satarupa22/MacromolecularLigandDB huggingface dataset:
Crystal Structure of EGFR-T790M/V948R in Complex with Poziotinib (PDB entry 7A6J)
Macromolecule: Epidermal growth factor receptor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 333 residues
Sequence: GSHMASGEAPNQALLRILKETEFKKIKVLGSGAFGTVYKGLWIPEGEKVKIPVAIKELREATSPKANKEILDEAYVMASVDNPHVCRLLGICLTSTVQLIMQLMPFGCLLDYVREHKDNIGSQYLLNWCVQIAKGMNYLEDRRLVHRDLAARNVLVKTPQHVKITDFGLAKLLGAEEKEYHAEGGKVPIKWMALESILHRIYTHQSDVWSYGVTVWELMTFGSKPYDGIPASEISSILEKGERLPQPPICTIDVYMIMRKCWMIDADSRPKFRELIIEFSKMARDPQRYLVIQGDERMHLPSPTDSNFYRALMDEEDMDDVVDADEYLIPQQG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.0
R work: 0.1902
R free: 0.2159
Average B factor: 48.7592
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 20.0 % PEG3350, 100 mM MgSO4, 4 % ethylen glycole, 7.5 mg/mL EGFR-T790M/V948R (in 100 mM NaCl, 25 mM Tris-HCl, 10 % glycerol, 1 mM TCEP, pH 8.0) 1 ul reservoir + 1 ul protein solution)
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: 2022-02-23
Crystal structure of I19V mutant human PTP1B (PTPN1) at room temperature (298 K) (PDB entry 9CYP)
Macromolecule: Tyrosine-protein phosphatase non-receptor type 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 321 residues
Sequence: MEMEKEFEQIDKSGSWAAVYQDIRHEASDFPCRVAKLPKNKNRNRYRDVSPFDHSRIKLHQEDNDYINASLIKMEEAQRSYILTQGPLPNTCGHFWEMVWEQKSRGVVMLNRVMEKGSLKCAQYWPQKEEKEMIFEDTNLKLTLISEDIKSYYTVRQLELENLTTQETREILHFHYTTWPDFGVPESPASFLNFLFKVRESGSLSPEHGPVVVHCSAGIGRSGTFCLADTCLLLMDKRKDPSSVDIKKVLLEMRKFRMGLIQTADQLRFSYLAVIEGAKFIMGDSSVQDQWKELSHEDLEPPPEHIPPPPRPPKRILEPHN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.99
R work: 0.182
R free: 0.2139
Average B factor: 42.08
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.3 M magnesium acetate, 0.1 M HEPES pH 7.5, 0.1% beta-mercaptoethanol, 13.5% PEG 8000, 2% ethanol
Matthews coefficient: 3.3
Solvent content (%): 66.94
Ligand: BETA-MERCAPTOETHANOL (BME)
Ligand formula: C2 H6 O S
Ligand molecular weight: 78.133
Ligand SMILES: C(CS)O
Ligand InChI: InChI=1S/C2H6OS/c3-1-2-4/h3-4H,1-2H2
Release date: 2024-08-21
Crystal Structure of a FVIIa-Trypsin Chimera (YT) in Complex with Soluble Tissue Factor (PDB entry 4Z6A)
Macromolecule: Coagulation factor VII
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.21
Sequence length: 96 residues
Sequence: DQCASSPCQNGGSCKDQLQSYICFCLPAFEGRNCETHKDDQLICVNENGGCEQYCSDHTGTKRSCRCHEGYSLLADGVSCTPTVEYPCGKIPILEK
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.25
R work: 0.1882
R free: 0.2405
Average B factor: 48.914
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.6
Crystallization temperature (K): 295
