satarupa22/MacromolecularLigandDB huggingface dataset:
SIRT2(56-356) with covalent intermediate between mechanism-based inhibitor Glucose-TM-1beta and 1'-SH ADP-ribose (PDB entry 6NR0)
Macromolecule: NAD-dependent protein deacetylase sirtuin-2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.5.1
Sequence length: 319 residues
Sequence: MDFLRNLFSQTLSLGSQKERLLDELTLEGVARYMQSERCRRVICLVGAGISTSAGIPDFRSPSTGLYDNLEKYHLPYPEAIFEISYFKKHPEPFFALAKELYPGQFKPTICHYFMRLLKDKGLLLRCYTQNIDTLERIAGLEQEDLVEAHGTFYTSHCVSASCRHEYPLSWMKEKIFSEVTPKCEDCQSLVKPDIVFFGESLPARFFSCMQSDFLKVDLLLVMGTSLQVQPFASLISKAPLSTPRLLINKEKAGQSDPFLGMIMGLGGGMDFDSKKAYRDVAWLGECDQGCLALAELLGWKKELEDLVRREHASIDAQS
Oligomeric state: Homo 2-mer
Stoichiometry: A2
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.45
R work: 0.2202
R free: 0.2562
Average B factor: 51.87
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5
Crystallization temperature (K): 293
Crystal growth procedure: Mixed solution of 0.44 mM protein (in buffer of 20 mM Tris/HCl pH 7.5, 160 mM NaCl) 2.5 mM NAD+, 2.5 mM Glucose-TM-1beta with an equal volume of well solution of 2 M (NH4)2SO4, 80 mM Na Acetate/HCl pH 5.0
Matthews coefficient: 2.49
Solvent content (%): 55.04
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
PanDDA analysis group deposition of models with modelled events (e.g. bound ligands) -- Crystal Structure of NUDT7 in complex with NU000443a (PDB entry 5QHH)
Macromolecule: Peroxisomal coenzyme A diphosphatase NUDT7
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.1
Sequence length: 196 residues
Sequence: SMLDDAKARLRKYDIGGKYSHLPYNKYSVLLPLVAKEGKLHLLFTVRSEKLRRAPGEVCFPGGKRDPTDMDDAATALREAQEEVGLRPHQVEVVCCLVPCLIDTDTLITPFVGLIDHNFQAQPNPAEVKDVFLVPLAYFLHPQVHDQHYVTRLGHRFINHIFEYTNPEDGVTYQIKGMTANLAVLVAFIILEKKPT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.52
R work: 0.1904
R free: 0.2052
Average B factor: 30.764
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M bis-tris pH 5.5 -- 0.1M ammonium acetate -- 5%(w/v) PEG10K
Matthews coefficient: 4.14
Solvent content (%): 70.26
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: 2019-03-27
FGFR1 kinase domain complex with fragment 2,2-dimethyl-2,3-dihydrobenzofuran-7-carboxamide (PDB entry 5UQ0)
Macromolecule: Fibroblast growth factor receptor 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 311 residues
Sequence: GAMSGVSEYELPEDPRWELPRDRLVLGKPLGEGAFGQVVLAEAIGLDKDKPNRVTKVAVKMLKSDATEKDLSDLISEMEMMKMIGKHKNIINLLGACTQDGPLYVIVEYASKGNLREYLQARRPPGLEYSYNPSHNPEEQLSSKDLVSCAYQVARGMEYLASKKCIHRDLAARNVLVTEDNVMKIADFGLARDIHHIDYYKKTTNGRLPVKWMAPEALFDRIYTHQSDVWSFGVLLWEIFTLGGSPYPGVPVEELFKLLKEGHRMDKPSNCTNELYMMMRDCWHAVPSQRPTFKQLVEDLDRIVALTSNQE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.3
R work: 0.2343
R free: 0.29351
Average B factor: 52.737
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 20% MPEG 5000, 0.1 M sodium cacodylate pH 7.5, 0.2 M ammonium sulfate
Matthews coefficient: 2.4
Solvent content (%): 48.83
Ligand: 2,2-dimethyl-2,3-dihydro-1-benzofuran-7-carboxamide (WP1)
Ligand formula: C11 H13 N O2
