satarupa22/MacromolecularLigandDB huggingface dataset:
Selection of fragments for kinase inhibitor design: decoration is key (PDB entry 4X2F)
Macromolecule: TGF-beta receptor type-1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.30
Sequence length: 305 residues
Sequence: GTIARTIVLQESIGKGRFGEVWRGKWRGEEVAVKIFSSREERSWFREAEIYQTVMLRHENILGFIAADNKDNGTWTQLWLVSDYHEHGSLFDYLNRYTVTVEGMIKLALSTASGLAHLHMEIVGTQGKPAIAHRDLKSKNILVKKNGTCCIADLGLAVRHDSATDTIDIAPNHRVGTKRYMAPEVLDDSINMKHFESFKRADIYAMGLVFWEIARRCSIGGIHEDYQLPYYDLVPSDPSVEEMRKVVCEQKLRPNIPNRWQSCEALRVMAKIMRECWYANGAARLTALRIKKTLSQLSQQEGIKM
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.49
R work: 0.1632
R free: 0.1911
Average B factor: 19.2
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M Tris-HCl, 240 mM Li2SO4, 24% PEG 4000, pH 7.5
Matthews coefficient: 2.11
Solvent content (%): 41.69
Ligand: 4-amino-8-(4-aminophenyl)pyrido[2,3-d]pyrimidin-5(8H)-one (3WJ)
Ligand formula: C13 H11 N5 O
Ligand molecular weight: 253.259
Ligand SMILES: c1cc(ccc1N)N2C=CC(=O)c3c2ncnc3N
Ligand InChI: InChI=1S/C13H11N5O/c14-8-1-3-9(4-2-8)18-6-5-10(19)11-12(15)16-7-17-13(11)18/h1-7H,14H2,(H2,15,16,17)
Release date: 2015-10-28
DNA Polymerase Mu, dGTP:At Pre-Catalytic Ground State Ternary Complex, 10 mM Ca2+ (960min) (PDB entry 7KSZ)
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): 1.417
R work: 0.1573
R free: 0.1747
Average B factor: 21.6426
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% PEG 4000
Matthews coefficient: 2.5
Solvent content (%): 50.89
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: 2022-01-19
MAP4K4 in complex with inhibitor (PDB entry 5J95)
Macromolecule: Mitogen-activated protein kinase kinase kinase kinase 4
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 312 residues
Sequence: ANDSPAKSLVDIDLSSLRDPAGIFELVEVVGNGTYGQVYKGRHVKTGQLAAIKVMDVTEDEEEEIKLEINMLKKYSHHRNIATYYGAFIKKSPPGHDDQLWLVMEFCGAGSITDLVKNTKGNTLKEDWIAYISREILRGLAHLHIHHVIHRDIKGQNVLLTENAEVKLVDFGVSAQLDRTVGRRNTFIGTPYWMAPEVIACDENPDATYDYRSDLWSCGITAIEMAEGAPPLCDMHPMRALFLIPRNPPPRLKSKKWSKKFFSFIEGCLVKNYMQRPSTEQLLKHPFIRDQPNERQVRIQLKDHIDRTRKKR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.5
R work: 0.215
R free: 0.2581
Average B factor: 77.06
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 0.1 M Bis-Tris pH=6.5, 0.2 M NaCl, 18% PEG 3350
Matthews coefficient: 2.49
Solvent content (%): 50.7
Ligand: 1-{4-[6-amino-5-(4-chlorophenyl)pyridin-3-yl]phenyl}cyclopentane-1-carboxylic acid (6HH)
Ligand formula: C23 H21 Cl N2 O2
Ligand molecular weight: 392.878
Ligand SMILES: c1cc(ccc1c2cc(c(nc2)N)c3ccc(cc3)Cl)C4(CCCC4)C(=O)O
Ligand InChI: InChI=1S/C23H21ClN2O2/c24-19-9-5-16(6-10-19)20-13-17(14-26-21(20)25)15-3-7-18(8-4-15)23(22(27)28)11-1-2-12-23/h3-10,13-14H,1-2,11-12H2,(H2,25,26)(H,27,28)
Release date: 2017-04-19
Crystal Structure of Factor VIIa in complex with N-(2-amino-1H-benzimidazol-5-yl)-2-[3-[(2-amino-2-oxoethyl)-methylsulfonylamino]phenyl]acetamide;2,2,2-trifluoroacetic acid (PDB entry 5PAU)