Crystal growth procedure: 0.1M NaCitrate, 16.6% PEG 3350, 12.5% 1-Propanol, with seeding
Matthews coefficient: 2.78
Solvent content (%): 55.76
Ligand: beta-D-glucopyranose (BGC)
Ligand formula: C6 H12 O6
Ligand molecular weight: 180.156
Ligand SMILES: C(C1C(C(C(C(O1)O)O)O)O)O
Ligand InChI: InChI=1S/C6H12O6/c7-1-2-3(8)4(9)5(10)6(11)12-2/h2-11H,1H2/t2-,3-,4+,5-,6-/m1/s1
Release date: 2015-12-30
Crystal Structure of the Human vaccinia-related kinase 1 (VRK1) bound to an N-propynyl-N-isopentyl-dihydropteridin inhibitor (PDB entry 6CNX)
Macromolecule: Serine/threonine-protein kinase VRK1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 364 residues
Sequence: SMRVKAAQAGRQSSAKRHLAEQFAVGEIITDMAAAAWKVGLPIGQGGFGCIYLADMNSSESVGSDAPCVVKVEPSDNGPLFTELKFYQRAAKPEQIQKWIRTRKLKYLGVPKYWGSGLHDKNGKSYRFMIMDRFGSDLQKIYEANAKRFSRKTVLQLSLRILDILEYIHEHEYVHGDIKASNLLLNYKNPDQVYLVDYGLAYRYCPEGVHKAYAADPKRCHDGTIEFTSIDAHNGVAPSRRGDLEILGYCMIQWLTGHLPWEDNLKDPKYVRDSKIRYRENIASLMDKCFPAANAPGEIAKYMETVKLLDYTEKPLYENLRDILLQGLKAIGSKDDGKLDLSVVENGGLKAKTITKKRAAEIEE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2
R work: 0.18707
R free: 0.21112
Average B factor: 31.898
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293.15
Crystal growth procedure: 30.25% PEG3350, 30mM LiSO4, 0.1M SBG (Sodium-tartrate, Bis-Tris, Glycylglycine)
Matthews coefficient: 2.81
Solvent content (%): 56.27
Ligand: (7R)-2-[(3,5-difluoro-4-hydroxyphenyl)amino]-7-methyl-8-(3-methylbutyl)-5-(prop-2-yn-1-yl)-7,8-dihydropteridin-6(5H)-one (F87)
Ligand formula: C21 H23 F2 N5 O2
Ligand molecular weight: 415.436
Ligand SMILES: CC1C(=O)N(c2cnc(nc2N1CCC(C)C)Nc3cc(c(c(c3)F)O)F)CC#C
Ligand InChI: InChI=1S/C21H23F2N5O2/c1-5-7-28-17-11-24-21(25-14-9-15(22)18(29)16(23)10-14)26-19(17)27(8-6-12(2)3)13(4)20(28)30/h1,9-13,29H,6-8H2,2-4H3,(H,24,25,26)/t13-/m1/s1
Release date: 2018-04-04
Pre-catalytic ternary complex of Human DNA Polymerase Beta With Gapped DNA substrate incoming (-)3TC-TP and Ca2+. (PDB entry 5U2S)
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): 2.3
R work: 0.23
R free: 0.284
Average B factor: 39.93
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
Matthews coefficient: 2.35
Solvent content (%): 47.75
Ligand: Lamivudine Triphosphate (1RZ)
Ligand formula: C8 H14 N3 O12 P3 S
Ligand molecular weight: 469.196
Ligand SMILES: C1C(OC(S1)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)N2C=CC(=NC2=O)N
Ligand InChI: InChI=1S/C8H14N3O12P3S/c9-5-1-2-11(8(12)10-5)6-4-27-7(21-6)3-20-25(16,17)23-26(18,19)22-24(13,14)15/h1-2,6-7H,3-4H2,(H,16,17)(H,18,19)(H2,9,10,12)(H2,13,14,15)/t6-,7+/m0/s1
Release date: 2017-05-24
COPS5(2-257) IN COMPLEX WITH A AZAINDOLE (COMPOUND 4) (PDB entry 5M5Q)