Ligand molecular weight: 191.226
Ligand SMILES: CC1(Cc2cccc(c2O1)C(=O)N)C
Ligand InChI: InChI=1S/C11H13NO2/c1-11(2)6-7-4-3-5-8(10(12)13)9(7)14-11/h3-5H,6H2,1-2H3,(H2,12,13)
Release date: 2017-02-22
PanDDA analysis group deposition -- Crystal structure of PTP1B in complex with compound_FMOPL000157a (PDB entry 5QDI)
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): 1.623
R work: 0.1883
R free: 0.2183
Average B factor: 38.4712
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: 3.33
Solvent content (%): 63.05
Ligand: N-(2-phenylethyl)methanesulfonamide (JFM)
Ligand formula: C9 H13 N O2 S
Ligand molecular weight: 199.27
Ligand SMILES: CS(=O)(=O)NCCc1ccccc1
Ligand InChI: InChI=1S/C9H13NO2S/c1-13(11,12)10-8-7-9-5-3-2-4-6-9/h2-6,10H,7-8H2,1H3
Release date: 2018-10-10
EphB3 kinase domain covalently bound to an irreversible inhibitor (compound 6) (PDB entry 5L6P)
Macromolecule: Ephrin type-B receptor 3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 298 residues
Sequence: GSSDPNEAVREFAKEIDVSCVKIEEVIGAGEFGEVCRGRLKQPGRREVFVAIKTLKVGYTERQRRDFLSEASIMGQFDHPNIIRLEGVVTKSRPVMILTEFMENCALDSFLRLNDGQFTVIQLVGMLRGIAAGMKYLSEMNYVHRDLAARNILVNSNLVCKVSDFGLSRFLEDDPSDPTYTSSLGGKIPIRWTAPEAIAYRKFTSASDVWSYGIVMWEVMSYGERPYWDMSNQDVINAVEQDYRLPPPMDCPTALHQLMLDCWVRDRNLRPKFSQIVNTLDKLIRNPASLKVIASAQS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.26
R work: 0.205
R free: 0.232
Average B factor: 55.84
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 293
Crystal growth procedure: 1,4-dioxane, Tris buffer, magnesium chloride
Matthews coefficient: 2.52
Solvent content (%): 51.28
Ligand: ~{N}-(4-phenylazanylquinazolin-7-yl)ethanamide (6P8)
Ligand formula: C16 H14 N4 O
Ligand molecular weight: 278.309
Ligand SMILES: CC(=O)Nc1ccc2c(c1)ncnc2Nc3ccccc3
Ligand InChI: InChI=1S/C16H14N4O/c1-11(21)19-13-7-8-14-15(9-13)17-10-18-16(14)20-12-5-3-2-4-6-12/h2-10H,1H3,(H,19,21)(H,17,18,20)
Release date: 2016-08-10
The crystal structure of CK2alpha in complex with compound 27 (PDB entry 5OTI)
Macromolecule: Casein kinase II subunit alpha
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 342 residues
Sequence: SGPVPSRARVYTDVNTHRPSEYWDYESHVVEWGNQDDYQLVRKLGRGKYSEVFEAINITNNEKVVVKILKPVAAAKIKREIKILENLRGGPNIITLADIVKDPVSRTPALVFEHVNNTDFKQLYQTLTDYDIRFYMYEILKALDYCHSMGIMHRDVKPHNVMIDHEHRKLRLIDWGLAEFYHPGQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRKEPFFHGHDNYDQLVRIAKVLGTEDLYDYIDKYNIELDPRFNDILGRHSRKRWERFVHSENQHLVSPEALDFLDKLLRYDHQSRLTAREAMEHPYFYTVVKREAMEHPYFYTVVK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.59
R work: 0.1898
R free: 0.2322
Average B factor: 33.84
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 298
Crystal growth procedure: 112.5mM Mes pH 6.5, 35% glycerol ethoxylate, 180 mM ammonium acetate
Matthews coefficient: 1.91
Solvent content (%): 35.68
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: 2018-02-28
Crystal structure of human JARID1B in complex with GSK467 (PDB entry 5FUN)
Macromolecule: LYSINE-SPECIFIC DEMETHYLASE 5B
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11
