satarupa22/MacromolecularLigandDB huggingface dataset:
An unusual natural product primary sulfonamide: synthesis, carbonic anhydrase inhibition and protein x-ray structure of Psammaplin C (PDB entry 5G0C)
Macromolecule: CARBONIC ANHYDRASE 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 260 residues
Sequence: MSHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHSFKVNFDDSQDKAVLKGGPLDGTYRLTQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDASKASQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTKGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLNETVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.28
R work: 0.12992
R free: 0.1631
Average B factor: 13.377
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystal growth procedure: SITTING DROP PLATES WITH 200 NL PROTEIN AT 5 MG/ML AND 200 NL RESERVOIR WITH 2.6 TO 2.8 M AMMONIUM SULFATE AND 100 MM TRIS AT PH 8.5
Matthews coefficient: 2.08
Solvent content (%): 40.9
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: 2016-05-25
Crystal structure of MKK7 (MAP2K7) covalently bound with type-II inhibitor SB1-G-23 (PDB entry 6YG7)
Macromolecule: Dual specificity mitogen-activated protein kinase kinase 7
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.12.2
Sequence length: 307 residues
Sequence: SMKQTGYLTIGGQRYQAEINDLENLGEMGSGTCGQVWKMRFRKTGHVIAVKQMRRSGNKEENKRILMDLDVVLKSHDCPYIVQCFGTFITNTDVFIAMELMGTCAEKLKKRMQGPIPERILGKMTVAIVKALYYLKEKHGVIHRDVKPSNILLDERGQIKLCDFGISGRLVDDKAKDRSAGCAAYMAPERIDPPDPTKPDYDIRADVWSLGISLVELATGQFPYKNCKTDFEVLTKVLQEEPPLLPGHMGFSGDFQSFVKDCLTKDHRKRPKYNKLLEHSFIKRYETLEVDVASWFKDVMAKTESPR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.2
R work: 0.2074
R free: 0.251
Average B factor: 65.103
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 293.15
Crystal growth procedure: 25% PEG3350, 0.1 M ammonium acetate,
0.1 M tris, pH 8.5
Matthews coefficient: 2.28
Solvent content (%): 45.97
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: 2020-08-12
Bone Marrow Tyrosine Kinase in Chromosome X in complex with a newly designed covalent inhibitor JS24 (PDB entry 6I99)
Macromolecule: Cytoplasmic tyrosine-protein kinase BMX
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 278 residues
Sequence: HHHHHHENLYFQGELKREEITLLKELGSGQFGVVKLGKWKGQYDVAVKMIKEGSMSEDEFFQEAQTMMKLSHPKLVKFYGVCSKEYPIYIVTEYISNGCLLNYLRSHGKGLEPSQLLEMCYDVCEGMAFLESHQFIHRDLAARNCLVDRDLCVKVSDFGMTRYVLDDQYVSSVGTKFPVKWSAPEVFHYFKYSSKSDVWAFGILMWEVFSLGKMPYDLYTNSEVVLKVSQGHRLYRPHLASDTIYQIMYSCWHELPEKRPTFQQLLSSIEPLREKDKH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.001
R work: 0.2321
R free: 0.2586
Average B factor: 23.6
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8
Crystallization temperature (K): 293.15
Crystal growth procedure: imidazole-malate, PEG 600
Matthews coefficient: 2.35
Solvent content (%): 50.1
Ligand: ~{N}-[2-methyl-5-[8-[4-(methylsulfonylamino)phenyl]-2-oxidanylidene-benzo[h][1,6]naphthyridin-1-yl]phenyl]-3-oxidanyl-propanamide (H88)
Ligand formula: C29 H26 N4 O5 S
Ligand molecular weight: 542.606
Ligand SMILES: Cc1ccc(cc1NC(=O)CCO)N2c3c4ccc(cc4ncc3C=CC2=O)c5ccc(cc5)NS(=O)(=O)C
Ligand InChI: InChI=1S/C29H26N4O5S/c1-18-3-10-23(16-25(18)31-27(35)13-14-34)33-28(36)12-7-21-17-30-26-15-20(6-11-24(26)29(21)33)19-4-8-22(9-5-19)32-39(2,37)38/h3-12,15-17,32,34H,13-14H2,1-2H3,(H,31,35)
Release date: 2020-05-27
