satarupa22/MacromolecularLigandDB huggingface dataset:
Crystal structure of the Fyn SH3 domain A95S-D99T mutant in C21 space group (PDB entry 7A2M)
Macromolecule: Tyrosine-protein kinase Fyn
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 60 residues
Sequence: GVTLFVALYDYESRTETDLSFHKGEKFQILNSSEGDWWEARSLTTGETGYIPSNYVAPVD
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.5
R work: 0.2126
R free: 0.255
Average B factor: 42.1828
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 4
Crystallization temperature (K): 298
Crystal growth procedure: 4.5 M sodium formate, 0.1 sodium acetate
Matthews coefficient: 2.66
Solvent content (%): 53.83
Ligand: SODIUM ION ()
Ligand formula: Na
Ligand molecular weight: 22.99
Ligand SMILES: [Na+]
Ligand InChI: InChI=1S/Na/q+1
Release date: 2021-08-25
Structure of human PARP1 catalytic domain bound to a quinazoline-2,4(1H,3H)-dione inhibitor (PDB entry 5KPP)
Macromolecule: Poly [ADP-ribose] polymerase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.4.2.30
Sequence length: 350 residues
Sequence: KSKLPKPVQDLIKMIFDVESMKKAMVEYEIDLQKMPLGKLSKRQIQAAYSILSEVQQAVSQGSSDSQILDLSNRFYTLIPHDFGMKKPPLLNNADSVQAKAEMLDNLLDIEVAYSLLRGGSDDSSKDPIDVNYEKLKTDIKVVDRDSEEAEIIRKYVKNTHATTHNAYDLEVIDIFKIEREGECQRYKPFKQLHNRRLLWHGSRTTNFAGILSQGLRIAPPEAPVTGYMFGKGIYFADMVSKSANYCHTSQGDPIGLILLGEVALGNMYELKHASHISKLPKGKHSVKGLGKTTPDPSANISLDGVDVPLGTGISSGVNDTSLLYNEYIVYDIAQVNLKYLLKLKFNFKT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.33
R work: 0.23889
R free: 0.28354
Average B factor: 48.719
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 298
Crystal growth procedure: 2.5M AMMONIUM SULFATE, 100mM TRIS
Matthews coefficient: 2.35
Solvent content (%): 47.73
Ligand: 1-[[4-fluoranyl-3-[(3R)-3-methyl-4-[2,2,2-tris(fluoranyl)ethyl]piperazin-1-yl]carbonyl-phenyl]methyl]quinazoline-2,4-dione (6WZ)
Ligand formula: C23 H22 F4 N4 O3
Ligand molecular weight: 478.439
Ligand SMILES: CC1CN(CCN1CC(F)(F)F)C(=O)c2cc(ccc2F)CN3c4ccccc4C(=O)NC3=O
Ligand InChI: InChI=1S/C23H22F4N4O3/c1-14-11-29(8-9-30(14)13-23(25,26)27)21(33)17-10-15(6-7-18(17)24)12-31-19-5-3-2-4-16(19)20(32)28-22(31)34/h2-7,10,14H,8-9,11-13H2,1H3,(H,28,32,34)/t14-/m1/s1
Release date: 2016-11-30
Crystal structure of inhibitory protein SOCS1 in complex with JAK1 kinase domain (PDB entry 6C7Y)
Macromolecule: Tyrosine-protein kinase JAK1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 286 residues
Sequence: AHFEKRFLKRIRDLGEGHFGKVELCRYDPEGDNTGEQVAVKSLKPESGGNHIADLKKEIEILRNLYHENIVKYKGICTEDGGNGIKLIMEFLPSGSLKEYLPKNKNKINLKQQLKYAVQICKGMDYLGSRQYVHRDLAARNVLVESEHQVKIGDFGLTKAIETDKEYYTVKDDRDSPVFWYAPECLMQSKFYIASDVWSFGVTLHELLTYCDSDSSPMALFLKMIGPTHGQMTVTRLVNTLKEGKRLPCPPNCPDEVYQLMRKCWEFQPSNRTSFQNLIEGFEALL
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.499
R work: 0.2067
R free: 0.2414
Average B factor: 86.2543
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7
