satarupa22/MacromolecularLigandDB huggingface dataset:
Discovery of A Dual Inhibitor of NQO1 and GSTP1 for Treating Malignant Glioblastoma (PDB entry 6LLX)
Macromolecule: Glutathione S-transferase P
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.5.1.18
Sequence length: 215 residues
Sequence: SHMASMPPYTVVYFPVRGRCAALRMLLADQGQSWKEEVVTVETWQEGSLKASCLYGQLPKFQDGDLTLYQSNTILRHLGRTLGLYGKDQQEAALVDMVNDGVEDLRCKYISLIYTNYEAGKDDYVKALPGQLKPFETLLSQNQGGKTFIVGDQISFADYNLLDLLLIHEVLAPGCLDAFPLLSAYVGRLSARPKLKAFLASPEYVNLPINGNGKQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.581
R work: 0.2001
R free: 0.2229
Average B factor: 11.7893
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M MES PH5.8 ,30% PEG6000 ,10mM DTT
Matthews coefficient: 2.71
Solvent content (%): 54.64
Ligand: GLUTATHIONE (GSH)
Ligand formula: C10 H17 N3 O6 S
Ligand molecular weight: 307.323
Ligand SMILES: C(CC(=O)NC(CS)C(=O)NCC(=O)O)C(C(=O)O)N
Ligand InChI: InChI=1S/C10H17N3O6S/c11-5(10(18)19)1-2-7(14)13-6(4-20)9(17)12-3-8(15)16/h5-6,20H,1-4,11H2,(H,12,17)(H,13,14)(H,15,16)(H,18,19)/t5-,6-/m0/s1
Release date: 2020-11-25
Human DNA polymerase eta-DNA ternary complex: reaction with 10 mM Mn2+ for 30s (PDB entry 5KFG)
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): 1.55
R work: 0.1737
R free: 0.2042
Average B factor: 22.4785
Crystallization method: EVAPORATION
Crystallization pH: 6
Crystallization temperature (K): 298
Crystal growth procedure: 17% PEG 2000MME, 0.1 M MES
Matthews coefficient: 2.1
Solvent content (%): 41.4
Ligand: MANGANESE (II) ION (MN)
Ligand formula: Mn
Ligand molecular weight: 54.938
Ligand SMILES: [Mn+2]
Ligand InChI: InChI=1S/Mn/q+2
Release date: 2016-06-29
Complex structure of TRIM24 PHD-bromodomain and inhibitor 6 (PDB entry 5H1V)
Macromolecule: Transcription intermediary factor 1-alpha
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 6.3.2
Sequence length: 183 residues
Sequence: PNEDWCAVCQNGGELLCCEKCPKVFHLSCHVPTLTNFPSGEWICTFCRDLSKPEVEYDCDAPSHNSEKKKTEGLVKLTPIDKRKCERLLLFLYCHEMSLAFQDPVPLTVPDYYKIIKNPMDLSTIKKRLQEDYSMYSKPEDFVADFRLIFQNCAEFNEPDSEVANAGIKLENYFEELLKNLYP
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.002
R work: 0.1804
R free: 0.2203
Average B factor: 34.8989
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M HEPES sodium, 2%(v/v) Polyethylene glycol 400, 2.0 M Ammonium sulfate
Matthews coefficient: 2.39
Solvent content (%): 48.43
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: 2017-02-22
Crystal structure of GTB + B trisaccharide (mercury derivative) (PDB entry 5TJO)
Macromolecule: Histo-blood group ABO system transferase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.4.1.40
Sequence length: 297 residues
Sequence: AIGEFMVSLPRMVYPQPKVLTPCRKDVLVVTPWLAPIVWEGTFNIDILNEQFRLQNTTIGLTVFAIKKYVAFLKLFLETAEKHFMVGHRVHYYVFTDQPAAVPRVTLGTGRQLSVLEVGAYKRWQDVSMRRMEMISDFCERRFLSEVDYLVCVDVDMEFRDHVGVEILTPLFGTLHPSFYGSSREAFTYERRPQSQAYIPKDEGDFYYMGAFFGGSVQEVQRLTRACHQAMMVDQANGIEAVWHDESHLNKYLLRHKPTKVLSPEYLWDQQLLGWPAVLRKLRFTAVPKNHQAVRNP