Human jak1 kinase domain in complex with inhibitor (PDB entry 6SMB)
Macromolecule: Tyrosine-protein kinase JAK1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 301 residues
Sequence: DIVSEKKPATEVDPTHFEKRFLKRIRDLGEGHFGKVELCRYDPEGDNTGEQVAVKSLKPESGGNHIADLKKEIEILRNLYHENIVKYKGICTEDGGNGIKLIMEFLPSGSLKEYLPKNKNKINLKQQLKYAVQICKGMDYLGSRQYVHRDLAARNVLVESEHQVKIGDFGLTKAIETDKEYYTVKDDRDSPVFWYAPECLMQSKFYIASDVWSFGVTLHELLTYCDSDSSPMALFLKMIGPTHGQMTVTRLVNTLKEGKRLPCPPNCPDEVYQLMRKCWEFQPSNRTSFQNLIEGFEALLK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.04
R work: 0.221
R free: 0.265
Average B factor: 38.2
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 27% (m/v) PEG6000, 0.1 M MES/NaOH pH 6.0 and 5 mM DTT
Matthews coefficient: 2.45
Solvent content (%): 49.76
Ligand: ~{N}-[3-[2-[(3-methoxy-1-methyl-pyrazol-4-yl)amino]-5-methyl-pyrimidin-4-yl]-1~{H}-indol-7-yl]-2-methyl-pyridine-3-carboxamide (LKQ)
Ligand formula: C25 H24 N8 O2
Ligand molecular weight: 468.51
Ligand SMILES: Cc1cnc(nc1c2c[nH]c3c2cccc3NC(=O)c4cccnc4C)Nc5cn(nc5OC)C
Ligand InChI: InChI=1S/C25H24N8O2/c1-14-11-28-25(30-20-13-33(3)32-24(20)35-4)31-21(14)18-12-27-22-17(18)7-5-9-19(22)29-23(34)16-8-6-10-26-15(16)2/h5-13,27H,1-4H3,(H,29,34)(H,28,30,31)
Release date: 2020-04-29
Crystal structure of chimeric carbonic anhydrase IX with inhibitor (PDB entry 4Q07)
Macromolecule: Carbonic anhydrase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 260 residues
Sequence: MSHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHSFQVEFDDSQDKAVLKGGPLDGTYRLLQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDVGKALQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTKGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLAECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.15
R work: 0.128
R free: 0.158
Average B factor: 14.353
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 291
Crystal growth procedure: Crystallization buffer was 0.1M sodium BICINE, pH 9, 0.2 M ammonium sulfate and 2M sodium malonate pH 7 made from 1M sodium BICINE and 3.4M sodium malonate, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Matthews coefficient: 2.01
Solvent content (%): 38.4
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: 2015-01-28
Crystal structure of the core catalytic domain of human inositol phosphate multikinase in complex with rhamnetin (PDB entry 6M8E)
Macromolecule: Inositol polyphosphate multikinase,Inositol polyphosphate multikinase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.1.151
Sequence length: 261 residues
Sequence: GSFTSHQVAGHMYGKDKVGILQHPDGTVLKQLQPPPRGPRELEFYNMVYAADCFDGVLLELRKYLPKYYGIWSPPTAPNDLYLKLEDVTHKFNKPCIMDVKIGQKSYDPFASSEKIQQQVSKYPLMEEIGFLVLGMRVYHVHSDSYETENQHYGRSLTKETIKDGVSRFFHNGYCLRKDAVAASIQKIEKILQWFENQKQLNFYASSLLFVYEGSSQGGSGGEVEVRMIDFAHVFPSNTIDEGYVYGLKHLISVLRSILDN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2
R work: 0.18431
R free: 0.24508
Average B factor: 30.315
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6
Crystallization temperature (K): 298
Crystal growth procedure: 35% (w/v) PEG 400, 0.1 M Li2SO4, 100 mM MES Imidanzol buffer , pH 6.0, 50 mM beta-mercaptoethanol at 298K. To obtain complex structure, the apo crystal was further soaked under 35% (w/v) PEG 400, 0.1 M Li2SO4, 100 mM HEPES, pH 7.5 at 298K in the presence of 10 mM rhametine for 3 days.