Crystallization temperature (K): 281
Crystal growth procedure: 100mM HEPES pH 7.0, 14% (w/v) PEG8000, 100mM magnesium acetate, 2mM TCEP
Matthews coefficient: 3.09
Solvent content (%): 60.17
Ligand: ADENOSINE-5'-DIPHOSPHATE (ADP)
Ligand formula: C10 H15 N5 O10 P2
Ligand molecular weight: 427.201
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
Ligand InChI: InChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
Release date: 2018-05-02
Crystal structure for the complex of human carbonic anhydrase IV and topiramate (PDB entry 5JNA)
Macromolecule: Carbonic anhydrase 4
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 266 residues
Sequence: AESHWCYEVQAESSNYPCLVPVKWGGNCQKDRQSPINIVTTKAKVDKKLGRFFFSGYDKKQTWTVQNNGHSVMMLLENKASISGGGLPAPYQAKQLHLHWSDLPYKGSEHSLDGEHFAMEMHIVHEKEKGTSRNVKEAQDPEDEIAVLAFLVEAGTQVNEGFQPLVEALSNIPKPEMSTTMAESSLLDLLPKEEKLRHYFRYLGSLTTPTCDEKVVWTVFREPIQLHREQILAFSQKLYYDKEQTVSMKDNVRPLQQLGQRTVIKS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2
R work: 0.17223
R free: 0.21835
Average B factor: 27.743
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 4.6
Crystallization temperature (K): 277
Crystal growth procedure: 100 mM Na acetate, 200 mM AmSO4 and 21% PEG 4000
Matthews coefficient: 2.5
Solvent content (%): 51.3
Ligand: ZINC ION (ZN)
Ligand formula: Zn
Ligand molecular weight: 65.409
Ligand SMILES: [Zn+2]
Ligand InChI: InChI=1S/Zn/q+2
Release date: 2017-05-03
Crystal structure of human steroid carrier protein SL (SCP-2L) mutant V83C (PDB entry 6Z1X)
Macromolecule: Peroxisomal multifunctional enzyme type 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.1.1
Sequence length: 120 residues
Sequence: MEGGKLQSTFVFEEIGRRLKDIGPEVVKKVNAVFEWHITKGGNIGAKWTIDLKSGSGKVYQGPAKGAADTTIILSDEDFMEVCLGKLDPQKAFFSGRLKARGNIMLSQKLQMILKDYAKL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.09
R work: 0.1806
R free: 0.237
Average B factor: 20.315
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.4
Crystallization temperature (K): 277
Crystal growth procedure: 2.2 M ammonium sulfate, 0.2 M NaCl and 0.1 M citric acid
Matthews coefficient: 2.1
Solvent content (%): 41
Ligand: SULFATE ION (SO4)
Ligand formula: O4 S
Ligand molecular weight: 96.063
Ligand SMILES: [O-]S(=O)(=O)[O-]
Ligand InChI: InChI=1S/H2O4S/c1-5(2,3)4/h(H2,1,2,3,4)/p-2
Release date: 2021-03-03
Crystal Structure of R192F hFen1 in complex with DNA (PDB entry 5ZOG)
Macromolecule: Flap endonuclease 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1
Sequence length: 344 residues
Sequence: MGIQGLAKLIADVAPSAIRENDIKSYFGRKVAIDASMSIYQFLIAVRQGGDVLQNEEGETTSHLMGMFYRTIRMMENGIKPVYVFDGKPPQLKSGELAKRSERRAEAEKQLQQAQAAGAEQEVEKFTKRLVKVTKQHNDECKHLLSLMGIPYLDAPSEAEASCAALVKAGKVYAAATEDMDCLTFGSPVLMFHLTASEAKKLPIQEFHLSRILQELGLNQEQFVDLCILLGSDYCESIRGIGPKRAVDLIQKHKSIEEIVRRLDPNKYPVPENWLHKEAHQLFLEPEVLDPESVELKWSEPNEEELIKFMCGEKQFSEERIRSGVKRLSKSRQKLAAALEHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.299