Macromolecule: COP9 signalosome complex subunit 5
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4
Sequence length: 257 residues
Sequence: GAASGSGMAQKTWELANNMQEAQSIDEIYKYDKKQQQEILAAKPWTKDHHYFKYCKISALALLKMVMHARSGGNLEVMGLMLGKVDGETMIIMDSFALPVEGTETRVNAQAAAYEYMAAYIENAKQVGRLENAIGWYHSHPGYGCWLSGIDVSTQMLNQQFQEPFVAVVIDPTRTISAGKVNLGAFRTYPKGYKPPDEGPSEYQTIPLNKIEDFGVHCKQYYALEVSYFKSSLDRKLLELLWNKYWVNTLSSSSLLT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.2
R work: 0.197
R free: 0.219
Average B factor: 68.84
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6
Crystallization temperature (K): 277
Crystal growth procedure: 35% MPD, 0.2M LiSO4, 0,1 M Mes pH 6.0
Matthews coefficient: 3.12
Solvent content (%): 60.63
Ligand: (4S)-2-METHYL-2,4-PENTANEDIOL (MPD)
Ligand formula: C6 H14 O2
Ligand molecular weight: 118.174
Ligand SMILES: CC(CC(C)(C)O)O
Ligand InChI: InChI=1S/C6H14O2/c1-5(7)4-6(2,3)8/h5,7-8H,4H2,1-3H3/t5-/m0/s1
Release date: 2017-01-11
Structure of Mdm2 with low molecular weight inhibitor (PDB entry 4ZFI)
Macromolecule: E3 ubiquitin-protein ligase Mdm2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 6.3.2
Sequence length: 97 residues
Sequence: MQIPASEQETLVRPKPLLLKLLKSVGAQKDTYTMKEVLFYLGQYIMTKRLYDEKQQHIVYCSNDLLGDLFGVPSFSVKEHRKIYTMIYRNLVVVNQQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2
R work: 0.1977
R free: 0.2433
Average B factor: 30.395
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.1 M HEPES pH 7.5, 0.2 M sodium chloride, 25% (w/v) PEG 3350
Matthews coefficient: 2.46
Solvent content (%): 50.1
Ligand: (5S)-3,5-bis(4-chlorobenzyl)-4-(6-chloro-1H-indol-3-yl)-5-hydroxy-1-methyl-1,5-dihydro-2H-pyrrol-2-one (4NJ)
Ligand formula: C27 H21 Cl3 N2 O2
Ligand molecular weight: 511.827
Ligand SMILES: CN1C(=O)C(=C(C1(Cc2ccc(cc2)Cl)O)c3c[nH]c4c3ccc(c4)Cl)Cc5ccc(cc5)Cl
Ligand InChI: InChI=1S/C27H21Cl3N2O2/c1-32-26(33)22(12-16-2-6-18(28)7-3-16)25(23-15-31-24-13-20(30)10-11-21(23)24)27(32,34)14-17-4-8-19(29)9-5-17/h2-11,13,15,31,34H,12,14H2,1H3/t27-/m0/s1
Release date: 2016-10-19
INPP5D PanDDA analysis group deposition -- Crystal Structure of the phosphatase and C2 domains of SHIP1 in complex with Z275165822 (PDB entry 5RY0)
Macromolecule: Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.86
Sequence length: 463 residues
Sequence: SMEQPEPDMITIFIGTWNMGNAPPPKKITSWFLSKGQGKTRDDSADYIPHDIYVIGTQEDPLSEKEWLEILKHSLQEITSVTFKTVAIHTLWNIRIVVLAKPEHENRISHICTDNVKTGIANTLGNKGAVGVSFMFNGTSLGFVNSHLTSGSEKKLRRNQNYMNILRFLALGDKKLSPFNITHRFTHLFWFGDLNYRVDLPTWEAETIIQKIKQQQYADLLSHDQLLTERREQKVFLHFEEEEITFAPTYRFERLTRDKYAYTKQKATGMKYNLPSWCDRVLWKSYPLVHVVCQSYGSTSDIMTSDHSPVFATFEAGVTSQFVSKNGPGTVDSQGQIEFLRCYATLKTKSQTKFYLEFHSSCLESFVKSQEGENEEGSEGELVVKFGETLPKLKPIISDPEYLLDQHILISIKSSDSDESYGEGCIALRLEATETQLPIYTPLTHHGELTGHFQGEIKLQTSQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.98
