satarupa22/MacromolecularLigandDB huggingface dataset:
POLYADPRIBOSYL GLYCOSIDASE IN COMPLEX WITH PDD00014909 (PDB entry 6HMN)
Macromolecule: Poly(ADP-ribose) glycohydrolase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.2.1.143
Sequence length: 531 residues
Sequence: GSSPDKKWLGTPIEEMRRMPRCGIRLPLLRPSANHTVTIRVDLLRAGEVPKPFPTHYKDLWDNKHVKMPCSEQNLYPVEDENGERTAGSRWELIQTALLNKFTRPQNLKDAILKYNVAYSKKWDFTALIDFWDKVLEEAEAQHLYQSILPDMVKIALCLPNICTQPIPLLAAAMNHSITMSQEQIASLLANAFFCTFPRRNAKMKSEYSSYPDINFNRLFEGRSSRKPEKLKTLFCYFRRVTAAAPTGLVTFTRQSLEDFPEWERCEKPLTRLHVTYEGTIEENGQGMLQVDFANRFVGGGVTSAGLVQEEIRFLINPELIISRLFTEVLDHNECLIITGTEQYSEYTGYAETYRWSRSHEDGSERDDWQRRCTEIVAIDALHFRRYLDQFVPEKMRRELNKAYCGFLRPGVSSENLSAVATGNWGCGAFGGDARLKALIQILAAAAAERDVVYFTFGDSELMRDIYSMHIFLTERKLTVGDVYKLLLRYYNEECRNCSTPGPDIKLYPFIYHAVESCAETADHSGQRTGT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.87
R work: 0.1611
R free: 0.2388
Average B factor: 53.42
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: Protein at 7.5 mg/mL in 50 mM HEPES, pH 7.0, 150 mM NaCl, 2 mM DTT was mixed with precipitant consisting of 18 - 23 percent PEG-3350, 0.2 M ammonium sulphate, 0.1 M PCTP pH 7.5 in a 1:1 ratio to give a 4 microL drop
Matthews coefficient: 2.49
Solvent content (%): 50.63
Ligand: DIMETHYL SULFOXIDE (DMS)
Ligand formula: C2 H6 O S
Ligand molecular weight: 78.133
Ligand SMILES: CS(=O)C
Ligand InChI: InChI=1S/C2H6OS/c1-4(2)3/h1-2H3
Release date: 2018-11-14
Monoclinic structure of human protein kinase CK2 catalytic subunit in complex with a heparin oligo saccharide (PDB entry 7B8H)
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): 1.34
R work: 0.1536
R free: 0.1639
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293.15
Crystal growth procedure: 1 microliter protein stock solution (8 mg/ml CK2alpha, 2 mM Heparin dodecasaccharide, 285.7 mM NaCl, 15 mM Tris, pH 8.5) was mixed with 2.5 microliter reservoir solution (32 %(w/v) PEG4000, 0.2 M malonate, 0.1 M Tris, pH 7.5). The resulting drop was equilibrated against 800 microliter reservoir solution. After equilibration the crystallization process was initialized by addition of 150 nanoliter micro seeding suspension. CK2alpha/heparin crystals grown in this way were prepared for cryo diffractometry by soaking them into a cryo solution consisting of 32 % (w/v) PEG4000, 0.2 M NaCl, 0.5 mM Heparin dodecasaccharide.