R work: 0.2087
R free: 0.2313
Average B factor: 63.2635
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.8
Crystallization temperature (K): 298
Crystal growth procedure: PEG 3350, MgCl2, Tris, KCl
Matthews coefficient: 3.88
Solvent content (%): 68.33
Release date: 2019-01-30
Caspase-8 specific unnatural amino acid peptides (PDB entry 4PRY)
Macromolecule: Caspase-3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.22.56
Sequence length: 285 residues
Sequence: MENTENSVDSKSIKNLEPKIIHGSESMDSGISLDNSYKMDYPEMGLCIIINNKNFHKSTGMTSRSGTDVDAANLRETFRNLKYEVRNKNDLTREEIVELMRDVSKEDHSKRSSFVCVLLSHGEEGIIFGTNGPVDLKKITNFFRGDRCRSLTGKPKLFIIQACRGTELDCGIETDSGVDDDMACHKIPVEADFLYAYSTAPGYYSWRNSKDGSWFIQSLCAMLKQYADKLEFMHILTRVNRKVATEFESFSFDATFHAKKQIPCIVSMLTKELYFYHQLHHHHHH
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.7
R work: 0.1549
R free: 0.1868
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 295
Crystal growth procedure: 0.1 M Sodium citrate, pH 5.5, 12% PEG6000, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Matthews coefficient: 2.11
Solvent content (%): 41.68
Release date: 2015-01-21
Human Carbonic Anhydrase II native 07 atm CO2 (PDB entry 6KM4)
Macromolecule: Carbonic anhydrase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 260 residues
Sequence: MSHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHAFNVEFDDSQDKAVLKGGPLDGTYRLIQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDFGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTKGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLLECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.15
R work: 0.098
R free: 0.1242
Average B factor: 14.62
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.8
Crystallization temperature (K): 293
Crystal growth procedure: 1.3 M sodium citrate, 100 mM Tris-HCl
Matthews coefficient: 2.08
Solvent content (%): 41
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: 2020-08-05
Structure of human butyrylcholinesterase in complex with N-{[2-(benzyloxy)-3-methoxyphenyl]methyl}-N-[3-(2-fluorophenyl)propyl]cyclobutanamine (PDB entry 8CGO)
Macromolecule: Cholinesterase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.1.8
Sequence length: 529 residues
Sequence: EDDIIIATKNGKVRGMQLTVFGGTVTAFLGIPYAQPPLGRLRFKKPQSLTKWSDIWNATKYANSCCQNIDQSFPGFHGSEMWNPNTDLSEDCLYLNVWIPAPKPKNATVLIWIYGGGFQTGTSSLHVYDGKFLARVERVIVVSMNYRVGALGFLALPGNPEAPGNMGLFDQQLALQWVQKNIAAFGGNPKSVTLFGESAGAASVSLHLLSPGSHSLFTRAILQSGSFNAPWAVTSLYEARNRTLNLAKLTGCSRENETEIIKCLRNKDPQEILLNEAFVVPYGTPLSVNFGPTVDGDFLTDMPDILLELGQFKKTQILVGVNKDEGTAFLVYGAPGFSKDNNSIITRKEFQEGLKIFFPGVSEFGKESILFHYTDWVDDQRPENYREALGDVVGDYNFICPALEFTKKFSEWGNNAFFYYFEHRSSKLPWPEWMGVMHGYEIEFVFGLPLERRDQYTKAEEILSRSIVKRWANFAKYGNPQETQNQSTSWPVFKSTEQKYLTLNTESTRIMTKLRAQQCRFWTSFFPKV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.65
R work: 0.1776
R free: 0.2155
Average B factor: 69.9