Macromolecule: Coagulation factor VII heavy chain
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.21
Sequence length: 254 residues
Sequence: IVGGKVCPKGECPWQVLLLVNGAQLCGGTLINTIWVVSAAHCFDKIKNWRNLIAVLGEHDLSEHDGDEQSRRVAQVIIPSTYVPGTTNHDIALLRLHQPVVLTDHVVPLCLPERTFSERTLAFVRFSLVSGWGQLLDRGATALELMVLNVPRLMTQDCLQQSRKVGDSPNITEYMFCAGYSDGSKDSCKGDSGGPHATHYRGTWYLTGIVSWGQGCATVGHFGVYTRVSQYIEWLQKLMRSEPRPGVLLRAPFP
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.55
R work: 0.1808
R free: 0.204
Average B factor: 25.033
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 277
Crystal growth procedure: 16 mg/ml protein in 20mM Tris/HCl pH 8.4, 5 mM benzamidine, 0.1 M NaCl, 50 mM CaCl2 mixed 1+1 with 32-35% AMMONIUM SULPHATE, 2% PEG 4000, 0.1 M Bicine-NaOH pH 8.5, 15% glycerol
Matthews coefficient: 3.77
Solvent content (%): 67.38
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: 2017-06-21
Teranry complex of human DNA polymerase iota R96G inserting dCMPNPP opposite template G in the presence of Mn2+ (PDB entry 5KT5)
Macromolecule: DNA (5'-D(*CP*TP*GP*GP*GP*GP*TP*CP*CP*T)-3')
Type: DNA, polydeoxyribonucleotide
Source organism: synthetic construct
Sequence length: 10 residues
Sequence: CTGGGGTCCT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.798
R work: 0.2236
R free: 0.2664
Average B factor: 51.4303
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 277.15
Crystal growth procedure: 18% PEG MME 5000, 0.1M MES buffer, 0.3M ammonium sulfate
Matthews coefficient: 2.54
Solvent content (%): 51.64
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: 2016-08-31
Catalytic Improvement of an Artificial Metalloenzyme by Computational Design (PDB entry 5BRV)
Macromolecule: Carbonic anhydrase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 260 residues
Sequence: MAHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHAFNVEFDDSQDKAVLKGGPLDGTYRLIQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDFGKAVQQPDGMAVLGIFLKVGSAKPGLQKVVDVLDSIKTKGKSADFTNFDPRGLLPESLDYWTYPGSMTTPPLLESVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKLRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.6
R work: 0.1846
R free: 0.2296
Average B factor: 23.532
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.9
Crystallization temperature (K): 298
Crystal growth procedure: 2.6 M ammonium sulfate, 50 mM Tris-HCl
Matthews coefficient: 2.09
Solvent content (%): 41.29
Ligand: pentamethylcyclopentadienyl iridium [N-benzensulfonamide-(2-pyridylmethyl-4-benzensulfonamide)amin] chloride (9TH)
Ligand formula: C28 H31 Cl Ir N3 O4 S2
Ligand molecular weight: 765.363
Ligand SMILES: C[C-]12C3(=C4([Ir+3]1356(C2(=C54C)C)([N-](CC7=[N]6C=CC(=C7)c8ccc(cc8)S(=O)(=O)N)S(=O)(=O)c9ccccc9)[Cl-])C)C
Ligand InChI: InChI=1S/C18H16N3O4S2.C10H15.ClH.Ir/c19-26(22,23)17-8-6-14(7-9-17)15-10-11-20-16(12-15)13-21-27(24,25)18-4-2-1-3-5-18;1-6-7(2)9(4)10(5)8(6)3;;/h1-12H,13H2,(H2,19,22,23);1-5H3;1H;/q2*-1;;+3/p-1
Release date: 2015-06-24
Crystal structure of human RECQL5 helicase APO form in complex with engineered nanobody (Gluebody) G2*-006 (PDB entry 7ZMQ)
