQEHYGGTATFYLSQAADGAKVLCL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.3
R work: 0.2083
R free: 0.2577
Average B factor: 48.171
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M MOPS/sodium HEPES pH 7.0-7.5, 40-50 % Morpheus Precipitant Mix 4 (50% mix = 12.5% MPD, 12.5% PEG1000, 12.5% PEG3350), 0.1 M Morpheus Carboxylic acids mix (0.02M each of:sodium formate, ammonium acetate, sodium citrate tribasic dehydrate, sodium potassium tartrate tetrahydrate and sodium oxamate).
Matthews coefficient: 2.9
Solvent content (%): 57.54
Ligand: beta-D-galactopyranose (GAL)
Ligand formula: C6 H12 O6
Ligand molecular weight: 180.156
Ligand SMILES: C(C1C(C(C(C(O1)O)O)O)O)O
Ligand InChI: InChI=1S/C6H12O6/c7-1-2-3(8)4(9)5(10)6(11)12-2/h2-11H,1H2/t2-,3+,4+,5-,6-/m1/s1
Release date: 2022-05-25
Structure of the PTK6 kinase domain bound to a type I inhibitor (3-fluoro-4-{[6-methyl-3-(1H-pyrazol-4-yl)imidazo[1,2-a]pyrazin-8-yl]amino}phenyl)(morpholin-4-yl)methanone (PDB entry 6CZ3)
Macromolecule: Protein-tyrosine kinase 6
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 264 residues
Sequence: GSDDAERPREEFTLCRKLGSGYFGEVFEGLWKDRVQVAIKVISRDNLLHQQMLQSEIQAMKKLRHKHILALYAVVSVGDPVYIITELMAKGSLLELLRDSDEKVLPVSELLDIAWQVAEGMCYLESQNYIHRDLAARNILVGENTLCKVGDFGLARLIKEDVYLSHDHNIPYKWTAPEALSRGHYSTKSDVWSFGILLHEMFSRGQVPYPGMSNHEAFLRVDAGYRMPCPLECPPSVHKLMLTCWCRDPEQRPCFKALRERLSS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.196
R free: 0.213
Average B factor: 37.5
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 288
Crystal growth procedure: 3.4 M Potassium acetate, 0.1 M bicine, pH 7.5, 13oC
Matthews coefficient: 3.14
Solvent content (%): 60.84
Ligand: (3-fluoro-4-{[6-methyl-3-(1H-pyrazol-4-yl)imidazo[1,2-a]pyrazin-8-yl]amino}phenyl)(morpholin-4-yl)methanone (FLJ)
Ligand formula: C21 H20 F N7 O2
Ligand molecular weight: 421.428
Ligand SMILES: Cc1cn2c(cnc2c(n1)Nc3ccc(cc3F)C(=O)N4CCOCC4)c5c[nH]nc5
Ligand InChI: InChI=1S/C21H20FN7O2/c1-13-12-29-18(15-9-24-25-10-15)11-23-20(29)19(26-13)27-17-3-2-14(8-16(17)22)21(30)28-4-6-31-7-5-28/h2-3,8-12H,4-7H2,1H3,(H,24,25)(H,26,27)
Release date: 2018-06-20
The crystal structure of human carbonic anhydrase VII in complex with 4-(4-phenylpiperidine-1-carbonyl)benzenesulfonamide. (PDB entry 6H36)
Macromolecule: Carbonic anhydrase 7
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 274 residues
Sequence: MGMTGHHGWGYGQDDGPSHWHKLYPIAQGDRQSPINIISSQAVYSPSLQPLELSYEACMSLSITNNGHSVQVDFNDSDDRTVVTGGPLEGPYRLKQFHFHWGKKHDVGSEHTVDGKSFPSELHLVHWNAKKYSTFGEAASAPDGLAVVGVFLETGDEHPSMNRLTDALYMVRFKGTKAQFSCFNPKSLLPASRHYWTYPGSLTTPPLSESVTWIVLREPISISERQMGKFRSLLFTSEDDERIHMVNNFRPPQPLKGRVVKASFRALEHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.85
R work: 0.195
R free: 0.233
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 293
Crystal growth procedure: 25% v/v Peg3350, 0.2 M Ammonium acetate, 0.1 M Tris-HCl pH 8.5
Matthews coefficient: 2.07
Solvent content (%): 40.47
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: 2018-12-19
Crystal structure of the human DYRK1A kinase domain bound to abemaciclib (PDB entry 7O7K)
Macromolecule: Dual specificity tyrosine-phosphorylation-regulated kinase 1A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.12.1
Sequence length: 361 residues
Sequence: SMSSHKKERKVYNDGYDDDNYDYIVKNGEKWMDRYEIDSLIGKGSFGQVVKAYDRVEQEWVAIKIIKNKKAFLNQAQIEVRLLELMNKHDTEMKYYIVHLKRHFMFRNHLCLVFEMLSYNLYDLLRNTNFRGVSLNLTRKFAQQMCTALLFLATPELSIIHCDLKPENILLCNPKRSAIKIVDFGSSCQLGQRIYQYIQSRFYRSPEVLLGMPYDLAIDMWSLGCILVEMHTGEPLFSGANEVDQMNKIVEVLGIPPAHILDQAPKARKFFEKLPDGTWNLKKTKDGKREYKPPGTRKLHNILGVETGGPGGRRAGESGHTVADYLKFKDLILRMLDYDPKTRIQPYYALQHSFFKKTADE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.82
R work: 0.1774
R free: 0.2049
Average B factor: 47.5774
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 288