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: Ammonium Sulfate
Matthews coefficient: 3.11
Solvent content (%): 60.51
Ligand: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID (MES)
Ligand formula: C6 H13 N O4 S
Ligand molecular weight: 195.237
Ligand SMILES: C1COCC[NH+]1CCS(=O)(=O)[O-]
Ligand InChI: InChI=1S/C6H13NO4S/c8-12(9,10)6-3-7-1-4-11-5-2-7/h1-6H2,(H,8,9,10)
Release date: 2023-06-14
Linked KDM5A Jmj Domain Bound to the Inhibitor C49 (2-{[(2-{[(E)-2-(dimethylamino)ethenyl](ethyl)amino}-2-oxoethyl)amino]methyl}pyridine-4-carboxylic acid) (PDB entry 5ISL)
Macromolecule: Lysine-specific demethylase 5A
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): 1.694
R work: 0.1701
R free: 0.2019
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: 2.21
Solvent content (%): 44.23
Ligand: 2-{[(2-{[(E)-2-(dimethylamino)ethenyl](ethyl)amino}-2-oxoethyl)amino]methyl}pyridine-4-carboxylic acid (MMK)
Ligand formula: C15 H22 N4 O3
Ligand molecular weight: 306.36
Ligand SMILES: CCN(C=CN(C)C)C(=O)CNCc1cc(ccn1)C(=O)O
Ligand InChI: InChI=1S/C15H22N4O3/c1-4-19(8-7-18(2)3)14(20)11-16-10-13-9-12(15(21)22)5-6-17-13/h5-9,16H,4,10-11H2,1-3H3,(H,21,22)/b8-7+
Release date: 2016-07-27
Crystal structure of bat influenza A/H17N10 polymerase with viral RNA promoter bound to a 22-mer modified Pol II CTD peptide with serine 5 thiophosphorylated. (PDB entry 6FHH)
Macromolecule: Polymerase acidic protein
Type: Protein, polypeptide(L)
Source organism: Influenza A virus (A/little yellow-shouldered bat/Guatemala/060/2010(H17N10))
Sequence length: 738 residues
Sequence: GSHHHHHHHHGSGSMENFVRTNFNPMILERAEKTMKEYGENPQNEGNKFAAISTHMEVCFMYSDFHFIDLEGNTIVKENDDDNAMLKHRFEIIEGQERNIAWTIVNSICNMTENSKPRFLPDLYDYKTNKFIEIGVTRRKVEDYYYEKASKLKGENVYIHIFSFDGEEMATDDEYILDEESRARIKTRLFVLRQELATAGLWDSFRQSEKGEETLEEEFSYPPTFQRLANQSLPPSFKDYHQFKAYVSSFKANGNIEAKLGAMSEKVNAQIESFDPRTIRELELPEGKFCTQRSKFLLMDAMKLSVLNPAHEGEGIPMKDAKACLDTFWGWKKATIIKKHEKGVNTNYLMIWEQLLESIKEMEGKFLNLKKTNHLKWGLGEGQAPEKMDFEDCKEVPDLFQYKSEPPEKRKLASWIQSEFNKASELTNSNWIEFDELGNDVAPIEHIASRRRNFFTAEVSQCRASEYIMKAVYINTALLNSSCTAMEEYQVIPIITKCRDTSGQRRTNLYGFIIKGRSHLRNDTDVVNFISLEFSLTDPRNEIHKWEKYCVLEIGDMEIRTSISTIMKPVYLYVRTNGTSKIKMKWGMEMRRCLLQSLQQVESMIEAESAVKEKDMTEPFFRNRENDWPIGESPQGIEKGTIGKVCRVLLAKSVFNSIYASAQLEGFSAESRKLLLLIQAFRDNLDPGTFDLKGLYEAIEECIINDPWVLLNASWFNSFLKAVQLSMGSGSGENLYFQ
Oligomeric state: Hetero 5-mer
Stoichiometry: A1, B1, C1, D1, E1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.7
R work: 0.2129
R free: 0.25763
Average B factor: 90.198
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277
Crystal growth procedure: Bat FluA polymerase bound to the ends of the RNA promotor (5 prime end nts 1-16, 3 prime end nts 1-18) was co-crystallized in a 1:8 ratio with the thiophospho-serine-5 22-mer Pol II CTD peptide mimic in 0.8 M sodium-potassium phosphate at pH 5.0. Crystals were set at 4 C using seeding.