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.57
R work: 0.1736
R free: 0.1958
Average B factor: 24.013
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 277
Crystal growth procedure: The first crystals of GTA/GTB were grown as mercury derivatives (Patenaude, S.I., et al. 2002): 10 ul drops with 6-8 mg/ml protein, 70 mM N-(2-acetamido)-2-iminodiacetic acid (ADA) pH 7.5, 50 mM, sodium acetate pH 4.6, 40 mM NaCl, 5-8 mM MnCl2, 2.5% (v/v) 2-methyl-2,4-pentanediol (MPD), 5%(v/v) glycerol, 2%(w/v) PEG 4000, and 0.3-0.5 mM 3-chloromercuri-2-methoxypropylurea suspended over 1 ml of a resevoir solution: 50 mM ADA pH 7.5, 10 mM MnCl2, 100 mM ammonium sulfate, 5%(v/v) MPD, 10%(v/v) glycerol, and 8-10%(w/v) PEG 4000. Crystals were washed with artificial mother liquor ML-1 consisting of 10% polyethylene glycol (PEG) 4000, 30 mM N-(2-acetamido)-2-iminodiacetic acid (ADA) buffer pH 7.5, 30 mM sodium acetate buffer pH 4.6, 100 mM ammonium sulfate, 10 mM MnCl2 and 30% glycerol as the cryoprotectant. Crystals of GTA/GTB in complex with the A and B trisaccharides were obtained by soaking them in mother liquor ML-1 with 30% glycerol and 45-50 mM substrates for 2-5 days at 18 degrees Celsius
Matthews coefficient: 2.27
Solvent content (%): 45.76
Ligand: MERCURY (II) ION (HG)
Ligand formula: Hg
Ligand molecular weight: 200.59
Ligand SMILES: [Hg+2]
Ligand InChI: InChI=1S/Hg/q+2
Release date: 2017-06-14
p107 pocket domain complexed with HDAC1 peptide (PDB entry 7SME)
Macromolecule: Retinoblastoma-like protein 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 371 residues
Sequence: GEFTQSVSRLQSIVAGLKNAPSDQLINIFESCVRNPVENIMKILKGIGETFCQHYTQSTDEQPGSHIDFAVNRLKLAEILYYKILETVMVQETRRLHGMDMSVLLEQDIFHRSLMACCLEIVLFAYSSPRTFPWIIEVLNLQPFYFYKVIEVVIRSEEGLSRDMVKHLNSIEEQILESLAWSHDSALWEALQVSANKVPTCEEVIFPNNFETGNNRPKRTGSLALFYRKVYHLASVRLRDLCLKLDVSNELRRKIWTCFEFTLVHCPDLMKDRHLDQLLLCAFYIMAKVTKEERTFQEIMKSYRNQPQANSHVYRSVLLKSIKEERGDLIKFYNTIYVGRVKSFALKYDLANQDHMMDAPPLSPFPHIKQQ
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.64
R work: 0.2241
R free: 0.2771
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 100 mM MES, pH 6.5, 4% PEG400, 1.6 M ammonium sulfate
Matthews coefficient: 2.97
Solvent content (%): 58.27
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: 2022-06-29
Crystal structure of human polymerase eta complexed with syn N7-benzylguanine (PDB entry 7L69)
Macromolecule: DNA polymerase eta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 432 residues
Sequence: MATGQDRVVALVDMDCFFVQVEQRQNPHLRNKPCAVVQYKSWKGGGIIAVSYEARAFGVTRSMWADDAKKLCPDLLLAQVRESRGKANLTKYREASVEVMEIMSRFAVIERASIDEAYVDLTSAVQERLQKLQGQPISADLLPSTYIEGLPQGPTTAEETVQKEGMRKQGLFQWLDSLQIDNLTSPDLQLTVGAVIVEEMRAAIERETGFQCSAGISHNKVLAKLACGLNKPNRQTLVSHGSVPQLFSQMPIRKIRSLGGKLGASVIEILGIEYMGELTQFTESQLQSHFGEKNGSWLYAMCRGIEHDPVKPRQLPKTIGCSKNFPGKTALATREQVQWWLLQLAQELEERLTKDRNDNDRVATQLVVSIRVQGDKRLSSLRRCCALTRYDAHKMSHDAFTVIKNCNTSGIQTEWSPPLTMLFLCATKFSAS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.91
R work: 0.1867
R free: 0.2237
Average B factor: 35.31