Matthews coefficient: 2.22
Solvent content (%): 44.59
Ligand: 2-(3,4-dihydroxyphenyl)-3,5-dihydroxy-7-methoxy-4H-1-benzopyran-4-one (J8G)
Ligand formula: C16 H12 O7
Ligand molecular weight: 316.262
Ligand SMILES: COc1cc(c2c(c1)OC(=C(C2=O)O)c3ccc(c(c3)O)O)O
Ligand InChI: InChI=1S/C16H12O7/c1-22-8-5-11(19)13-12(6-8)23-16(15(21)14(13)20)7-2-3-9(17)10(18)4-7/h2-6,17-19,21H,1H3
Release date: 2019-01-23
Notum Fragment 722 (PDB entry 7BCF)
Macromolecule: Palmitoleoyl-protein carboxylesterase NOTUM
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.1.98
Sequence length: 383 residues
Sequence: ETGSAQQLNEDLRLHLLLNTSVTCNDGSPAGYYLKESRGSRRWLLFLEGGWYCFNRENCDSRYDTMRRLMSSRDWPRTRTGTGILSSQPEENPYWWNANMVFIPYCSSDVWSGASSKSEKNEYAFMGALIIQEVVRELLGRGLSGAKVLLLAGSSAGGTGVLLNVDRVAEQLEKLGYPAIQVRGLADSGWFLDNKQYRHTDCVDTITCAPTEAIRRGIRYWNGVVPERCRRQFQEGEEWNCFFGYKVYPTLRSPVFVVQWLFDEAQLTVDNVHLTGQPVQEGLRLYIQNLGRELRHTLKDVPASFAPACLSHEIIIRSHWTDVQVKGTSLPRALHCWDRSLHDSHKASKTPLKGCPVHLVDSCPWPHCNPSCPTGTKHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.86
R work: 0.2227
R free: 0.2592
Average B factor: 29.693
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 296
Crystal growth procedure: 1.5 M Ammonium Sulphate
0.1 M Sodium Citrate, pH4.2
Matthews coefficient: 2.01
Solvent content (%): 38.75
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: 2022-01-12
hALK in complex with 3-(3-methyl-1H-pyrazol-5-yl)pyridine (PDB entry 7JYT)
Macromolecule: ALK tyrosine kinase receptor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 322 residues
Sequence: GAMGSTDYNPNYCFAGKTSSISDLKEVPRKNITLIRGLGHGAFGEVYEGQVSGMPNDPSPLQVAVKTLPEVCSEQDELDFLMEALIISKFNHQNIVRCIGVSLQSLPRFILLELMAGGDLKSFLRETRPRPSQPSSLAMLDLLHVARDIACGCQYLEENHFIHRDIAARNCLLTCPGPGRVAKIGDFGMARDIYRASYYRKGGCAMLPVKWMPPEAFMEGIFTSKTDTWSFGVLLWEIFSLGYMPYPSKSNQEVLEFVTSGGRMDPPKNCPGPVYRIMTQCWQHQPEDRPNFAIILERIEYCTQDPDVINTALPIEYGPLVE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2
R work: 0.2077
R free: 0.2244
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 293
Crystal growth procedure: 20 mM Tris pH 8.0, 150 mM NaCl, 0.5 mM EDTA, 1 mM Benzamidine and 0.25 mM TCEP
Matthews coefficient: 2.41
Solvent content (%): 48.89
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: 2021-01-20
Phosphatase domain of PP5 bound to a phosphomimetic Cdc37 substrate peptide (PDB entry 5HPE)
Macromolecule: Serine/threonine-protein phosphatase 5,Hsp90 co-chaperone Cdc37
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.16
Sequence length: 350 residues
Sequence: EYSGPKLEDGKVTISFMKELMQWYKDQKKLHRKCAYQILVQVKEVLSKLSTLVETTLKETEKITVCGDTHGQFYDLLNIFELNGLPSETNPYIFNGDFVDRGSFSVEVILTLFGFKLLYPDHFHLLRGNHETDNMNQIYGFEGEVKAKYTAQMYELFSEVFEWLPLAQCINGKVLIMHGGLFSEDGVTLDDIRKIERNRQPPDSGPMCDLLWSDPQPQNGRSISKRGVSCQFGPDVTKAFLEENNLDYIIRSHEVKAEGYEVAHGGRCVTVFSAPNYCDQMGNKASYIHLQGSDLRPQFHQFTAVPHPNVKPMAYANTLLQLGMMGSGSGSASRSVWDHIEVEDDEDETH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.27
R work: 0.1684
R free: 0.2359
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 277
Crystal growth procedure: 18% PEG, 8% ethylene glycol, 0.1M Hepes pH 7.5, 20mM hexamine cobolt chloride
Matthews coefficient: 2.31