Matthews coefficient: 3.09
Solvent content (%): 60.2
Ligand: PHOSPHATE ION (PO4)
Ligand formula: O4 P
Ligand molecular weight: 94.971
Ligand SMILES: [O-]P(=O)([O-])[O-]
Ligand InChI: InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4)/p-3
Release date: 2019-01-30
Hybrid structural analysis of the Arp2/3 regulator Arpin identifies its acidic tail as a primary binding epitope (PDB entry 4Z68)
Macromolecule: Tankyrase-2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.4.2.30
Sequence length: 155 residues
Sequence: SEADRQLLEAAKAGDVETVKKLCTVQSVNCRDIEGRQSTPLHFAAGYNRVSVVEYLLQHGADVHAKDKGGLVPLHNACSYGHYEVAELLVKHGAVVNVADLWKFTPLHEAAAKGKYEICKLLLQHGADPTKKNRDGNTPLDLVKDGDTDIQDLLR
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.859
R work: 0.1698
R free: 0.2166
Average B factor: 20.6
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 291
Crystal growth procedure: ammonium sulfate, isopropanol
Matthews coefficient: 1.9
Solvent content (%): 35.22
Ligand: SULFATE ION (SO4)
Ligand formula: O4 S
Ligand molecular weight: 96.063
Ligand SMILES: [O-]S(=O)(=O)[O-]
Ligand InChI: InChI=1S/H2O4S/c1-5(2,3)4/h(H2,1,2,3,4)/p-2
Release date: 2015-12-30
LOW-SALT STRUCTURE OF PROTEIN KINASE CK2 CATALYTIC SUBUNIT (ISOFORM CK2ALPHA) IN COMPLEX WITH THE INDENOINDOLE-TYPE INHIBITOR 4P (PDB entry 5ONI)
Macromolecule: Casein kinase II subunit alpha
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 391 residues
Sequence: MSGPVPSRARVYTDVNTHRPREYWDYESHVVEWGNQDDYQLVRKLGRGKYSEVFEAINITNNEKVVVKILKPVKKKKIKREIKILENLRGGPNIITLADIVKDPVSRTPALVFEHVNNTDFKQLYQTLTDYDIRFYMYEILKALDYCHSMGIMHRDVKPHNVMIDHEHRKLRLIDWGLAEFYHPGQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRKEPFFHGHDNYDQLVRIAKVLGTEDLYDYIDKYNIELDPRFNDILGRHSRKRWERFVHSENQHLVSPEALDFLDKLLRYDHQSRLTAREAMEHPYFYTVVKDQARMGSSSMPGGSTPVSSANMMSGISSVPTPSPLGPLAGSPVIAAANPLGMPVPAAAGAQQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2
R work: 0.1751
R free: 0.2042
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 90 MICROLITER ENZYME STOCK SOLUTION (6 MG/ML IN 500 MM NACL, 25 MM
TRIS/HCL, PH 8.5) WAS MIXED WITH 10 MIKROLITER 4P STOCK
SOLUTION (10 MM 4P IN DMSO). THIS MIXTURE WAS INCUBATED FOR 30
MIN AT ROOM TEMPERATURE. THE RESERVOIR SOLUTION OF THE
CRYSTALLIZATION EXPERIMENT WAS 25 % (W/V) PEG5000, 0.2 M
AMMONIUM SULPHATE, 0.1 M MES BUFFER, PH 6.5. PRIOR TO
EQUILIBRATION THE CRYSTALLIZATION DROP WAS COMPOSED OF 1
MICROLITER RESERVOIR SOLUTION PLUS 1 MICROLITER ENZYME/4P
MIXTURE., VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K
Matthews coefficient: 3.2
Solvent content (%): 61.62
Ligand: 4-(3-methylbut-2-enoxy)-5-propan-2-yl-7,8-dihydro-6~{H}-indeno[1,2-b]indole-9,10-dione (9YE)
Ligand formula: C23 H25 N O3
Ligand molecular weight: 363.45
Ligand SMILES: CC(C)n1c2c(c3c1-c4c(cccc4OCC=C(C)C)C3=O)C(=O)CCC2
Ligand InChI: InChI=1S/C23H25NO3/c1-13(2)11-12-27-18-10-5-7-15-19(18)22-21(23(15)26)20-16(24(22)14(3)4)8-6-9-17(20)25/h5,7,10-11,14H,6,8-9,12H2,1-4H3
Release date: 2017-12-27
RING-DTC domain of Deltex1 bound to NAD (PDB entry 6Y5P)