Macromolecule: ATP-dependent DNA helicase Q5
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.4.12
Sequence length: 445 residues
Sequence: SMDPERRVRSTLKKVFGFDSFKTPLQESATMAVVKGNKDVFVCMPTGAGKSLCYQLPALLAKGITIVVSPLIALIQDQVDHLLTLKVRVSSLNSKLSAQERKELLADLEREKPQTKILYITPEMAASSSFQPTLNSLVSRHLLSYLVVDEAHCVSQWGHDFRPDYLRLGALRSRLGHAPCVALTATATPQVQEDVFAALHLKKPVAIFKTPCFRANLFYDVQFKELISDPYGNLKDFCLKALGQEADKGLSGCGIVYCRTREACEQLAIELSCRGVNAKAYHAGLKASERTLVQNDWMEEKVPVIVATISFGMGVDKANVRFVAHWNIAKSMAGYYQESGRAGRDGKPSWCRLYYSRNDRDQVSFLIRKEVAKLQEKRGNKASDKATIMAFDALVTFCEELGCRHAAIAKYFGDALPACAKGCDHCQNPTAVRRRLEALERSSSW
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.7
R work: 0.225
R free: 0.2583
Average B factor: 61.392
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.2M lithium sulfate -- 25% PEG3350 -- 0.1M tris pH 8.5
Matthews coefficient: 3.94
Solvent content (%): 68.79
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: 2022-06-22
Crystal structure of phospholipase A2 (PDB entry 6KQU)
Macromolecule: Group IIE secretory phospholipase A2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.1.4
Sequence length: 123 residues
Sequence: NLVQFGVMIEKMTGKSALQYGDYGCYCGIGGSHWPVDQTDWCCHAHDCCYGRLEKLGCEPKLEKYLFSVSERGIFCAGRTTCQRLTCECDKRAALCFRRNLGTYNRKYAHYPNKLCTGPTPPC
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2
R work: 0.1972
R free: 0.2385
Average B factor: 17.841
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 277
Crystal growth procedure: 2.2M Sodium chloride, 0.1M BIS-TRIS propane pH 7.0
Matthews coefficient: 3.45
Solvent content (%): 64.38
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: 2020-08-19
FACTOR XIA IN COMPLEX WITH THE INHIBITOR methyl ~{N}-[4-[[(1~{S})-2-[(~{E})-3-[3-chloranyl-2-fluoranyl-6-(1,2,3,4-tetrazol-1-yl)phenyl]prop-2-enoyl]-3,4-dihydro-1~{H}-isoquinolin-1-yl]carbonylamino]phenyl]carbamate (PDB entry 5QCM)
Macromolecule: Coagulation factor XI
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.27
Sequence length: 244 residues
Sequence: IVGGTASVRGEWPWQVTLHTTSPTQRHLCGGSIIGNQWILTAAHCFYGVESPKILRVYSGILNQSEIKEDTSFFGVQEIIIHDQYKMAESGYDIALLKLETTVGYGDSQRPICLPSKGDRNVIYTDCWVTGWGYRKLRDKIQNTLQKAKIPLVTNEECQKRYRGHKITHKMICAGYREGGKDACKGDSGGPLSCKHNEVWHLVGITSWGEGCAQRERPGVYTNVVEYVDWILEKTQAVHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.2
R work: 0.215
R free: 0.244
Average B factor: 34.04
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7
Crystallization temperature (K): 277
Crystal growth procedure: 100 mM sodium acetate, pH 4.6, 25% (w/v) MePEG2000, 200 mM ammonium sulfate, then transferred to 100 mM Tris-HCl, pH 7.0, 25% (w/v) MePEG2000, 200 MM ammonium sulfate
Matthews coefficient: 3.48
Solvent content (%): 64.64
Ligand: methyl ~{N}-[4-[[(1~{S})-2-[(~{E})-3-[3-chloranyl-2-fluoranyl-6-(1,2,3,4-tetrazol-1-yl)phenyl]prop-2-enoyl]-3,4-dihydro-1~{H}-isoquinolin-1-yl]carbonylamino]phenyl]carbamate (BVJ)
Ligand formula: C28 H23 Cl F N7 O4
Ligand molecular weight: 575.978