R work: 0.1577
R free: 0.2041
Average B factor: 17.673
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 30 mM sodium nitrate, 30 mM dibasic sodium phosphate, 30 mM ammonium sulfate, 100 mM MES/imidazole, pH 6.5, 20% PEG500 MME, 10% PEG20000
Matthews coefficient: 2.08
Solvent content (%): 40.82
Ligand: 1-[4-(4-chlorophenyl)piperazin-1-yl]ethan-1-one (WNY)
Ligand formula: C12 H15 Cl N2 O
Ligand molecular weight: 238.713
Ligand SMILES: CC(=O)N1CCN(CC1)c2ccc(cc2)Cl
Ligand InChI: InChI=1S/C12H15ClN2O/c1-10(16)14-6-8-15(9-7-14)12-4-2-11(13)3-5-12/h2-5H,6-9H2,1H3
Release date: 2020-11-11
Discovery of N-(3-(5-((3-acrylamido-4-(morpholine-4-carbonyl)phenyl)amino)-1-methyl-6-oxo-1,6-dihydropyridin-3-yl)-2-methylphenyl)-4-(tert-butyl)benzamide (CHMFL-BTK-01) as a Highly Selective Irreversible BTK Kinase Inhibitor (PDB entry 5J87)
Macromolecule: Tyrosine-protein kinase BTK
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 274 residues
Sequence: PSTAGLGYGSWEIDPKDLTFLKELGTGQFGVVKYGKWRGQYDVAIKMIKEGSMSEDEFIEEAKVMMNLSHEKLVQLYGVCTKQRPIFIITEYMANGCLLNYLREMRHRFQTQQLLEMCKDVCEAMEYLESKQFLHRDLAARNCLVNDQGVVKVSDFGLSRYVLDDEYTSSVGSKFPVRWSPPEVLMYSKFSSKSDIWAFGVLMWEIYSLGKMPYERFTNSETAEHIAQGLRLYRPHLASEKVYTIMYSCWHEKADERPTFKILLSNILDVMDEE
Oligomeric state: Homo 4-mer
Stoichiometry: A4
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.59
R work: 0.2165
R free: 0.2477
Crystallization method: EVAPORATION
Crystallization pH: 6.5
Crystallization temperature (K): 298
Crystal growth procedure: 0.2M magnesium chloride ,0.1M sodium cacodylate pH6.5, 31% PEG 2000 , 0.1M sodium iodide
Matthews coefficient: 2.29
Solvent content (%): 46.36
Ligand: N-[3-(5-{[3-(acryloylamino)-4-(morpholine-4-carbonyl)phenyl]amino}-1-methyl-6-oxo-1,6-dihydropyridin-3-yl)-2-methylphenyl]-4-tert-butylbenzamide (N42)
Ligand formula: C38 H41 N5 O5
Ligand molecular weight: 647.763
Ligand SMILES: Cc1c(cccc1NC(=O)c2ccc(cc2)C(C)(C)C)C3=CN(C(=O)C(=C3)Nc4ccc(c(c4)NC(=O)C=C)C(=O)N5CCOCC5)C
Ligand InChI: InChI=1S/C38H41N5O5/c1-7-34(44)40-32-22-28(15-16-30(32)36(46)43-17-19-48-20-18-43)39-33-21-26(23-42(6)37(33)47)29-9-8-10-31(24(29)2)41-35(45)25-11-13-27(14-12-25)38(3,4)5/h7-16,21-23,39H,1,17-20H2,2-6H3,(H,40,44)(H,41,45)
Release date: 2017-04-19
Discovery and Optimisation of Potent, Efficacious and Selective Inhibitors Targeting EGFR Exon20 Insertion Mutations. Compound 18 bound to EGFR[V948R] (PDB entry 8PO3)
Macromolecule: Epidermal growth factor receptor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 330 residues