Crystal growth procedure: 14-16% PEG 4000, 0.1 M sodium citrate (pH 6.5) and 0.1 M ammonium sulfate
Matthews coefficient: 2.82
Solvent content (%): 56.37
Ligand: CITRATE ANION (FLC)
Ligand formula: C6 H5 O7
Ligand molecular weight: 189.1
Ligand SMILES: C(C(=O)[O-])C(CC(=O)[O-])(C(=O)[O-])O
Ligand InChI: InChI=1S/C6H8O7/c7-3(8)1-6(13,5(11)12)2-4(9)10/h13H,1-2H2,(H,7,8)(H,9,10)(H,11,12)/p-3
Release date: 2021-11-24
Crystal structure of a fentanyl derivative in complex with human CA VII (PDB entry 8Q3U)
Macromolecule: Carbonic anhydrase 7
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 274 residues
Sequence: MGMTGHHGWGYGQDDGPSHWHKLYPIAQGDRQSPINIISSQAVYSPSLQPLELSYEACMSLSITNNGHSVQVDFNDSDDRTVVTGGPLEGPYRLKQFHFHWGKKHDVGSEHTVDGKSFPSELHLVHWNAKKYSTFGEAASAPDGLAVVGVFLETGDEHPSMNRLTDALYMVRFKGTKAQFSCFNPKSLLPASRHYWTYPGSLTTPPLSESVTWIVLREPISISERQMGKFRSLLFTSEDDERIHMVNNFRPPQPLKGRVVKASFRALEHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.1
R work: 0.14956
R free: 0.15322
Average B factor: 15.03
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 293
Crystal growth procedure: 19% (w/v) PEG 3350, 0.2 M ammonium acetate, 0.1 M TRIS-HCl
Matthews coefficient: 2.14
Solvent content (%): 42.6
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: 2023-09-20
The structure of NTMT1 in complex with compound 11 (PDB entry 6PVA)
Macromolecule: N-terminal Xaa-Pro-Lys N-methyltransferase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1.244
Sequence length: 241 residues
Sequence: MGSSHHHHHHSSGLVPRGSTSEVIEDEKQFYSKAKTYWKQIPPTVDGMLGGYGHISSIDINSSRKFLQRFLREGPNKTGTSCALDCGAGIGRITKRLLLPLFREVDMVDITEDFLVQAKTYLGEEGKRVRNYFCCGLQDFTPEPDSYDVIWIQWVIGHLTDQHLAEFLRRCKGSLRPNGIIVIKDNMAQEGVILDDVDSSVCRDLDVVRRIICSAGLSLLAEERQENLPDEIYHVYSFALR
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.84
R work: 0.1958
R free: 0.2318
Average B factor: 38.0236
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 1.5 M lithium sulfate; 0.1 M sodium HEPES 7.5
Matthews coefficient: 2.31
Solvent content (%): 46.85
Release date: 2020-08-19
Structure of the Wnt deacylase Notum in complex with isoquinoline 45 (PDB entry 6R8R)
Macromolecule: Palmitoleoyl-protein carboxylesterase NOTUM
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.1.98
Sequence length: 383 residues
Sequence: ETGSAQQLNEDLRLHLLLNTSVTCNDGSPAGYYLKESRGSRRWLLFLEGGWYCFNRENCDSRYDTMRRLMSSRDWPRTRTGTGILSSQPEENPYWWNANMVFIPYCSSDVWSGASSKSEKNEYAFMGALIIQEVVRELLGRGLSGAKVLLLAGSSAGGTGVLLNVDRVAEQLEKLGYPAIQVRGLADSGWFLDNKQYRHTDCVDTITCAPTEAIRRGIRYWNGVVPERCRRQFQEGEEWNCFFGYKVYPTLRSPVFVVQWLFDEAQLTVDNVHLTGQPVQEGLRLYIQNLGRELRHTLKDVPASFAPACLSHEIIIRSHWTDVQVKGTSLPRALHCWDRSLHDSHKASKTPLKGCPVHLVDSCPWPHCNPSCPTGTKHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.27
R work: 0.1478
R free: 0.1777
Average B factor: 23.2508
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 4
Crystallization temperature (K): 300
Crystal growth procedure: 1.4 M ammonium sulphate, 0.1 M citric acid, pH 4
Matthews coefficient: 1.94
Solvent content (%): 36.6
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: 2019-05-08
Carbonic anhydrase 9 in complex with SB4197 (PDB entry 6U4T)
Macromolecule: Carbonic anhydrase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 257 residues
Sequence: HWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHSFQVTFDDSQDKAVLKGGPLDGTYRLLQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDVGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTEGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLAECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.356
R work: 0.154
R free: 0.1729
Average B factor: 21.9586
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 298
Crystal growth procedure: 1.6 M NaCitrate, 50 mM Tris
Matthews coefficient: 2.12
Solvent content (%): 41.98
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: 2020-01-22