Ligand SMILES: COC(=O)Nc1ccc(cc1)NC(=O)C2c3ccccc3CCN2C(=O)C=Cc4c(ccc(c4F)Cl)n5cnnn5
Ligand InChI: InChI=1S/C28H23ClFN7O4/c1-41-28(40)33-19-8-6-18(7-9-19)32-27(39)26-20-5-3-2-4-17(20)14-15-36(26)24(38)13-10-21-23(37-16-31-34-35-37)12-11-22(29)25(21)30/h2-13,16,26H,14-15H2,1H3,(H,32,39)(H,33,40)/b13-10+/t26-/m0/s1
Release date: 2017-11-08
Crystal structure of human protein N-terminal asparagine amidohydrolase (NTAN1) C75S mutant (PDB entry 6A0I)
Macromolecule: Protein N-terminal asparagine amidohydrolase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.5.1
Sequence length: 318 residues
Sequence: MPLLVEGRRVRLPQSAGDLVRAHPPLEERARLLRGQSVQQVGPQGLLYVQQRELAVTSPKDGSISILGSDDATTSHIVVLRHTGNGATCLTHCDGTDTKAEVPLIMNSIKSFSDHAQCGRLEVHLVGGFSDDRQLSQKLTHQLLSEFDRQEDDIHLVTLCVTELNDREENENHFPVIYGIAVNIKTAEIYRASFQDRGPEEQLRAARTLAGGPMISIYDAETEQLRIGPYSWTPFPHVDFWLHQDDKQILENLSTSPLAEPPHFVEHIRSTLMFLKKHPSPAHTLFSGNKALLYKKNEDGLWEKISSPGSLEHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.996
R work: 0.164
R free: 0.2108
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 4.8
Crystallization temperature (K): 295
Crystal growth procedure: PEG 3350, potassium phosphate monobasic
Matthews coefficient: 2.13
Solvent content (%): 42.18
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: 2019-12-11
Human Plasma Coagulation Factor XI in complex with peptide P39 (PDB entry 5EOK)
Macromolecule: Coagulation factor XI
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.27
Sequence length: 606 residues
Sequence: CVTQLLKDTCFEGGDITTVFTPSAKYCQVVCTYHPRCLLFTFTAESPSEDPTRWFTCVLKDSVTETLPRVNRTAAISGYSFKQCSHQISACNKDIYVDLDMKGINYNSSVAKSAQECQERCTDDVHCHFFTYATRQFPSLEHRNICLLKHTQTGTPTRITKLDKVVSGFSLKSCALSNLACIRDIFPNTVFADSNIDSVMAPDAFVCGRICTHHPGCLFFTFFSQEWPKESQRNLCLLKTSESGLPSTRIKKSKALSGFSLQSCRHSIPVFCHSSFYHDTDFLGEELDIVAAKSHEACQKLCTNAVRCQFFTYTPAQASCNEGKGKCYLKLSSNGSPTKILHGRGGISGYTLRLCKMDNECTTKIKPRIVGGTASVRGEWPWQVTLHTTSPTQRHLCGGSIIGNQWILTAAHCFYGVESPKILRVYSGILNQSEIKEDTSFFGVQEIIIHDQYKMAESGYDIALLKLETTVNYTDSQRPICLPSKGDRNVIYTDCWVTGWGYRKLRDKIQNTLQKAKIPLVTNEECQKRYRGHKITHKMICAGYREGGKDACKGDSGGPLSCKHNEVWHLVGITSWGEGCAQRERPGVYTNVVEYVDWILEKTQAV
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.8
R work: 0.20135
R free: 0.26412
Average B factor: 71.558
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293.15
Crystal growth procedure: 0.1M HEPES pH7.5, 20% PEG1500
Matthews coefficient: 2.59
Solvent content (%): 52.6
Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose (NAG)
Ligand formula: C8 H15 N O6
Ligand molecular weight: 221.208
Ligand SMILES: CC(=O)NC1C(C(C(OC1O)CO)O)O
Ligand InChI: InChI=1S/C8H15NO6/c1-3(11)9-5-7(13)6(12)4(2-10)15-8(5)14/h4-8,10,12-14H,2H2,1H3,(H,9,11)/t4-,5-,6-,7-,8-/m1/s1
Release date: 2016-04-06
Crystal structure of PLK1 in complex with a novel 5,6-dihydroimidazolo[1,5-f]pteridine inhibitor (PDB entry 5TA8)
Macromolecule: Serine/threonine-protein kinase PLK1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.21
Sequence length: 358 residues