Macromolecule: E3 ubiquitin-protein ligase DTX1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2.27
Sequence length: 235 residues
Sequence: GSKSKNPEDVVRRYMQKVKNPPDEDCTICMERLVTASGYEGVLRHKGVRPELVGRLGRCGHMYHLLCLVAMYSNGNKDGSLQCPTCKAIYGEKTGTQPPGKMEFHLIPHSLPGFPDTQTIRIVYDIPTGIQGPEHPNPGKKFTARGFPRHCYLPNNEKGRKVLRLLITAWERRLIFTIGTSNTTGESDTVVWNEIHHKTEFGSNLTGHGYPDASYLDNVLAELTAQGVSEAAAKA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.74
R work: 0.1853
R free: 0.2137
Average B factor: 44.4615
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.6
Crystallization temperature (K): 292
Crystal growth procedure: 0.16M Calcium acetate hydrate, 0.08MSodium cacodylate pH 6.5, 14.4% w/v PEG 8000, 20% v/v Glycerol
Matthews coefficient: 3.64
Solvent content (%): 66.23
Ligand: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NAD)
Ligand formula: C21 H27 N7 O14 P2
Ligand molecular weight: 663.425
Ligand SMILES: c1cc(c[n+](c1)C2C(C(C(O2)COP(=O)([O-])OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)O)O)O)O)C(=O)N
Ligand InChI: InChI=1S/C21H27N7O14P2/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(32)14(30)11(41-21)6-39-44(36,37)42-43(34,35)38-5-10-13(29)15(31)20(40-10)27-3-1-2-9(4-27)18(23)33/h1-4,7-8,10-11,13-16,20-21,29-32H,5-6H2,(H5-,22,23,24,25,33,34,35,36,37)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
Release date: 2020-09-30
Human DNA polymerase eta in a non-productive ternary complex with Ca2+ and dTTP oppositing cdA (PDB entry 6M7T)
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): 2.8
R work: 0.2201
R free: 0.2612
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 295
Crystal growth procedure: 16 % PEG 2000 MME
100 mM MES, pH 6.0
Matthews coefficient: 3.43
Solvent content (%): 64.12
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: 2018-09-12
Structure of human PARG complexed with JA2120 (PDB entry 6OA1)
Macromolecule: Poly(ADP-ribose) glycohydrolase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.2.1.143
Sequence length: 533 residues
Sequence: GPHMSPDKKWLGTPIEEMRRMPRCGIRLPLLRPSANHTVTIRVDLLRAGEVPKPFPTHYKDLWDNKHVKMPCSEQNLYPVEDENGERTAGSRWELIQTALLNKFTRPQNLKDAILKYNVAYSKKWDFTALIDFWDKVLEEAEAQHLYQSILPDMVKIALCLPNICTQPIPLLAAAMNHSITMSQEQIASLLANAFFCTFPRRNAKMKSEYSSYPDINFNRLFEGRSSRKPEKLKTLFCYFRRVTAAAPTGLVTFTRQSLEDFPEWERCEKPLTRLHVTYEGTIEENGQGMLQVDFANRFVGGGVTSAGLVQEEIRFLINPELIISRLFTEVLDHNECLIITGTEQYSEYTGYAETYRWSRSHEDGSERDDWQRRCTEIVAIDALHFRRYLDQFVPEKMRRELNKAYCGFLRPGVSSENLSAVATGNWGCGAFGGDARLKALIQILAAAAAERDVVYFTFGDSELMRDIYSMHIFLTERKLTVGDVYKLLLRYYNEECRNCSTPGPDIKLYPFIYHAVESCAETADHSGQRTGT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.16694
R free: 0.19937
Average B factor: 20.79
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 295
Crystal growth procedure: 20% PEG 3350, 0.05 M PCTP pH 7.5, 0.1 M NaCl, 0.15 M MgCl2
Matthews coefficient: 2.24
Solvent content (%): 45.06
Ligand: 1,3-dimethyl-8-{[2-(morpholin-4-yl)ethyl]sulfanyl}-3,7-dihydro-1H-purine-2,6-dione (M0P)
Ligand formula: C13 H19 N5 O3 S
Ligand molecular weight: 325.387
Ligand SMILES: CN1c2c([nH]c(n2)SCCN3CCOCC3)C(=O)N(C1=O)C