Matthews coefficient: 1.98
Solvent content (%): 38
Ligand: NICOTINIC ACID (NIO)
Ligand formula: C6 H5 N O2
Ligand molecular weight: 123.109
Ligand SMILES: c1cc(cnc1)C(=O)O
Ligand InChI: InChI=1S/C6H5NO2/c8-6(9)5-2-1-3-7-4-5/h1-4H,(H,8,9)
Release date: 2021-02-03
PanDDA analysis group deposition of models with modelled events (e.g. bound ligands) -- Crystal Structure of NUDT7 in complex with NUOOA000180 (PDB entry 5QH0)
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): 1.57
R work: 0.1958
R free: 0.2059
Average B factor: 31.373
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: 4.09
Solvent content (%): 69.91
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
Crystal structure of human aspartate beta-hydroxylase isoform a (PDB entry 5APA)
Macromolecule: ASPARTYL/ASPARAGINYL BETA-HYDROXYLASE
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11.16
Sequence length: 220 residues
Sequence: MHHHHHHSSGVDLGTENLYFQSMRSLYNVNGLKAQPWWTPKETGYTELVKSLERNWKLIRDEGLAVMDKAKGLFLPEDENLREKGDWSQFTLWQQGRRNENACKGAPKTCTLLEKFPETTGCRRGQIKYSIMHPGTHVWPHTGPTNCRLRMHLGLVIPKEGCKIRCANETKTWEEGKVLIFDDSFEHEVWQDASSFRLIFIVDVWHPELTPQQRRSLPAI
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.05
R work: 0.1529
R free: 0.1855
Crystal growth procedure: 50MM SODIUM MALATE, 20% PEG3350, 3% DEXTRAN SULFATE, 20MM NISO4
Matthews coefficient: 4.47
Solvent content (%): 72.52
Ligand: NICKEL (II) ION (NI)
Ligand formula: Ni
Ligand molecular weight: 58.693
Ligand SMILES: [Ni+2]
Ligand InChI: InChI=1S/Ni/q+2
Release date: 2015-09-23
Crystal structure of CTSB in complex with 212-148 (PDB entry 8HEN)
Macromolecule: Cathepsin B
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.22.1
Sequence length: 257 residues
Sequence: DLKLPASFDAREQWPQCPTIKEIRDQGSCGSCWAFGAVEAISDRICIHTNAHVSVEVSAEDLLTCCGSMCGDGCNGGYPAEAWNFWTRKGLVSGGLYESHVGCRPYSIPPCEHHVNGSRPPCTGEGDTPKCSKICEPGYSPTYKQDKHYGYNSYSVSNSEKDIMAEIYKNGPVEGAFSVYSDFLLYKSGVYQHVTGEMMGGHAIRILGWGVENGTPYWLVANSWNTDWGDNGFFKILRGQDHCGIESEVVAGIPRTD
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.95
R work: 0.1854
R free: 0.2315
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.2 M Magnesium chloride hexahydrate, 0.1 M NaAc pH 5.2, 28% w/v PEG 3350
Matthews coefficient: 2.14
Solvent content (%): 42.55
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: 2023-12-13
Fragment-based discovery of a highly potent, orally bioavailable inhibitor which modulates the phosphorylation and catalytic activity of ERK1/2 (PDB entry 6G9H)
Macromolecule: Mitogen-activated protein kinase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.24
Sequence length: 368 residues
Sequence: MAHHHHHHMAAAAAAGAGPEMVRGQVFDVGPRYTNLSYIGEGAYGMVCSAYDNVNKVRVAIKKISPFEHQTYCQRTLREIKILLRFRHENIIGINDIIRAPTIEQMKDVYIVQDLMETDLYKLLKTQHLSNDHICYFLYQILRGLKYIHSANVLHRDLKPSNLLLNTTCDLKICDFGLARVADPDHDHTGFLTEYVATRWYRAPEIMLNSKGYTKSIDIWSVGCILAEMLSNRPIFPGKHYLDQLNHILGILGSPSQEDLNCIINLKARNYLLSLPHKNKVPWNRLFPNADSKALDLLDKMLTFNPHKRIEVEQALAHPYLEQYYDPSDEPIAEAPFKFDMELDDLPKEKLKELIFEETARFQPGYRS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.73
R work: 0.162
R free: 0.213