Sequence: MSYYHHHHHHDYDIPTTENLYFQGAAPADPGKAGVPGVAAPGAPAAAPPAKEIPEVLVDPRSRRRYVRGRFLGKGGFAKCFEISDADTKEVFAGKIVPKSLLLKPHQREKMSMEISIHRSLAHQHVVGFHGFFEDNDFVFVVLELCRRRSLLELHKRRKALTEPEARYYLRQIVLGCQYLHRNRVIHRDLKLGNLFLNEDLEVKIGDFGLATKVEYDGERKKVLCGTPNYIAPEVLSKKGHSFEVDVWSIGCIMYTLLVGKPPFETSCLKETYLRIKKNEYSIPKHINPVAASLIQKMLQTDPTARPTINELLNDEFFTSGYIPARLPITCLTIPPRFSIAPSSLDPSNRKPLTVLNK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.6
R work: 0.1815
R free: 0.2467
Average B factor: 94.267
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 0.95 mM succinic acid, 1.7% PEG2000 MME, 0.4 mM zinc acetate, 100 mM HEPES, pH 7.0, temperature 277K
Matthews coefficient: 2.45
Solvent content (%): 49.83
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
Structure-based Design, Synthesis, and Biological Evaluation of Imidazo[4,5-b]pyridine-2-one based p38 MAP Kinase Inhibitors by scaffold hopping - compound 10 (PDB entry 6M9L)
Macromolecule: Mitogen-activated protein kinase 14
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.24
Sequence length: 388 residues
Sequence: MSYYHHHHHHDYDIPTTENLYFQGAMGSMSQERPTFYRQELNKTIWEVPERYQNLSPVGSGAYGSVCAAFDTKTGLRVAVKKLSRPFQSIIHAKRTYRELRLLKHMKHENVIGLLDVFTPARSLEEFNDVYLVTHLMGADLNNIVKCQKLTDDHVQFLIYQILRGLKYIHSADIIHRDLKPSNLAVNEDSELKILDFGLARHTDDEMTGYVATRWYRAPEIMLNWMHYNQTVDIWSVGCIMAELLTGRTLFPGTDHIDQLKLILRLVGTPGAELLKKISSESARNYIQSLTQMPKMNFANVFIGANPLAVDLLEKMLVLDSDKRITAAQALAHAYFAQYHDPDDEPVADPYDQSFESRDLLIDEWKSLTYDEVISFVPPPLDQEEMES
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.45
R work: 0.2134
R free: 0.2697
Average B factor: 24.22
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.4
Crystallization temperature (K): 277.2
Crystal growth procedure: 24.% PEG MME 5000, 0.1M MES_Na
Matthews coefficient: 2.03
Solvent content (%): 39.54
Ligand: 3-benzyl-6-[(2,4-difluorophenyl)amino]-1,3-dihydro-2H-imidazo[4,5-b]pyridin-2-one (J9G)
Ligand formula: C19 H14 F2 N4 O
Ligand molecular weight: 352.337
Ligand SMILES: c1ccc(cc1)CN2c3c(cc(cn3)Nc4ccc(cc4F)F)NC2=O
Ligand InChI: InChI=1S/C19H14F2N4O/c20-13-6-7-16(15(21)8-13)23-14-9-17-18(22-10-14)25(19(26)24-17)11-12-4-2-1-3-5-12/h1-10,23H,11H2,(H,24,26)
Release date: 2019-04-17
Crystal structure of human MTH1 in complex with inhibitor 6-[(2-phenylethyl)sulfanyl]-7H-purin-2-amine (PDB entry 5NGS)
Macromolecule: 7,8-dihydro-8-oxoguanine triphosphatase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.1.55
Sequence length: 159 residues
Sequence: GSHMGASRLYTLVLVLQPQRVLLGMKKRGFGAGRWNGFGGKVQEGETIEDGARRELQEESGLTVDALHKVGQIVFEFVGEPELMDVHVFCTDSIQGTPVESDEMRPCWFQLDQIPFKDMWPDDSYWFPLLLQKKKFHGYFKFQGQDTILDYTLREVDTV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.85
R work: 0.21563
R free: 0.24832
Average B factor: 28.804
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 5 mmol/L compound and 6 mmol/L MgCl2 were added to MTH1. Sitting drop vapor diffusion experiments at 293K were performed, and MTH1 (9.34 mg/mL) was mixed with reservoir solution (28% (w/v) PEG8000, 0.1 mol/L Sodium Acetate pH 4.0 and 0.2 mol/L LiSO4) in a 3:5 ratio.