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 100 mM MES pH 6.5
20% PEG2000 MME
5 mM magnesium chloride
Matthews coefficient: 2.12
Solvent content (%): 41.87
Release date: 2022-01-05
Crystal structure of human KDM4A in complex with compound 34g (PDB entry 6H4V)
Macromolecule: Lysine-specific demethylase 4A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11
Sequence length: 360 residues
Sequence: SMASESETLNPSARIMTFYPTMEEFRNFSRYIAYIESQGAHRAGLAKVVPPKEWKPRASYDDIDDLVIPAPIQQLVTGQSGLFTQYNIQKKAMTVREFRKIANSDKYCTPRYSEFEELERKYWKNLTFNPPIYGADVNGTLYEKHVDEWNIGRLRTILDLVEKESGITIEGVNTPYLYFGMWKTSFAWHTEDMDLYSINYLHFGEPKSWYSVPPEHGKRLERLAKGFFPGSAQSCEAFLRHKMTLISPLMLKKYGIPFDKVTQEAGEFMITFPYGYHAGFNHGFNCAESTNFATRRWIEYGKQAVLCSCRKDMVKISMDVFVRKFQPERYKLWKAGKDNTVIDHTLPTPEAAEFLKESEL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.15
R work: 0.176
R free: 0.211
Average B factor: 61.31
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: Crystallisation solution is 0.1M Bis-Tris-Propane pH7.5, 12-16% PEG-4000. Inhibitor is soaked in crystals by addition directly to the drops of DMSO dissolved compound
Matthews coefficient: 2.59
Solvent content (%): 52.52
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: 2019-06-12
DNA Polymerase Mu Reactant Complex, Mn2+ (4 min) (PDB entry 5TYU)
Macromolecule: DNA-directed DNA/RNA polymerase mu
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 356 residues
Sequence: GSAAAPLSPAWMPAYACQRPTPLTHHNTGLSEALEILAEAAGFEGSEGRLLTFCRAASVLKALPSPVTTLSQLQGLPHFGEHSSRVVQELLEHGVCEEVERVRRSERYQTMKLFTQIFGVGVKTADRWYREGLRTLDDLREQPQKLTQQQKAGLQHHQDLSTPVLRSDVDALQQVVEEAVGQALPGATVTLTGGFRRGKLQGHDVDFLITHPKEGQEAGLLPRVMCRLQDQGLILYHQHQHSCCESPTRLAQQSHMDAFERSFCIFRLPQPGSWKAVRVDLVVAPVSQFPFALLGWTGSKLFQRELRRFSRKEKGLWLNSHGLFDPEQKTFFQAASEEDIFRHLGLEYLPPEQRNA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.048
R work: 0.1868
R free: 0.2125
Average B factor: 32.3326
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 85-90mM HEPES pH 7.5, 17-18% PEG4000
Matthews coefficient: 2.62
Solvent content (%): 53.07
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: 2017-08-30
Macrocyclic plasmin inhibitor (PDB entry 7THS)
Macromolecule: Plasminogen
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.7
Sequence length: 250 residues
Sequence: AAPSFDCGKPQVEPKKCPGRVVGGCVAHPHSWPWQVSLRTRFGMHFCGGTLISPEWVLTAAHCLEKSPRPSSYKVILGAHQEVNLEPHVQEIEVSRLFLEPTRKDIALLKLSSPAVITDKVIPACLPSPNYVVADRTECFITGWGETQGTFGAGLLKEAQLPVIENKVCNRYEFLNGRVQSTELCAGHLAGGTDSCQGDAGGPLVCFEKDKYILQGVTSWGLGCARPNKPGVYVRVSRFVTWIEGVMRNN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.1852
R free: 0.208
Average B factor: 22.2901
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5
Crystallization temperature (K): 293
Crystal growth procedure: 13-18% PEG 4000, 150 mM Ammonium sulfate, 100 mM MES
Matthews coefficient: 2.13
Solvent content (%): 42.2
Ligand: (6S,9R,20R,23S)-N-{[4-(aminomethyl)phenyl]methyl}-20-[(benzenesulfonyl)amino]-3,13,21-trioxo-2,6,9,14,22-pentaazatetracyclo[23.2.2.2~6,9~.2~15,18~]tritriaconta-1(27),15,17,25,28,30-hexaene-23-carboxamide (I5Y)