Average B factor: 34.003
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.2
Crystallization temperature (K): 293
Crystal growth procedure: 0.3M (NH4)2SO4, 32.0%w/v MPEG 2000, 0.1M HEPES/NaOHpH=7.2, 0.02M Mercaptoethanol
Matthews coefficient: 2.32
Solvent content (%): 46.97
Ligand: ~{N}-~{tert}-butyl-2-[5-[5-chloranyl-2-(oxan-4-ylamino)pyrimidin-4-yl]-3-oxidanylidene-1~{H}-isoindol-2-yl]-~{N}-methyl-ethanamide (ERW)
Ligand formula: C24 H30 Cl N5 O3
Ligand molecular weight: 471.98
Ligand SMILES: CC(C)(C)N(C)C(=O)CN1Cc2ccc(cc2C1=O)c3c(cnc(n3)NC4CCOCC4)Cl
Ligand InChI: InChI=1S/C24H30ClN5O3/c1-24(2,3)29(4)20(31)14-30-13-16-6-5-15(11-18(16)22(30)32)21-19(25)12-26-23(28-21)27-17-7-9-33-10-8-17/h5-6,11-12,17H,7-10,13-14H2,1-4H3,(H,26,27,28)
Release date: 2018-05-30
Crystal Structure of human phosphodiesterase 10 in complex with 4-(azetidine-1-carbonyl)-2-methyl-N-(1-quinolin-2-ylimidazol-4-yl)pyrazole-3-carboxamide (PDB entry 5SEN)
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): 2.04
R work: 0.212
R free: 0.2507
Average B factor: 40.339
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 (%): 53.16
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: 2022-10-12
Crystal structure of CK2a1 V116I with hematein (PDB entry 6L23)
Macromolecule: Casein kinase II subunit alpha
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 340 residues
Sequence: GPLGSMSGPVPSRARVYTDVNTHRPREYWDYESHVVEWGNQDDYQLVRKLGRGKYSEVFEAINITNNEKVVVKILKPVKKKKIKREIKILENLRGGPNIITLADIVKDPVSRTPALVFEHINNTDFKQLYQTLTDYDIRFYMYEILKALDYCHSMGIMHRDVKPHNVMIDHEHRKLRLIDWGLAEFYHPGQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRKEPFFHGHDNYDQLVRIAKVLGTEDLYDYIDKYNIELDPRFNDILGRHSRKRWERFVHSENQHLVSPEALDFLDKLLRYDHQSRLTAREAMEHPYFYTVVKDQARMG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.9744942746
R work: 0.179110694155
R free: 0.228733919588
Average B factor: 21.9822130972
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277
Crystal growth procedure: Ethylene glycol
Matthews coefficient: 2.01
Solvent content (%): 38.9
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: 2021-03-31
Crystal structure of MTH1 in complex with alpha-mangostin (cocktail No. 9) (PDB entry 6AA4)
Macromolecule: 7,8-dihydro-8-oxoguanine triphosphatase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.1.55
Sequence length: 163 residues
Sequence: MASRLYTLVLVLQPQRVLLGMKKRGFGAGRWNGFGGKVQEGETIEDGARRELQEESGLTVDALHKVGQIVFEFVGEPELMDVHVFCTDSIQGTPVESDEMRPCWFQLDQIPFKDMWPDDSYWFPLLLQKKKFHGYFKFQGQDTILDYTLREVDTVLEHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.9
R work: 0.2056
R free: 0.2436
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 25% PEG3350, 1.8mM ZnSO4, 6% sucrose, 0.1M Bis-Tris pH 6.1
Matthews coefficient: 2.07
Solvent content (%): 40.44
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: 2019-03-06
Crystal structure of CHK1-10pt-mutant complex with compound 45 (PDB entry 7BK3)
Macromolecule: Serine/threonine-protein kinase Chk1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 297 residues