Sequence: GSSGEAPNQALLRILKETEFKKIKVLGSGAFGTVYKGLWIPEGEKVKIPVAIKELREATSPKANKEILDEAYVMASVDNPHVCRLLGICLTSTVQLITQLMPFGCLLDYVREHKDNIGSQYLLNWCVQIAKGMNYLEDRRLVHRDLAARNVLVKTPQHVKITDFGLAKLLGAEEKEYHAEGGKVPIKWMALESILHRIYTHQSDVWSYGVTVWELMTFGSKPYDGIPASEISSILEKGERLPQPPICTIDVYMIMRKCWMIDADSRPKFRELIIEFSKMARDPQRYLVIQGDERMHLPSPTDSNFYRALMDEEDMDDVVDADEYLIPQQG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.13
R work: 0.2191
R free: 0.2688
Average B factor: 23.67
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293.15
Crystal growth procedure: PEG 8K 12%w/v pH 0, PCPT 0.1M pH 5.5
Matthews coefficient: 2.15
Solvent content (%): 42.66
Ligand: 2-methyl-5-[[3-[1-[(3~{S})-1-propanoylpyrrolidin-3-yl]-4-pyridin-4-yl-pyrazol-3-yl]phenoxy]methyl]-3~{H}-isoindol-1-one (2II)
Ligand formula: C31 H31 N5 O3
Ligand molecular weight: 521.61
Ligand SMILES: CCC(=O)N1CCC(C1)n2cc(c(n2)c3cccc(c3)OCc4ccc5c(c4)CN(C5=O)C)c6ccncc6
Ligand InChI: InChI=1S/C31H31N5O3/c1-3-29(37)35-14-11-25(18-35)36-19-28(22-9-12-32-13-10-22)30(33-36)23-5-4-6-26(16-23)39-20-21-7-8-27-24(15-21)17-34(2)31(27)38/h4-10,12-13,15-16,19,25H,3,11,14,17-18,20H2,1-2H3/t25-/m0/s1
Release date: 2024-06-05
Structure of ASK1 bound to BIO-1772961 (PDB entry 6VRE)
Macromolecule: Mitogen-activated protein kinase kinase kinase 5
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.25
Sequence length: 291 residues
Sequence: TEEGDCESDLLEYDYEYDENGDRVVLGKGTYGIVYAGRDLSNQVRIAIKEIPERDSRYSQPLHEEIALHKHLKHKNIVQYLGSFSENGFIKIFMEQVPGGSLSALLRSKWGPLKDNEQTIGFYTKQILEGLKYLHDNQIVHRDIKGDNVLINTYSGVLKISDFGTSKRLAGINPCTEEFTGTLQYMAPEIIDKGPRGYGKAADIWSLGCTIIEMATGKPPFYELGEPQAAMFKVGMFKVHPEIPESMSAEAKAFILKCFEPDPDKRACANDLLVDEFLKVSSKKKKTQPKL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.29
R work: 0.19
R free: 0.24
Average B factor: 68.3043
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 5.5
Crystallization temperature (K): 300
Crystal growth procedure: 0.1M BisTRIS pH 5.5, 0.2M ammonium acetate, 3% sorbitol and 12% PEG3350
Matthews coefficient: 2.74
Solvent content (%): 55.14
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: 2020-05-06
Tick salivary cystatin Ricistatin in complex with cathepsin V (PDB entry 7PK4)
Macromolecule: Putative salivary cystatin
Type: Protein, polypeptide(L)
Source organism: Ixodes ricinus
Sequence length: 116 residues
Sequence: MELALRGGYRERPNHQEDPKYLELAHYATSTWSAQQPGKTPFDTVVEVLKVETQTVAGTNYRLTLKVAESTCELTSTYSKDACQPNANAAQRTCTTVIYQNLEGEKSVSSFGCAAA
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.92
R work: 0.1859
R free: 0.2261
Average B factor: 27.591
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 4.5