Sequence length: 481 residues
Sequence: SMFLPPPECPVFEPSWEEFADPFAFIHKIRPIAEQTGICKVRPPPDWQPPFACDVDKLHFTPRIQRLNELEAQTRVKLGGGGARDYTLRTFGEMADAFKSDYFNMPVHMVPTELVEKEFWRLVSTIEEDVTVEYGADIASKEFGSGFPVRDGKIKLSPEEEEYLDSGWNLNNMPVMEQSVLAHITADICGMKLPWLYVGMCFSSFCWHIEDHWSYSINYLHWGEPKTWYGVPGYAAEQLENVMKKLAPELFVSQPDLLHQLVTIMNPNTLMTHEVPVYRTNQCAGEFVITFPRAYHSGFNQGFNFAEAVNFCTVDWLPLGRQCVEHYRLLHRYCVFSHDEMICKMASKADVLDVVVASTVQKDMAIMIEDEKALRETVRKLGVIDSERMDFELLPDDERQCVKCKTTCFMSAISCSCKPGLLVCLHHVKELCSCPPYKYKLRYRYTLDDLYPMMNALKLRAESYNEWALNVNEALEAKINK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.3
R work: 0.1805
R free: 0.2117
Average B factor: 65
Crystallization pH: 8
Crystal growth procedure: 0.1M HEPES PH 8.0, 0.8M POTASSIUM PHOSPHATE-DIBASIC, 0.8M SODIUM PHOSPHATE MONOBASIC
Matthews coefficient: 3.98
Solvent content (%): 70.37
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: 2016-04-13
Structure of the complex of human DNA ligase III-alpha and XRCC1 BRCT domains (PDB entry 6WH1)
Macromolecule: X-ray repair cross complementing protein 1 variant
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 96 residues
Sequence: ELPDFFQGKHFFLYGEFPGDERRKLIRYVTAFNGELEDYMSDRVQFVITAQEWDPSFEEALMDNPSLAFVRPRWIYSCNEKQKLLPHQLYGVVPQA
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.4
R work: 0.221
R free: 0.272
Average B factor: 67.21
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 295
Crystal growth procedure: 8-10% isopropanol and 0.1M Bis-Tris pH 5.5
Matthews coefficient: 2.36
Solvent content (%): 47.97
Release date: 2020-12-02
Crystal Structure of Human UBA6 in Complex with ATP (PDB entry 7PVN)
Macromolecule: Ubiquitin-like modifier-activating enzyme 6
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 6.2.1.45
Sequence length: 1052 residues
Sequence: MEGSEPVAAHQGEEASCSSWGTGSTNKNLPIMSTASVEIDDALYSRQRYVLGDTAMQKMAKSHVFLSGMGGLGLEIAKNLVLAGIKAVTIHDTEKCQAWDLGTNFFLSEDDVVNKRNRAEAVLKHIAELNPYVHVTSSSVPFNETTDLSFLDKYQCVVLTEMKLPLQKKINDFCRSQCPPIKFISADVHGIWSRLFCDFGDEFEVLDTTGEEPKEIFISNITQANPGIVTCLENHPHKLETGQFLTFREINGMTGLNGSIQQITVISPFSFSIGDTTELEPYLHGGIAVQVKTPKTVFFESLERQLKHPKCLIVDFSNPEAPLEIHTAMLALDQFQEKYSRKPNVGCQQDSEELLKLATSISETLEEKPDVNADIVHWLSWTAQGFLSPLAAAVGGVASQEVLKAVTGKFSPLCQWLYLEAADIVESLGKPECEEFLPRGDRYDALRACIGDTLCQKLQNLNIFLVGCGAIGCEMLKNFALLGVGTSKEKGMITVTDPDLIEKSNLNRQFLFRPHHIQKPKSYTAADATLKINSQIKIDAHLNKVCPTTETIYNDEFYTKQDVIITALDNVEARRYVDSRCLANLRPLLDSGTMGTKGHTEVIVPHLTESYNSHRDPPEEEIPFATLKSFPAAIEHTIQWARDKFESSFSHKPSLFNKFWQTYSSAEEVLQKIQSGHSLEGCFQVIKLLSRRPRNWSQCVELARLKFEKYFNHKALQLLHCFPLDIRLKDGSLFWQSPKRPPSPIKFDLNEPLHLSFLQNAAKLYATVYCIPFAEEDLSADALLNILSEVKIQEFKPSNKVVQTDETARKPDHVPISSEDERNAIFQLEKAILSNEATKSDLQMAVLSFEKDDDHNGHIDFITAASNLRAKMYSIEPADRFKTKRIAGKIIPAIATTTATVSGLVALEMIKVTGGYPFEAYKNCFLNLAIPIVVFTETTEVRKTKIRNGISFTIWDRWTVHGKEDFTLLDFINAVKEKYGIEPTMVVQGVKMLYVPVMPGHAKRLKLTMHKLVKPTTEKKYVDLTVSFAPDIDGDEDLPGPPVRYYFSHDTD
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.71
R work: 0.2326
R free: 0.2617
Average B factor: 77.09
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M Na-cacodylate, 0.16 M Ca-acetate, 15% PEG 8000 and 16% Glycerol