Ligand formula: C43 H52 N8 O6 S
Ligand molecular weight: 808.988
Ligand SMILES: c1ccc(cc1)S(=O)(=O)NC2Cc3ccc(cc3)NC(=O)CCCN4CCN(CCC(=O)Nc5ccc(cc5)CC(NC2=O)C(=O)NCc6ccc(cc6)CN)CC4
Ligand InChI: InChI=1S/C43H52N8O6S/c44-29-33-8-10-34(11-9-33)30-45-42(54)38-27-31-12-16-36(17-13-31)47-41(53)20-22-51-25-23-50(24-26-51)21-4-7-40(52)46-35-18-14-32(15-19-35)28-39(43(55)48-38)49-58(56,57)37-5-2-1-3-6-37/h1-3,5-6,8-19,38-39,49H,4,7,20-30,44H2,(H,45,54)(H,46,52)(H,47,53)(H,48,55)/t38-,39+/m0/s1
Release date: 2023-01-18
Diphosphoinositol polyphosphate phosphohydrolase 1 (DIPP1/NUDT3) in complex with Scyllo-L-1,4-[PP]2-(2,3)IP2, Mg, and Fluoride ion (PDB entry 8T99)
Macromolecule: Diphosphoinositol polyphosphate phosphohydrolase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.1.52
Sequence length: 148 residues
Sequence: MMKLKSNQTRTYDGDGYKKRAACLCFRSESEEEVLLVSSSRHPDRWIVPGGGMEPEEEPSVAAVREVCEEAGVKGTLGRLVGIFENQERKHRTYVYVLIVTEVLEDWEDSVNIGRKREWFKIEDAIKVLQYHKPVQASYFETLRQGYS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.5
R work: 0.156
R free: 0.18271
Average B factor: 18.491
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 298
Crystal growth procedure: 10% w/v PEG8000, 10% v/v isopropanol, 200 mM lithium sulfate, 100 mM sodium acetate, pH 5.0, 5 mM IP6, soaked in 200 mM lithium chloride, 20% w/v PEG8000, 20% v/v isopropanol, 100 mM sodium acetate, pH 5.0, 20 mM magnesium chloride, 100 mM sodium fluoride in presence of TvIPK reaction solution with L-scyllo-(1,2,3,4)IP4
Matthews coefficient: 2.5
Solvent content (%): 50.82
Ligand: (1R,2S,3S,4R,5S,6S)-2,3-dihydroxy-5,6-bis(phosphonooxy)cyclohexane-1,4-diyl bis[trihydrogen (diphosphate)] (ZOW)
Ligand formula: C6 H18 O24 P6
Ligand molecular weight: 660.035
Ligand SMILES: C1(C(C(C(C(C1OP(=O)(O)OP(=O)(O)O)OP(=O)(O)O)OP(=O)(O)O)OP(=O)(O)OP(=O)(O)O)O)O
Ligand InChI: InChI=1S/C6H18O24P6/c7-1-2(8)4(28-36(23,24)30-34(18,19)20)6(26-32(12,13)14)5(25-31(9,10)11)3(1)27-35(21,22)29-33(15,16)17/h1-8H,(H,21,22)(H,23,24)(H2,9,10,11)(H2,12,13,14)(H2,15,16,17)(H2,18,19,20)/t1-,2-,3+,4+,5-,6-/m0/s1
Release date: 2023-11-15
Crystal structure of CLK1 in complexed with furo[3,2-b]pyridine compound VN316 (derivative of compound 12h) (PDB entry 6I5L)
Macromolecule: Dual specificity protein kinase CLK1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.12.1
Sequence length: 339 residues
Sequence: SMHLICQSGDVLSARYEIVDTLGEGAFGKVVECIDHKAGGRHVAVKIVKNVDRYCEAARSEIQVLEHLNTTDPNSTFRCVQMLEWFEHHGHICIVFELLGLSTYDFIKENGFLPFRLDHIRKMAYQICKSVNFLHSNKLTHTDLKPENILFVQSDYTEAYNPKIKRDERTLINPDIKVVDFGSATYDDEHHSTLVSTRHYRAPEVILALGWSQPCDVWSIGCILIEYYLGFTVFPTHDSKEHLAMMERILGPLPKHMIQKTRKRKYFHHDRLDWDEHSSAGRYVSRACKPLKEFMLSQDVEHERLFDLIQKMLEYDPAKRITLREALKHPFFDLLKKSI
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.55
R work: 0.19345
R free: 0.22146
Average B factor: 51.62
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 24-28% 1,2-propanediol, 5% glycerol, 0.1M sodium/potassium phosphate
Matthews coefficient: 2.58