Sequence: MAVPFVEDWDLVQTLGEGAYGEVQLAVNRVTEEAVAVKIVDMKRAVDCPENIKKEICILKMLNHENVIKFYGHRREGNIQYLFMELASGGSLFDRIEPDIGMPEPDAQRFFHQLMAGVVYLHGIGITHRDIKPHNLLLDERDNLKIADYSLATVFRYNNRERLLNKMCGTLPYVAPELLKRREFHAEPVDVWSCGIVLTAMLAGELPWDQPSDSCQEYSDWKEKKTYLNPWKKIDSAPLALLHKILVENPSARITIPDIKKDRWYNKPLKKGAKRPRVTSGGVSESPSGHHHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.0
R work: 0.1705
R free: 0.2245
Average B factor: 32.305
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 7% PEG 8000, 0.1 M MES buffer pH 6.5, 20% ethylene glycol
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: 2021-07-07
EGFR kinase in complex with TAS6417 (CLN-081) (PDB entry 8F1H)
Macromolecule: Epidermal growth factor receptor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 331 residues
Sequence: GSTSGEAPNQALLRILKETEFKKIKVLGSGAFGTVYKGLWIPEGEKVKIPVAIKELREATSPKANKEILDEAYVMASVDNPHVCRLLGICLTSTVQLITQLMPFGCLLDYVREHKDNIGSQYLLNWCVQIAKGMNYLEDRRLVHRDLAARNVLVKTPQHVKITDFGLAKLLGAEEKEYHAEGGKVPIKWMALESILHRIYTHQSDVWSYGVTVWELMTFGSKPYDGIPASEISSILEKGERLPQPPICTIDVYMIMVKCWMIDADSRPKFRELIIEFSKMARDPQRYLVIQGDERMHLPSPTDSNFYRALMDEEDMDDVVDADEYLIPQQG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.8
R work: 0.1845
R free: 0.2122
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M MES pH=6.5, 1.1 M Sodium Citrate
Matthews coefficient: 3.47
Solvent content (%): 64.53
Ligand: N-[(5P,8S,10R)-4-amino-6-methyl-5-(quinolin-3-yl)-8,9-dihydropyrimido[5,4-b]indolizin-8-yl]prop-2-enamide (X9H)
Ligand formula: C23 H20 N6 O
Ligand molecular weight: 396.445
Ligand SMILES: CC1=CC(Cn2c1c(c3c2ncnc3N)c4cc5ccccc5nc4)NC(=O)C=C
Ligand InChI: InChI=1S/C23H20N6O/c1-3-18(30)28-16-8-13(2)21-19(15-9-14-6-4-5-7-17(14)25-10-15)20-22(24)26-12-27-23(20)29(21)11-16/h3-10,12,16H,1,11H2,2H3,(H,28,30)(H2,24,26,27)/t16-/m0/s1
Release date: 2023-11-08
Crystal structure of human methionine aminopeptidase 12 (MAP12) in complex with two cobalt ions (PDB entry 8KHN)
Macromolecule: Methionine aminopeptidase 1D, mitochondrial
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.11.18
Sequence length: 313 residues
Sequence: MGSSHHHHHHSSGLVPRGSHMRQRDISHSIVLPAAVSSAHPVPKHIKKPDYVTTGIVPDWGDSIEVKNEDQIQGLHQACQLARHVLLLAGKSLKVDMTTEEIDALVHREIISHNAYPSPLGYGGFPKSVCTSVNNVLCHGIPDSRPLQDGDIINIDVTVYYNGYHGDTSETFLVGNVDECGKKLVEVARRCRDEAIAACRAGAPFSVIGNTISHITHQNGFQVCPHFVGHGIGSYFHGHPEIWHHANDSDLPMEEGMAFTIEPIITEGSPEFKVLEDAWTVVSLDNQRSAQFEHTVLITSRGAQILTKLPHEA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.51
R work: 0.1926
R free: 0.2136
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 287
Crystal growth procedure: 0.1M HEPES pH 7.2, 0.1M Carboxylic acids, 17% (v/v) MPD, 17% (w/v) PEG 1000, 17% (w/v) PEG 3350
Matthews coefficient: 2.23
Solvent content (%): 44.76
Ligand: COBALT (II) ION (CO)
Ligand formula: Co
Ligand molecular weight: 58.933
Ligand SMILES: [Co+2]
Ligand InChI: InChI=1S/Co/q+2
Release date: 2024-01-24
Tankyrase-2 in complex with compound 15d (PDB entry 6A84)
Macromolecule: Tankyrase-2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.4.2.30
Sequence length: 48 residues
Sequence: MAHSPPGHHSVTGRPSVNGLALAEYVIYRGEQAYPEYLITYQIMRPEG
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.98