Crystallization temperature (K): 291.15
Crystal growth procedure: 0.07 M Ammonium acetate 4.5 18.9% w/v PEG 10,000
Matthews coefficient: 2.01
Solvent content (%): 38.88
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: 2022-12-14
The FK1 domain of FKBP51 in complex with (1S,5S,6R)-10-((S)-(3,5-dichlorophenyl)sulfinyl)-3-(pyridin-2-ylmethyl)-5-vinyl-3,10-diazabicyclo[4.3.1]decan-2-one (PDB entry 8CHP)
Macromolecule: Peptidyl-prolyl cis-trans isomerase FKBP5
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 5.2.1.8
Sequence length: 128 residues
Sequence: GAPATVTEQGEDITSKKDRGVLKIVKRVGNGEETPMIGDKVYVHYKGKLSNGKKFDSSHDRNEPFVFSLGKGQVIKAWDIGVATMKKGEIAHLLIKPEYAYGSAGSLPKIPSNATLFFEIELLDFKGE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1
R work: 0.1751
R free: 0.1871
Average B factor: 9.241
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 32% PEG3350, 0.2 M ammonium acetate, 0.1M HEPES-NaOH pH 7.5
Matthews coefficient: 2.32
Solvent content (%): 46.97
Ligand: (1~{S},5~{S},6~{R})-10-[3,5-bis(chloranyl)phenyl]sulfinyl-5-ethenyl-3-(pyridin-2-ylmethyl)-3,10-diazabicyclo[4.3.1]decan-2-one (UT6)
Ligand formula: C22 H23 Cl2 N3 O2 S
Ligand molecular weight: 464.408
Ligand SMILES: C=CC1CN(C(=O)C2CCCC1N2S(=O)c3cc(cc(c3)Cl)Cl)Cc4ccccn4
Ligand InChI: InChI=1S/C22H23Cl2N3O2S/c1-2-15-13-26(14-18-6-3-4-9-25-18)22(28)21-8-5-7-20(15)27(21)30(29)19-11-16(23)10-17(24)12-19/h2-4,6,9-12,15,20-21H,1,5,7-8,13-14H2/t15-,20+,21-,30+/m0/s1
Release date: 2023-09-06
STRUCTURE OF PROTEIN KINASE CK2 CATALYTIC SUBUNIT (ISOFORM CK2ALPHA'; CSNK2A2 GENE PRODUCT) IN COMPLEX WITH THE INHIBITOR CX-4945 AND THE ALPHA-D-POCKET LIGAND 3,4-DICHLORO PHENETHYLAMINE (DPA) (PDB entry 8QBU)
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): 1.09
R work: 0.1593
R free: 0.1793
Average B factor: 18.8
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 293
Crystal growth procedure: THE CK2ALPHA' SOLUTION AFTER PROTEIN PURIFICATION (5 MG/ML CK2ALPHA' IN 500 MM NACL, 25 MM TRIS/HCl, PH 8.5) WAS MIXED IN 1:10 VOLUME RATIO WITH 10 MM SOLUTION OF THE INHIBITOR MB002 IN DMSO. THIS SOLUTION WAS MIXED IN 2:1 RATIO WITH RESERVOIR SOLUTION [900 MM LICL, 28 % (W/V) PEG 6000, 250 MM TRIS/HCL, PH 8.5] IN SITTING DROP PLATES (VAPOUR DIFFUSION). THE CRYSTAL GROWTH WAS INDUCED BY MICROSEEDING. THE CRYSTALS WERE OPTIMIZED BY MACROSEEDING. A CRYSTAL WAS PURGED TWICE WITH RESERVOIR SOLUTION BEFORE ADDING 1 MIKROLITER DPA (50 MM IN DMSO) AND 1 MIKROLITER CX-4945 (10 MM IN DMSO) TO THE CRYSTAL MOTHOR LIQUOR FOR EXTENSIVE SOAKING AND REPLACEMENT OF THE INITIAL INHIBITOR MB002. ALL STEPS WERE PERFORMED AT A TEMPERATURE OF 293 K.