Solvent content (%): 52.26
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: 2019-01-09
Crystal Structure of Cathepsin-G and Neutrophil Elastase Inhibited by S. aureus EapH2 at pH 5.5 (PDB entry 8G24)
Macromolecule: Neutrophil elastase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.37
Sequence length: 218 residues
Sequence: IVGGRRARPHAWPFMVSLQLRGGHFCGATLIAPNFVMSAAHCVANVNVRAVRVVLGAHNLSRREPTRQVFAVQRIFENGYDPVNLLNDIVILQLNGSATINANVQVAQLPAQGRRLGNGVQCLAMGWGLLGRNRGIASVLQELNVTVVTSLCRRSNVCTLVRGRQAGVCFGDSGSPLVCNGLIHGIASFVRGGCASGLYPDAFAPVAQFVNWIDSIIQ
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.82
R work: 0.212
R free: 0.2491
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M Bis-Tris, 0.2 M sodium chloride, 26% w/v PDB3350
Matthews coefficient: 2.19
Solvent content (%): 43.83
Release date: 2023-04-26
Postcatalytic ternary complex of Human DNA Polymerase Beta with Gapped DNA substrate, incorporated (-)3TC and PPi. (PDB entry 5TBA)
Macromolecule: DNA polymerase beta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 343 residues
Sequence: MGMSKRKAPQETLNGGITDMLTELANFEKNVSQAIHKYNAYRKAASVIAKYPHKIKSGAEAKKLPGVGTKIAEKIDEFLATGKLRKLEKIRQDDTSSSINFLTRVSGIGPSAARKFVDEGIKTLEDLRKNEDKLNHHQRIGLKYFGDFEKRIPREEMLQMQDIVLNEVKKVDSEYIATVCGSFRRGAESSGDMDVLLTHPSFTSESTKQPKLLHQVVEQLQKVHFITDTLSKGETKFMGVCQLPSKNDEKEYPHRRIDIRLIPKDQYYCGVLYFTGSDIFNKNMRAHALEKGFTINEYTIRPLGVTGVAGEPLPVDSEKDIFDYIQWKYREPKDRSEHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.49
R work: 0.205
R free: 0.273
Average B factor: 41.5
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8
Crystallization temperature (K): 295
Crystal growth procedure: 50 MM IMIDAZOLE, 350 MM SODIUM
 ACETATE, 17% PEG3350 , PH 8.0
Matthews coefficient: 2.34
Solvent content (%): 47.42
Ligand: PYROPHOSPHATE (PPV)
Ligand formula: H4 O7 P2
Ligand molecular weight: 177.975
Ligand SMILES: OP(=O)(O)OP(=O)(O)O
Ligand InChI: InChI=1S/H4O7P2/c1-8(2,3)7-9(4,5)6/h(H2,1,2,3)(H2,4,5,6)
Release date: 2017-01-11
IDO1/BMS-978587 crystal structure (PDB entry 6AZV)
Macromolecule: Indoleamine 2,3-dioxygenase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.13.11.52
Sequence length: 402 residues
Sequence: GSHMENSWTISKEYHIDEEVGFALPNPQENLPDFYNDWMFIAKHLPDLIESGQLRERVEKLNMLSIDHLTDHKSQRLARLVLGCITMAYVWGKGHGDVRKVLPRNIAVPYCQLSKKLELPPILVYADCVLANWKKKDPNKPLTYENMDVLFSFRDGDCSKGFFLVSLLVEIAAASAIKVIPTVFKAMQMQERDTLLKALLEIASCLEKALQVFHQIHDHVNPKAFFSVLRIYLSGWKGNPQLSDGLVYEGFWEDPKEFAGGSAGQSSVFQCFDVLLGIQQTAGGGHAAQFLQDMRRYMPPAHRNFLCSLESNPSVREFVLSKGDAGLREAYDACVKALVSLRSYHLQIVTKYILIPASQQPKENKTSEDPSKLEAKGTGGTDLMNFLKTVRSTTEKSLLKEG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.755
R work: 0.1947
R free: 0.2719
Average B factor: 68.3118
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 298
Crystal growth procedure: 22% PEG-3350, 0.2 M NH4 citrate pH 7
Matthews coefficient: 3.01
Solvent content (%): 59.16
Ligand: (1R,2S)-2-(4-[bis(2-methylpropyl)amino]-3-{[(4-methylphenyl)carbamoyl]amino}phenyl)cyclopropane-1-carboxylic acid (C4V)