Matthews coefficient: 2.29
Solvent content (%): 46.19
Ligand: 6-(2-phenylethylsulfanyl)-7~{H}-purin-2-amine (8WW)
Ligand formula: C13 H13 N5 S
Ligand molecular weight: 271.341
Ligand SMILES: c1ccc(cc1)CCSc2c3c(nc[nH]3)nc(n2)N
Ligand InChI: InChI=1S/C13H13N5S/c14-13-17-11-10(15-8-16-11)12(18-13)19-7-6-9-4-2-1-3-5-9/h1-5,8H,6-7H2,(H3,14,15,16,17,18)
Release date: 2017-10-04
Structure of human DNA polymerase beta complexed with 8-ClG as the template base in a 1-nucleotide gapped DNA (PDB entry 6CLY)
Macromolecule: DNA polymerase beta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 335 residues
Sequence: MSKRKAPQETLNGGITDMLTELANFEKNVSQAIHKYNAYRKAASVIAKYPHKIKSGAEAKKLPGVGTKIAEKIDEFLATGKLRKLEKIRQDDTSSSINFLTRVSGIGPSAARKFVDEGIKTLEDLRKNEDKLNHHQRIGLKYFGDFEKRIPREEMLQMQDIVLNEVKKVDSEYIATVCGSFRRGAESSGDMDVLLTHPSFTSESTKQPKLLHQVVEQLQKVHFITDTLSKGETKFMGVCQLPSKNDEKEYPHRRIDIRLIPKDQYYCGVLYFTGSDIFNKNMRAHALEKGFTINEYTIRPLGVTGVAGEPLPVDSEKDIFDYIQWKYREPKDRSE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.186
R work: 0.2188
R free: 0.2678
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 298
Crystal growth procedure: 14% to 23% PEG3400, and 350 mM sodium acetate in 50 mM imidazole (pH 7.5)
Matthews coefficient: 2.42
Solvent content (%): 49.17
Ligand: SODIUM ION ()
Ligand formula: Na
Ligand molecular weight: 22.99
Ligand SMILES: [Na+]
Ligand InChI: InChI=1S/Na/q+1
Release date: 2019-03-06
The crystal structure of the G45V mutant of human GlnRS (PDB entry 4YE9)
Macromolecule: Glutamine--tRNA ligase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 6.1.1.18
Sequence length: 776 residues
Sequence: HMAALDSLSLFTSLGLSEQKARETLKNSALSAQLREAATQAQQTLVSTIDKATGILLYGLASRLRDTRRLSFLVSYIASKKIHTEPQLSAALEYVRSHPLDPIDTVDFERECGVGVIVTPEQIEEAVEAAINRHRPQLLVERYHFNMGLLMGEARAVLKWADGKMIKNEVDMQVLHLLGPKLEADLEKKFKVAKARLEETDRRTAKDVVENGETADQTLSLMEQLRGEALKFHKPGENYKTPGYVVTPHTMNLLKQHLEITGGQVRTRFPPEPNGILHIGHAKAINFNFGYAKANNGICFLRFDDTNPEKEEAKFFTAICDMVAWLGYTPYKVTYASDYFDQLYAWAVELIRRGLAYVCHQRGEELKGHNTLPSPWRDRPMEESLLLFEAMRKGKFSEGEATLRMKLVMEDGKMDPVAYRVKYTPHHRTGDKWCIYPTYDYTHCLCDSIEHITHSLCTKEFQARRSSYFWLCNALDVYCPVQWEYGRLNLHYAVVSKRKILQLVATGAVRDWDDPRLFTLTALRRRGFPPEAINNFCARVGVTVAQTTMEPHLLEACVRDVLNDTAPRAMAVLESLRVIITNFPAAKSLDIQVPNFPADETKGFHQVPFAPIVFIERTDFKEEPEPGFKRLAWGQPVGLRHTGYVIELQHVVKGPSGCVESLEVTCRRADAGEKPKAFIHWVSQPLMCEVRLYERLFQHKNPEDPTEVPGGFLSDLNLASLHVVDAALVDCSVALAKPFDKFQFERLGYFSVDPDSHQGKLVFNRTVTLKEDPGKV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.7
R work: 0.2282
R free: 0.2623
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 289