Matthews coefficient: 2.6
Solvent content (%): 52.69
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: 2023-12-06
HUMAN IDO1 IN COMPLEX WITH COMPOUND 4-A (PDB entry 6WJY)
Macromolecule: Indoleamine 2,3-dioxygenase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.13.11.52
Sequence length: 394 residues
Sequence: MISKEYHIDEEVGFALPNPQENLPDFYNDWMFIAKHLPDLIESGQLRERVEKLNMLSIDHLTDHKSQRLARLVLGCITMAYVWGKGHGDVRKVLPRNIAVPYCQLSKKLELPPILVYADCVLANWKKKDPNKPLTYENMDVLFSFRDGDCSKGFFLVSLLVEIAAASAIKVIPTVFKAMQMQERDTLLKALLEIASCLEKALQVFHQIHDHVNPKAFFSVLRIYLSGWKGNPQLSDGLVYEGFWEDPKEFAGGSAGQSSVFQCFDVLLGIQQTAGGGHAAQFLQDMRRYMPPAHRNFLCSLESNPSVREFVLSKGDAGLREAYDACVKALVSLRSYHLQIVTKYILIPASQQPKENKTSEDPSKLEAKGTGGTDLMNFLKTVRSTTEKSLLKEG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.91
R work: 0.1796
R free: 0.2076
Average B factor: 46.657
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 mM Tris, 16% (w/v) PEG4000, 0.2 M NH4OAc
Matthews coefficient: 2.84
Solvent content (%): 56.68
Ligand: 3-chloro-N-(3-{(2S)-1-[(4-fluorophenyl)amino]-1-oxopropan-2-yl}bicyclo[1.1.1]pentan-1-yl)benzamide (U41)
Ligand formula: C21 H20 Cl F N2 O2
Ligand molecular weight: 386.847
Ligand SMILES: CC(C(=O)Nc1ccc(cc1)F)C23CC(C2)(C3)NC(=O)c4cccc(c4)Cl
Ligand InChI: InChI=1S/C21H20ClFN2O2/c1-13(18(26)24-17-7-5-16(23)6-8-17)20-10-21(11-20,12-20)25-19(27)14-3-2-4-15(22)9-14/h2-9,13H,10-12H2,1H3,(H,24,26)(H,25,27)/t13-,20-,21+/m1/s1
Release date: 2020-08-26
PTP1B F225I in complex with TCS401 (PDB entry 7MOW)
Macromolecule: Tyrosine-protein phosphatase non-receptor type 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 308 residues
Sequence: GHMASMEMEKEFEQIDKSGSWAAIYQDIRHEASDFPCRVAKLPKNKNRNRYRDVSPFDHSRIKLHQEDNDYINASLIKMEEAQRSYILTQGPLPNTCGHFWEMVWEQKSRGVVMLNRVMEKGSLKCAQYWPQKEEKEMIFEDTNLKLTLISEDIKSYYTVRQLELENLTTQETREILHFHYTTWPDFGVPESPASFLNFLFKVRESGSLSPEHGPVVVHCSAGIGRSGTICLADTCLLLMDKRKDPSSVDIKKVLLEMRKFRMGLIQTADQLRFSYLAVIEGAKFIMGDSSVQDQWKELSHEDLEPHN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.1547
R free: 0.1757
Average B factor: 29.61
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 0.2 M MgCl2, 0.1 M Tris pH 8, 17.5% PEG 8000
Matthews coefficient: 3.28
Solvent content (%): 62.52
Ligand: 2-(OXALYL-AMINO)-4,5,6,7-TETRAHYDRO-THIENO[2,3-C]PYRIDINE-3-CARBOXYLIC ACID (OTA)
Ligand formula: C10 H10 N2 O5 S
Ligand molecular weight: 270.262
Ligand SMILES: C1CNCc2c1c(c(s2)NC(=O)C(=O)O)C(=O)O
Ligand InChI: InChI=1S/C10H10N2O5S/c13-7(10(16)17)12-8-6(9(14)15)4-1-2-11-3-5(4)18-8/h11H,1-3H2,(H,12,13)(H,14,15)(H,16,17)
Release date: 2022-05-18
Crystal structure of the pre-catalytic ternary complex of DNA polymerase lambda with a templating A and an incoming dTTP (PDB entry 4XUS)
Macromolecule: DNA polymerase lambda
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 325 residues
Sequence: NHNLHITEKLEVLAKAYSVQGDKWRALGYAKAINALKSFHKPVTSYQEACSIPGIGKRMAEKIIEILESGHLRKLDHISESVPVLELFSNIWGAGTKTAQMWYQQGFRSLEDIRSQASLTTQQAIGLKHYSDFLERMPREEATEIEQTVQKAAQAFNSGLLCVACGSYRRGKATCGDVDVLITHPDGRSHRGIFSRLLDSLRQEGFLTDDLVSQEENGQQQKYLGVCRLPGPGRRHRRLDIIVVPYSEFACALLYFTGSAHFNRSMRALAKTKGMSLSEHALSTAVVRNTHGCKVGPGRVLPTPTEKDVFRLLGLPYREPAERDW
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.4
R work: 0.1874
R free: 0.2358
Average B factor: 29.24
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 278
Crystal growth procedure: 0.1 M sodium acetate trihydrate
2.0 M sodium formate
Matthews coefficient: 2.94
Solvent content (%): 58.19
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: 2016-02-03