Ligand formula: C26 H35 N3 O3
Ligand molecular weight: 437.574
Ligand SMILES: Cc1ccc(cc1)NC(=O)Nc2cc(ccc2N(CC(C)C)CC(C)C)C3CC3C(=O)O
Ligand InChI: InChI=1S/C26H35N3O3/c1-16(2)14-29(15-17(3)4)24-11-8-19(21-13-22(21)25(30)31)12-23(24)28-26(32)27-20-9-6-18(5)7-10-20/h6-12,16-17,21-22H,13-15H2,1-5H3,(H,30,31)(H2,27,28,32)/t21-,22-/m1/s1
Release date: 2018-03-21
Crystal structure of human protein kinase CK2alpha' (CSNK2A2 gene product) in complex with the 2-aminothiazole-type inhibitor 27 (PDB entry 6TEW)
Macromolecule: Casein kinase II subunit alpha'
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 364 residues
Sequence: MGSSHHHHHHSQDPMPGPAAGSRARVYAEVNSLRSREYWDYEAHVPSWGNQDDYQLVRKLGRGKYSEVFEAINITNNERVVVKILKPVKKKKIKREVKILENLRGGTNIIKLIDTVKDPVSKTPALVFEYINNTDFKQLYQILTDFDIRFYMYELLKALDYCHSKGIMHRDVKPHNVMIDHQQKKLRLIDWGLAEFYHPAQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRREPFFHGQDNYDQLVRIAKVLGTEELYGYLKKYHIDLDPHFNDILGQHSRKRWENFIHSENRHLVSPEALDLLDKLLRYDHQQRLTAKEAMEHPYFYPVVKEQSQPSADNAVLSSGLTAAR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.082
R work: 0.1461
R free: 0.1687
Average B factor: 21.15
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 293
Crystal growth procedure: RESERVOIR COMPOSITION: 28 % (W/V) PEG6000, 0.9 M LICL, 0.1 M, TRIS/HCL, PH 8.5; CRYSTALLIZATION DROP COMPOSITION PRIOR TO EQUILIBRATION: 0.01 ML RESERVOIR SOLUTION PLUS 0.02 ML CK2ALPHA' (MUTANT CYS336SER)/INHIBITOR MB002 MIXTURE (0.180 ML 6 MG/ML CK2ALPHA-'CYS336SER, 0.5 M NACL, 25 MM TRIS/HCL, PH 8.5, MIXED AND PRE-EQUILIBRATED WITH 0.02 ML 10 MM MB002 IN DIMETHYL SULFOXIDE); the inhibitor MB002 was replaced by extensive soaking with the 2-aminothiazole-type inhibitor 27; VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K
Matthews coefficient: 2.35
Solvent content (%): 47.59
Ligand: 4-[(4-naphthalen-2-yl-1,3-thiazol-2-yl)amino]-2-oxidanyl-benzoic acid (N5Q)
Ligand formula: C20 H14 N2 O3 S
Ligand molecular weight: 362.402
Ligand SMILES: c1ccc2cc(ccc2c1)c3csc(n3)Nc4ccc(c(c4)O)C(=O)O
Ligand InChI: InChI=1S/C20H14N2O3S/c23-18-10-15(7-8-16(18)19(24)25)21-20-22-17(11-26-20)14-6-5-12-3-1-2-4-13(12)9-14/h1-11,23H,(H,21,22)(H,24,25)
Release date: 2020-07-08
PKA in complex with a halogenated phthalazinone fragment compound. (PDB entry 5BX6)
Macromolecule: cAMP-dependent protein kinase catalytic subunit alpha
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.11
Sequence length: 351 residues
Sequence: MGNAAAAKKGSEQESVKEFLAKAKEDFLKKWESPAQNTAHLDQFERIKTLGTGSFGRVMLVKHKETGNHYAMKILDKQKVVKLKQIEHTLNEKRILQAVNFPFLVKLEFSFKDNSNLYMVMEYVPGGEMFSHLRRIGRFSEPHARFYAAQIVLTFEYLHSLDLIYRDLKPENLLIDQQGYIQVTDFGFAKRVKGRTWTLCGTPEYLAPEIILSKGYNKAVDWWALGVLIYEMAAGYPPFFADQPIQIYEKIVSGKVRFPSHFSSDLKDLLRNLLQVDLTKRFGNLKNGVNDIKNHKWFATTDWIAIYQRKVEAPFIPKFKGPGDTSNFDDYEEEEIRVSINEKCGKEFSEF
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.89
R work: 0.1696
R free: 0.2178
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7
Crystallization temperature (K): 277
Crystal growth procedure: The droplets, containing 10 mg/ml PKA.