Matthews coefficient: 2.75
Solvent content (%): 55.3
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: 2022-08-31
DNA polymerase beta substrate complex with incoming 5-FdUTP (PDB entry 5WNY)
Macromolecule: DNA (5'-D(*CP*CP*GP*AP*CP*AP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')
Type: DNA, polydeoxyribonucleotide
Source organism: synthetic construct
Sequence length: 16 residues
Sequence: CCGACAGCGCATCAGC
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.1
R work: 0.1806
R free: 0.2372
Average B factor: 35.9008
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 295
Crystal growth procedure: 50 mM imidazole, pH 7.5, 16% PEG3350 and 350 mM sodium acetate
Matthews coefficient: 2.29
Solvent content (%): 46.31
Ligand: SODIUM ION ()
Ligand formula: Na
Ligand molecular weight: 22.99
Ligand SMILES: [Na+]
Ligand InChI: InChI=1S/Na/q+1
Release date: 2017-09-13
Crystal structure of Neprilysin in complex with Sampatrilat. (PDB entry 6XVP)
Macromolecule: Neprilysin
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.24.11
Sequence length: 699 residues
Sequence: YDDGICKSSDCIKSAARLIQNMDATTEPCTDFFKYACGGWLKRNVIPETSSRYGNFDILRDELEVVLKDVLQEPKTEDIVAVQKAKALYRSCINESAIDSRGGEPLLKLLPDIYGWPVATENWEQKYGASWTAEKAIAQLNSKYGKKVLINLFVGTDDKNSVNHVIHIDQPRLGLPSRDYYECTGIYKEACTAYVDFMISVARLIRQEERLPIDENQLALEMNKVMELEKEIANATAKPEDRNDPMLLYNKMTLAQIQNNFSLEINGKPFSWLNFTNEIMSTVNISITNEEDVVVYAPEYLTKLKPILTKYSARDLQNLMSWRFIMDLVSSLSRTYKESRNAFRKALYGTTSETATWRRCANYVNGNMENAVGRLYVEAAFAGESKHVVEDLIAQIREVFIQTLDDLTWMDAETKKRAEEKALAIKERIGYPDDIVSNDNKLNNEYLELNYKEDEYFENIIQNLKFSQSKQLKKLREKVDKDEWISGAAVVNAFYSSGRNQIVFPAGILQPPFFSAQQSNSLNYGGIGMVIGHEITHGFDDNGRNFNKDGDLVDWWTQQSASNFKEQSQCMVYQYGNFSWDLAGGQHLNGINTLGENIADNGGLGQAYRAYQNYIKKNGEEKLLPGLDLNHKQLFFLNFAQVWCGTYRPEYAVNSIKTDVHSPGNFRIIGTLQNSAEFSEAFHCRKNSYMNPEKKCRVW
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.65
R work: 0.191
R free: 0.2373
Average B factor: 61.47
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 291
Crystal growth procedure: 0.2 M NH4Cl, 22% PEG3350
Matthews coefficient: 2.38
Solvent content (%): 48.33
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: 2020-05-13
Crystal Structure of human phosphodiesterase 10 in complex with 2-(4-fluorophenyl)-4-(2-isoquinolin-3-yloxyethyl)-5-methyl-1,3-oxazole (PDB entry 5SK2)
Macromolecule: cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.4.17
Sequence length: 343 residues
Sequence: GSSICTSEEWQGLMQFTLPVRLCKEIELFHFDIGPFENMWPGIFVYMVHRSCGTSCFELEKLCRFIMSVKKNYRRVPYHNWKHAVTVAHCMYAILQNNHTLFTDLERKGLLIACLCHDLDHRGFSNSYLQKFDHPLAALYSTSTMEQHHFSQTVSILQLEGHNIFSTLSSSEYEQVLEIIRKAIIATDLALYFGNRKQLEEMYQTGSLNLNNQSHRDRVIGLMMTACDLCSVTKLWPVTKLTANDIYAEFWAEGDEMKKLGIQPIPMMDRDKKDEVPQGQLGFYNAVAIPCYTTLTQILPPTEPLLKACRDNLSQWEKVIRGEETATWISSPSVAQKAAASED
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.14
R work: 0.1786
R free: 0.2291
Average B factor: 43.428
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 295