R work: 0.1691
R free: 0.2136
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.1M Tris pH 8.5, 2.4M (NH4)2HPO4
Matthews coefficient: 2.64
Solvent content (%): 53.36
Ligand: 2-(4-chloro-1,2-dihydro-1'H-spiro[indole-3,4'-piperidin]-1'-yl)-5,6,7,8-tetrahydroquinazolin-4(3H)-one (9SU)
Ligand formula: C20 H23 Cl N4 O
Ligand molecular weight: 370.876
Ligand SMILES: c1cc2c(c(c1)Cl)C3(CCN(CC3)C4=NC5=C(CCCC5)C(=O)N4)CN2
Ligand InChI: InChI=1S/C20H23ClN4O/c21-14-5-3-7-16-17(14)20(12-22-16)8-10-25(11-9-20)19-23-15-6-2-1-4-13(15)18(26)24-19/h3,5,7,22H,1-2,4,6,8-12H2,(H,23,24,26)
Release date: 2019-04-03
Crystal structure of PDE4D catalytic domain complexed with 17 (PDB entry 7W4X)
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): 2.20007326465
R work: 0.228741688885
R free: 0.252792779593
Average B factor: 32.9562702411
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% PEG 3350, 10% isopropanol, and 25% ethylene glycol
Matthews coefficient: 2.21
Solvent content (%): 44.45
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
Crystal structure of the dimethylarginine dimethylaminohydrolase adduct with N5-(1-imino-2-chloroethyl)-L-lysine (PDB entry 6DGE)
Macromolecule: N(G),N(G)-dimethylarginine dimethylaminohydrolase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.5.3.18
Sequence length: 308 residues
Sequence: MGSSHHHHHHSSGLVPRGSHMASMAGLGHPAAFGRATHAVVRALPESLGQHALRSAKGEEVDVARAERQHQLYVGVLGSKLGLQVVELPADESLPDCVFVEDVAVVCEETALITRPGAPSRRKEVDMMKEALEKLQLNIVEMKDENATLDGGDVLFTGREFFVGLSKRTNQRGAEILADTFKDYAVSTVPVADGLHLKSFCSMAGPNLIAIGSSESAQKALKIMQQMSDHRYDKLTVPDDIAANCIYLNIPNKGHVLLHRTPEEYPESAKVYEKLKDHMLIPVSMSELEKVDGLLTCCSVLINKKVDS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.91
R work: 0.2148
R free: 0.2507
Average B factor: 24.68
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.3
Crystallization temperature (K): 277
Crystal growth procedure: 20% PEG 3350
0.2 M NaCl
Matthews coefficient: 2.03
Solvent content (%): 39.42
Ligand: N~6~-[(1E)-2-chloroethanimidoyl]-L-lysine (GBG)
Ligand formula: C8 H16 Cl N3 O2
Ligand molecular weight: 221.685
Ligand SMILES: C(CCNC(=N)CCl)CC(C(=O)O)N
Ligand InChI: InChI=1S/C8H16ClN3O2/c9-5-7(11)12-4-2-1-3-6(10)8(13)14/h6H,1-5,10H2,(H2,11,12)(H,13,14)/t6-/m0/s1
Release date: 2018-07-25
CCT068127 in complex with CDK2 (PDB entry 5MHQ)
Macromolecule: Cyclin-dependent kinase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.22
Sequence length: 306 residues
Sequence: GPLGSPEFMENFQKVEKIGEGTYGVVYKARNKLTGEVVALKKIRLDTETEGVPSTAIREISLLKELNHPNIVKLLDVIHTENKLYLVFEFLHQDLKKFMDASALTGIPLPLIKSYLFQLLQGLAFCHSHRVLHRDLKPQNLLINTEGAIKLADFGLARAFGVPVRTYTHEVVTLWYRAPEILLGCKYYSTAVDIWSLGCIFAEMVTRRALFPGDSEIDQLFRIFRTLGTPDEVVWPGVTSMPDYKPSFPKWARQDFSKVVPPLDEDGRSLLSQMLHYDPNKRISAKAALAHPFFQDVTKPVPHLRL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.3
R work: 0.1885
R free: 0.22597
Average B factor: 24.36
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.4
Crystallization temperature (K): 293
Crystal growth procedure: 10mg/ml CDK2
10% V/V PEG3350, 50 mM HEPES/NAOH, 50 mM NA/K PHOSPHATE, pH 7.5.