25 mM Bis-Tris-HCl, pH 7.0, 150 mM KCl, 1.5mM octanoyl-N-methylglucamide and 0.8 mM PKI peptide, were equilibrated against 12-26 % (v/v) methanol.
Matthews coefficient: 2.51
Solvent content (%): 51.02
Ligand: 4-chlorophthalazin-1(2H)-one (495)
Ligand formula: C8 H5 Cl N2 O
Ligand molecular weight: 180.591
Ligand SMILES: c1ccc2c(c1)C(=O)NN=C2Cl
Ligand InChI: InChI=1S/C8H5ClN2O/c9-7-5-3-1-2-4-6(5)8(12)11-10-7/h1-4H,(H,11,12)
Release date: 2016-09-14
UCH-L5 in complex with the RPN13 DEUBAD domain (PDB entry 4UEM)
Macromolecule: UBIQUITIN CARBOXYL-TERMINAL HYDROLASE ISOZYME L5
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.19.12
Sequence length: 331 residues
Sequence: GPGMTGNAGEWCLMESDPGVFTELIKGFGCRGAQVEEIWSLEPENFEKLKPVHGLIFLFKWQPGEEPAGSVVQDSRLDTIFFAKQVINNACATQAIVSVLLNCTHQDVHLGETLSEFKEFSQSFDAAMKGLALSNSDVIRQVHNSFARQQMFEFDTKTSAKEEDAFHFVSYVPVNGRLYELDGLREGPIDLGACNQDDWISAVRPVIEKRIQKYSEGEIRFNLMAIVSDRKMIYEQKIAELQRQLAEEPMDTDQGNSMLSAIQSEVAKNQMLIEEEVQKLKRYKIENIRRKHNYLPFIMELLKTLAEHQQLIPLVEKAKEKQNAKKAQETK
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.82
R work: 0.2318
R free: 0.2813
Crystallization temperature (K): 277
Crystal growth procedure: 100 MM BIS-TRIS-PROPANE PH 6.4, 230 MM NABR, 21% PEG3350. 4 DEGREES CELSIUS
Matthews coefficient: 2.7
Solvent content (%): 54
Release date: 2015-03-04
Crystal Structure of Human Pseudouridylate Synthase 7 (PDB entry 5KKP)
Macromolecule: Pseudouridylate synthase 7
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 5.4.99
Sequence length: 563 residues
Sequence: ESFADMMKHGLTEADVGITKFVSSHQGFSGILKERYSDFVVHEIGKDGRISHLNDLSIPVDEEDPSEDIFTVLTAEEKQRLEELQLFKNKETSVAIEVIEDTKEKRTIIHQAIKSLFPGLETKTEDREGKKYIVAYHAAGKKALANPRKHSWPKSRGSYCHFVLYKENKDTMDAINVLSKYLRVKPNIFSYMGTKDKRAITVQEIAVLKITAQRLAHLNKCLMNFKLGNFSYQKNPLKLGELQGNHFTVVLRNITGTDDQVQQAMNSLKEIGFINYYGMQRFGTTAVPTYQVGRAILQNSWTEVMDLILKPRSGAEKGYLVKCREEWAKTKDPTAALRKLPVKRCVEGQLLRGLSKYGMKNIVSAFGIIPRNNRLMYIHSYQSYVWNNMVSKRIEDYGLKPVPGDLVLKGATATYIEEDDVNNYSIHDVVMPLPGFDVIYPKHKIQEAYREMLTADNLDIDNMRHKIRDYSLSGAYRKIIIRPQNVSWEVVAYDDPKIPLFNTDVDNLEGKTPPVFASEGKYRALKMDFSLPPSTYATMAIREVLKMDTSIKNQTQLNTTWLR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.26
R work: 0.209
R free: 0.263
Average B factor: 59.6
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 293
Crystal growth procedure: 23% PEG 3350, 0.2 M Sodium formate, pH7.0
Matthews coefficient: 2.22
Solvent content (%): 44.52
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: 2016-08-17