Crystal growth procedure: ammonium acetate, bis-tris, PEG 20,000, EDTA
Matthews coefficient: 4.85
Solvent content (%): 74.64
Release date: 2016-02-17
c-KIT kinase domain in complex with avapritinib derivative 11 (PDB entry 8PQE)
Macromolecule: Mast/stem cell growth factor receptor Kit
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 327 residues
Sequence: GSMPMYEVQWKVVEESNGNNYSYIDPTQLPYDHKWEFPRNRLSFGKTLGAGAFGKVVEATAQGLIKSDAAMTVAVKMLKPSAHSTEREALMSELKVLSYLGNHENIVNLLGACTHGGPTLVITEYCCYGDLLNFLRRKRDEFVPYKVAPEDLYKDFLTLEHLLSFSYQVAKGMAFLASKNCIHRDLAARNILLTHGNITKICDFGLARDIKNDSNYVDKGNARLPVKWMAPESIFNSVYTFESDVWSYGIFLWELFSLGSSPYPGMPVDSKFYKMIKEGFRMSSPEYAPAEMYDIMKTCWDADPDKRPTFKQIVQDIEKQISESTNH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.0
R work: 0.2135
R free: 0.2556
Average B factor: 62.55
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 9.5
Crystallization temperature (K): 285.15
Crystal growth procedure: 7.5 mg/mL, 12% PEG8000 20% Ethylen glycole, 30 mM NaI, 30 mM NaF, 30 mM NaBr, 100 mM Tris-Bicine, pH 9.5
Matthews coefficient: 2.04
Solvent content (%): 39.6
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: 2023-12-27
Human Sirt6 in complex with ADP-ribose and fragment 4-amino-6-chlorobenzene-1,3-disulfonamide (PDB entry 8AKG)
Macromolecule: NAD-dependent protein deacetylase sirtuin-6
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1.286
Sequence length: 302 residues
Sequence: GIDPFTADKGKCGLPEIFDPPEELERKVWELARLVWQSSSVVFHTGAGISTASGIPDFRGPHGVWTMEERGLAPKFDTTFESARPTQTHMALVQLERVGLLRFLVSQNVDGLHVRSGFPRDKLAELHGNMFVEECAKCKTQYVRDTVVGTMGLKATGRLCTVAKARGLRACRGELRDTILDWEDSLPDRDLALADEASRNADLSITLGTSLQIRPSGNLPLATKRRGGRLVIVNLQPTKHDRHADLRIHGYVDEVMTRLMKHLGLEIPAWDGPRVLERALPPLPRPPTPKLEPKEESPTRIN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.82
R work: 0.1734
R free: 0.1929
Average B factor: 36.079
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.7
Crystallization temperature (K): 293
Crystal growth procedure: 1.6 M (NH4)2SO4, 10% PEG 400, and Bis-Tris buffer pH 5.7
Matthews coefficient: 2.6
Solvent content (%): 52.76
Ligand: [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL
[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE (AR6)
Ligand formula: C15 H23 N5 O14 P2
Ligand molecular weight: 559.316
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)O)O)O)O)O)N
Ligand InChI: InChI=1S/C15H23N5O14P2/c16-12-7-13(18-3-17-12)20(4-19-7)14-10(23)8(21)5(32-14)1-30-35(26,27)34-36(28,29)31-2-6-9(22)11(24)15(25)33-6/h3-6,8-11,14-15,21-25H,1-2H2,(H,26,27)(H,28,29)(H2,16,17,18)/t5-,6-,8-,9-,10-,11-,14-,15+/m1/s1
Release date: 2023-08-16