Ligand InChI: InChI=1S/C13H19N5O3S/c1-16-10-9(11(19)17(2)13(16)20)14-12(15-10)22-8-5-18-3-6-21-7-4-18/h3-8H2,1-2H3,(H,14,15)
Release date: 2019-12-25
Non-receptor Protein Tyrosine Phosphatase SHP2 F285S in Complex with Allosteric Inhibitor JLR-2 (PDB entry 6BN5)
Macromolecule: Tyrosine-protein phosphatase non-receptor type 11
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 526 residues
Sequence: SMTSRRWFHPNITGVEAENLLLTRGVDGSFLARPSKSNPGDFTLSVRRNGAVTHIKIQNTGDYYDLYGGEKFATLAELVQYYMEHHGQLKEKNGDVIELKYPLNCADPTSERWFHGHLSGKEAEKLLTEKGKHGSFLVRESQSHPGDFVLSVRTGDDKGESNDGKSKVTHVMIRCQELKYDVGGGERFDSLTDLVEHYKKNPMVETLGTVLQLKQPLNTTRINAAEIESRVRELSKLAETTDKVKQGFWEEFETLQQQECKLLYSRKEGQRQENKNKNRYKNILPSDHTRVVLHDGDPNEPVSDYINANIIMPEFETKCNNSKPKKSYIATQGCLQNTVNDFWRMVFQENSRVIVMTTKEVERGKSKCVKYWPDEYALKEYGVMRVRNVKESAAHDYTLRELKLSKVGQGNTERTVWQYHFRTWPDHGVPSDPGGVLDFLEEVHHKQESIMDAGPVVVHCSAGIGRTGTFIVIDILIDIIREKGVDCDIDVPKTIQMVRSQRSGMVQTEAQYRFIYMAVQHYIETL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.22
R work: 0.236
R free: 0.2917
Average B factor: 45.16
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8.6
Crystallization temperature (K): 298.15
Crystal growth procedure: 100 mM Tris pH 8.6, 20% PEG 3350, 1 mM TCEP
Matthews coefficient: 2.24
Solvent content (%): 45.14
Ligand: 3-benzyl-8-chloro-2-hydroxy-4H-pyrimido[2,1-b][1,3]benzothiazol-4-one (DZJ)
Ligand formula: C17 H11 Cl N2 O2 S
Ligand molecular weight: 342.799
Ligand SMILES: c1ccc(cc1)CC2=C(N=C3N(C2=O)c4ccc(cc4S3)Cl)O
Ligand InChI: InChI=1S/C17H11ClN2O2S/c18-11-6-7-13-14(9-11)23-17-19-15(21)12(16(22)20(13)17)8-10-4-2-1-3-5-10/h1-7,9,21H,8H2
Release date: 2017-12-13
Discovery of a Novel, Highly Potent, and Selective Thieno[3,2-d]pyrimidinone-Based Cdc7 inhibitor with a Quinuclidine Moiety (TAK-931) as an Orally Active Investigational Anti-Tumor Agent (PDB entry 6P5M)
Macromolecule: Rho-associated protein kinase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 405 residues
Sequence: GAMGSPGDGAGASRQRKLEALIRDPRSPINVESLLDGLNSLVLDLDFPALRKNKNIDNFLNRYEKIVKKIRGLQMKAEDYDVVKVIGRGAFGEVQLVRHKASQKVYAMKLLSKFEMIKRSDSAFFWEERDIMAFANSPWVVQLFYAFQDDRYLYMVMEYMPGGDLVNLMSNYDVPEKWAKFYTAEVVLALDAIHSMGLIHRDVKPDNMLLDKHGHLKLADFGTCMKMDETGMVHCDTAVGTPDYISPEVLKSQGGDGYYGRECDWWSVGVFLYEMLVGDTPFYADSLVGTYSKIMDHKNSLCFPEDAEISKHAKNLICAFLTDREVRLGRNGVEEIRQHPFFKNDQWHWDNIRETAAPVVPELSSDIDSSNFDDIEDDKGDVETFPIPKAFVGNQLPFIGFTYYR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.65
R work: 0.1934
R free: 0.225
Average B factor: 57.52
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.1
Crystallization temperature (K): 293
Crystal growth procedure: 0.8 M trisodium citrate, 0.1 M citrate, pH 5.1
Matthews coefficient: 4.01
Solvent content (%): 69.31
Ligand: 6-(5-methyl-1H-pyrazol-4-yl)-2-[(pyrrolidin-1-yl)methyl]thieno[3,2-d]pyrimidin-4(3H)-one (O1S)
Ligand formula: C15 H17 N5 O S
Ligand molecular weight: 315.393
Ligand SMILES: Cc1c(cn[nH]1)c2cc3c(s2)C(=O)NC(=N3)CN4CCCC4
Ligand InChI: InChI=1S/C15H17N5OS/c1-9-10(7-16-19-9)12-6-11-14(22-12)15(21)18-13(17-11)8-20-4-2-3-5-20/h6-7H,2-5,8H2,1H3,(H,16,19)(H,17,18,21)
Release date: 2020-01-15