Matthews coefficient: 1.91
Solvent content (%): 35.77
Ligand: (2~{R},3~{S})-3-[[9-propan-2-yl-6-(pyridin-3-ylmethylamino)purin-2-yl]amino]pentan-2-ol (8QT)
Ligand formula: C19 H27 N7 O
Ligand molecular weight: 369.464
Ligand SMILES: CCC(C(C)O)Nc1nc(c2c(n1)n(cn2)C(C)C)NCc3cccnc3
Ligand InChI: InChI=1S/C19H27N7O/c1-5-15(13(4)27)23-19-24-17(21-10-14-7-6-8-20-9-14)16-18(25-19)26(11-22-16)12(2)3/h6-9,11-13,15,27H,5,10H2,1-4H3,(H2,21,23,24,25)/t13-,15+/m1/s1
Release date: 2017-12-20
The tandem SH2 domains of SYK with a bound CD3G diphospho-ITAM peptide (PDB entry 7Q5U)
Macromolecule: Tyrosine-protein kinase SYK
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 265 residues
Sequence: SMADSANHLPFFFGNITREEAEDYLVQGGMSDGLYLLRQSRNYLGGFALSVAHGRKAHHYTIERELNGTYAIAGGRTHASPADLCHYHSQESDGLVCLLKKPFNRPQGVQPKTGPFEDLKENLIREYVKQTWNLQGQALEQAIISQKPQLEKLIATTAHEKMPWFHGKISREESEQIVLIGSKTNGKFLIRARDNNGSYALCLLHEGKVLHYRIDKDKTGKLSIPEGKKFDTLWQLVEHYSYKADGLLRVLTVPCQKIGTQGNVN
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.4
R work: 0.2165
R free: 0.2588
Average B factor: 45.203
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6
Crystallization temperature (K): 293
Crystal growth procedure: 100 mM MMT buffer, 30% PEG 1000
Matthews coefficient: 2.91
Solvent content (%): 57.67
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: 2021-11-24
HUMAN GAR TRANSFORMYLASE IN COMPLEX WITH GAR AND (S)-2-({4-[3-(2-AMINO-4-OXO-4,7-DIHYDRO-3H-PYRROLO[2,3-D]PYRIMIDIN-6-YL)-PROPYL]-THIOPHENE-2-CARBONYL}-AMINO)-PENTANEDIOIC ACID (PDB entry 4ZZ1)
Macromolecule: Trifunctional purine biosynthetic protein adenosine-3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 6.3.4.13
Sequence length: 210 residues
Sequence: MARVAVLISGTGSNLQALIDSTREPNSSAQIDIVISNKAAVAGLDKAERAGIPTRVINHKLYKNRVEFDSAIDLVLEEFSIDIVCLAGFMRILSGPFVQKWNGKMLNIHPSLLPSFKGSNAHEQALETGVTVTGCTVHFVAEDVDAGQIILQEAVPVKRGDTVATLSERVKLAEHKIFPAALQLVASGTVQLGENGKICWVKEEHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.351
R work: 0.1396
R free: 0.1577
Average B factor: 23.5851
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 18 % PEG4000, 2 % PEG400, 0.33 M NaCl
Matthews coefficient: 3.86
Solvent content (%): 68.1
Ligand: GLYCINAMIDE RIBONUCLEOTIDE (GAR)
Ligand formula: C7 H13 N2 O8 P
Ligand molecular weight: 284.16
Ligand SMILES: C(C1C(C(C(O1)NC(=O)CN)O)O)OP(=O)([O-])[O-]
Ligand InChI: InChI=1S/C7H15N2O8P/c8-1-4(10)9-7-6(12)5(11)3(17-7)2-16-18(13,14)15/h3,5-7,11-12H,1-2,8H2,(H,9,10)(H2,13,14,15)/p-2/t3-,5-,6-,7-/m1/s1
Release date: 2015-12-16
CRYSTAL STRUCTURE OF HUMAN DNA POLYMERASE ETA INSERTING dTTP ACROSS A DNA TEMPLATE CONTAINING 1,N6-ETHENODEOXYADENOSINE LESION (PDB entry 5DG7)
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): 2.26
R work: 0.1559
R free: 0.2123
Average B factor: 29.7
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 291
Crystal growth procedure: 0.1M MES pH 5.5, 5mM calcium chloride, 16% PEG 2000 MME
Matthews coefficient: 2.12
Solvent content (%): 41.91
Ligand: THYMIDINE-5'-TRIPHOSPHATE (TTP)
Ligand formula: C10 H17 N2 O14 P3
Ligand molecular weight: 482.168
Ligand SMILES: CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O
Ligand InChI: InChI=1S/C10H17N2O14P3/c1-5-3-12(10(15)11-9(5)14)8-2-6(13)7(24-8)4-23-28(19,20)26-29(21,22)25-27(16,17)18/h3,6-8,13H,2,4H2,1H3,(H,19,20)(H,21,22)(H,11,14,15)(H2,16,17,18)/t6-,7+,8+/m0/s1
Release date: 2016-06-08