Crystal growth procedure: 5-20 mg/mL protein in 25mM HEPES/NaOH pH7.5, 150mM NaCl, 50mM BME mixed 1:1 with reservoir 0.1M HEPES/NaOH pH7.5, 30% PEG550MME, 50mM MgCl2
Matthews coefficient: 2.63
Solvent content (%): 53.26
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: 2022-10-12
Crystal structure of Tdp1 catalytic domain in complex with compound XZ532 (PDB entry 6DJJ)
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): 1.741
R work: 0.1736
R free: 0.2064
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 292
Crystal growth procedure: 0.1 M MOPS/HEPES-Na pH 7.5
10% w/v PEG 8000
20% v/v ethylene glycol
0.03M sodium fluoride
0.03M sodium bromide
0.03M sodium iodide
Matthews coefficient: 2.43
Solvent content (%): 49.48
Ligand: 4-aminobenzene-1,2-dicarboxylic acid (GM7)
Ligand formula: C8 H7 N O4
Ligand molecular weight: 181.145
Ligand SMILES: c1cc(c(cc1N)C(=O)O)C(=O)O
Ligand InChI: InChI=1S/C8H7NO4/c9-4-1-2-5(7(10)11)6(3-4)8(12)13/h1-3H,9H2,(H,10,11)(H,12,13)
Release date: 2019-05-29
Fragment-based screening of HSP70 sheds light on the functional role of ATP-binding site residues (PDB entry 5AQH)
Macromolecule: HEAT SHOCK COGNATE 71 KDA PROTEIN
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.3.51
Sequence length: 386 residues
Sequence: GPLGSMSKGPAVGIDLGTTYSCVGVFQHGKVEIIANDQGNRTTPSYVAFTDTERLIGDAAKNQVAMNPTNTVFDAKRLIGRRFDDAVVQSDMKHWPFMVVNDAGRPKVQVEYKGETKSFYPEEVSSMVLTKMKEIAEAYLGKTVTNAVVTVPAYFNDSQRQATKDAGTIAGLNVLRIINEPTAAAIAYGLDKKVGAERNVLIFDLGGGTFDVSILTIEDGIFEVKSTAGDTHLGGEDFDNRMVNHFIAEFKRKHKKDISENKRAVRRLRTACERAKRTLSSSTQASIEIDSLYEGIDFYTSITRARFEELNADLFRGTLDPVEKALRDAKLDKSQIHDIVLVGGSTRIPKIQKLLQDFFNGKELNKSINPDEAVAYGAAVQAAILS
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.0
R work: 0.1841
R free: 0.2277
Average B factor: 36.91
Crystallization pH: 8.5
Crystal growth procedure: 16-26% (W/V) PEG3350, 0.1 M K-NA TARTRATE, 0.1 M TRIS.HCL PH 8.5 AND 25% (V/V) GLYCEROL
Matthews coefficient: 2.5
Solvent content (%): 50.76
Ligand: 5-methyl-1,5-dihydro-1,4,5,6,8-pentaazaacenaphthylen-3-amine (ZVO)
Ligand formula: C8 H8 N6
Ligand molecular weight: 188.189
Ligand SMILES: CN1c2c3c(c[nH]c3ncn2)C(=N1)N
Ligand InChI: InChI=1S/C8H8N6/c1-14-8-5-4(6(9)13-14)2-10-7(5)11-3-12-8/h2-3H,1H3,(H2,9,13)(H,10,11,12)
Release date: 2016-10-05
Crystal structure of TRIM24 PHD-bromodomain complexed with N-{1,3-dimethyl-2-oxo-6-[3-(oxolan-3-ylmethoxy)phenoxy]-2,3-dihydro-1H-1,3-benzodiazol-5-yl}-1-methyl-1H-imidazole-4-sulfonamide (7l) (PDB entry 4YBT)
Macromolecule: Transcription intermediary factor 1-alpha
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 6.3.2
Sequence length: 184 residues
Sequence: SPNEDWCAVCQNGGELLCCEKCPKVFHLSCHVPTLTNFPSGEWICTFCRDLSKPEVEYDCDAPSHNSEKKKTEGLVKLTPIDKRKCERLLLFLYCHEMSLAFQDPVPLTVPDYYKIIKNPMDLSTIKKRLQEDYSMYSKPEDFVADFRLIFQNCAEFNEPDSEVANAGIKLENYFEELLKNLYP
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.82
R work: 0.167
R free: 0.209
Average B factor: 42.04
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 298
Crystal growth procedure: 2.2-2.4M ammonium sulfate, 0.1M HEPES buffer pH 7.5, 2% PEG400 and 8-9% glycerol
Matthews coefficient: 2.37
Solvent content (%): 48.01
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: 2015-06-24
complex of human thrombin with XC-43 (PDB entry 7MJ5)
Macromolecule: Putative secreted salivary protein
Type: Protein, polypeptide(L)
Source organism: Xenopsylla cheopis
Sequence length: 36 residues
Sequence: KPVEAEVAQPKLYQRGEGGNGMEPIPEDVLNEALNA
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.15
R work: 0.1645
R free: 0.1927
Average B factor: 43.0751
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 298
Crystal growth procedure: 0.2 M magnesium acetate, 9 % PEG 8000
Matthews coefficient: 3.32
Solvent content (%): 62.94
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: 2021-12-22
Crystal structure of P21-activated kinase 4 in complex with an inhibitor compound 29 (PDB entry 5BMS)
Macromolecule: Serine/threonine-protein kinase PAK 4
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 293 residues
Sequence: GSHEQFRAALQLVVDPGDPRSYLDNFIKIGEGSTGIVCIATVRSSGKLVAVKKMDLRKQQRRELLFNEVVIMRDYQHENVVEMYNSYLVGDELWVVMEFLEGGALTDIVTHTRMNEEQIAAVCLAVLQALSVLHAQGVIHRDIKSDSILLTHDGRVKLSDFGFCAQVSKEVPRRKSLVGTPYWMAPELISRLPYGPEVDIWSLGIMVIEMVDGEPPYFNEPPLKAMKMIRDNLPPRLKNLHKVSPSLKGFLDRLLVRDPAQRATAAELLKHPFLAKAGPPASIVPLMRQNRTR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.903
R work: 0.1735
R free: 0.2303
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 0.2 M Tri-Potassium citrate and 20% PEG3350
Matthews coefficient: 2.9
Solvent content (%): 57.64
Ligand: N~2~-[(7-chloro-1H-benzimidazol-6-yl)methyl]-N~4~-(5-cyclopropyl-1H-pyrazol-3-yl)pyrimidine-2,4-diamine (4T6)
Ligand formula: C18 H17 Cl N8
Ligand molecular weight: 380.834
Ligand SMILES: c1cc2c(c(c1CNc3nccc(n3)Nc4cc([nH]n4)C5CC5)Cl)[nH]cn2
Ligand InChI: InChI=1S/C18H17ClN8/c19-16-11(3-4-12-17(16)23-9-22-12)8-21-18-20-6-5-14(25-18)24-15-7-13(26-27-15)10-1-2-10/h3-7,9-10H,1-2,8H2,(H,22,23)(H3,20,21,24,25,26,27)
Release date: 2015-07-01
Crystal structure of PDE4D catalytic domain complexed with 33a (PDB entry 7W4Y)
Macromolecule: cAMP-specific 3',5'-cyclic phosphodiesterase 4D
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.4.53
Sequence length: 373 residues
Sequence: SIPRFGVKTEQEDVLAKELEDVNKWGLHVFRIAELSGNRPLTVIMHTIFQERDLLKTFKIPVDTLITYLMTLEDHYHADVAYHNNIHAADVVQSTHVLLSTPALEAVFTDLEILAAIFASAIHDVDHPGVSNQFLINTNSELALMYNDSSVLENHHLAVGFKLLQEENCDIFQNLTKKQRQSLRKMVIDIVLATDMSKHMNLLADLKTMVETKKVTSSGVLLLDNYSDRIQVLQNMVHCADLSNPTKPLQLYRQWTDRIMEEFFRQGDRERERGMEISPMCDKHNASVEKSQVGFIDYIVHPLWETWADLVHPDAQDILDTLEDNREWYQSTIPQSPSPAPDDPEEGRQGQTEKFQFELTLEEDGESDTEKDA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.10002940118
R work: 0.196501567225
R free: 0.24396145707
Average B factor: 22.8378426616
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.4
Crystallization temperature (K): 277
Crystal growth procedure: 0.1 M Hepes (pH 7.4), 0.1 M MgCl2, 15% PEG3350, 10% isopropanol, 25% ethylene glycol
Matthews coefficient: 2.25
Solvent content (%): 45.32
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: 2022-03-16