Solvent content (%): 46.69
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: 2016-07-27
Crystal Structure of Human Myt1 Kinase domain Bounded with RP-6306 (PDB entry 8D6E)
Macromolecule: Membrane-associated tyrosine- and threonine-specific cdc2-inhibitory kinase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 311 residues
Sequence: MHHHHHHSSGVDLGTENLYFQSMHQLQPRRVSFRGEASETLQSPGYDPSRPESFFQQSFQRLSRLGHGSYGEVFKVRSKEDGRLYAVKRSMSPFRGPKDRARKLAEVGSHEKVGQHPCCVRLEQAWEEGGILYLQTELCGPSLQQHCEAWGASLPEAQVWGYLRDTLLALAHLHSQGLVHLDVKPANIFLGPRGRCKLGDFGLLVELGTAGAGEVQEGDPRYMAPELLQGSYGTAADVFSLGLTILEVACNMELPHGGEGWQQLRQGYLPPEFTAGLSSELRSVLVMMLEPDPKLRATAEALLALPVLRQP
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.15
R work: 0.19
R free: 0.2177
Average B factor: 89.4569
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8.25
Crystallization temperature (K): 293
Crystal growth procedure: 5.6 to 6.6% PEG3350, 0.2 M Na2SO4, 0.1 M Tris-HCl and 10% EG
Matthews coefficient: 2.78
Solvent content (%): 55.8
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: 2022-07-27
Human Xylosyltransferase 1 in complex with UDP-xylose and peptide QEEEGAGGGQGG (PDB entry 6EJ7)
Macromolecule: Xylosyltransferase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.4.2.26
Sequence length: 751 residues
Sequence: APLVHHHHHHALDENLYFQGALADVSRPPHARKTGGSSPETKYDQPPKCDISGKEAISALSRAKSKHCRQEIGETYCRHKLGLLMPEKVTRFCPLEGKANKNVQWDEDSVEYMPANPVRIAFVLVVHGRASRQLQRMFKAIYHKDHFYYIHVDKRSNYLHRQVLQVSRQYSNVRVTPWRMATIWGGASLLSTYLQSMRDLLEMTDWPWDFFINLSAADYPIRTNDQLVAFLSRYRDMNFLKSHGRDNARFIRKQGLDRLFLECDAHMWRLGDRRIPEGIAVDGGSDWFLLNRRFVEYVTFSTDDLVTKMKQFYSYTLLPAESFFHTVLENSPHCDTMVDNNLRITNWNRKLGCKCQYKHIVDWCGCSPNDFKPQDFHRFQQTARPTFFARKFEAVVNQEIIGQLDYYLYGNYPAGTPGLRSYWENVYDEPDGIHSLSDVTLTLYHSFARLGLRRAETSLHTDGENSCRYYPMGHPASVHLYFLADRFQGFLIKHHATNLAVSKLETLETWVMPKKVFKIASPPSDFGRLQFSEVGTDWDAKERLFRNFGGLLGPMDEPVGMQKWGKGPNVTVTVIWVDPVNVIAATYDILIESTAEFTHYKPPLNLPLRPGVWTVKILHHWVPVAETKFLVAPLTFSNRQPIKPEEALKLHNGPLRNAYMEQSFQSLNPVLSLPINPAQVEQARRNAASTGTALEGWLDSLVGGMWTAMDICATGPTACPVMQTCSQTAWSSFSPDPKSELGAVKPDGRLR
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2
R work: 0.1985
R free: 0.2298
Average B factor: 45.9448
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: 55-65% Morpheus precipitant mix 2 (PEG8000 and ethylene glycol), 
0.1M Bicine/Tris buffer at pH 7.5
0.1 M of Morpheus NPS mix.
Matthews coefficient: 2.72
Solvent content (%): 54.86
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: 2018-05-02
Crystal structure of mRNA cap guanine-N7 methyltransferase in complex with RAM (PDB entry 5E8J)
Macromolecule: mRNA cap guanine-N7 methyltransferase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1.56
Sequence length: 312 residues
Sequence: SQSRIFYLRNFNNWMKSVLIGEFLEKVRQKKKRDITVLDLGCGKGGDLLKWKKGRINKLVCTDIADVSVKQCQQRYEDMKNRRDSEYIFSAEFITADSSKELLIDKFRDPQMCFDICSCQFVCHYSFESYEQADMMLRNACERLSPGGYFIGTTPNSFELIRRLEASETESFGNEIYTVKFQKKGDYPLFGCKYDFNLEGVVDVPEFLVYFPLLNEMAKKYNMKLVYKKTFLEFYEEKIKNNENKMLLKRMQALEPYPANESSKLVSEKVDDYEHAAKYMKNSQVRLPLGTLSKSEWEATSIYLVFAFEKQQ
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.35
R work: 0.2105
R free: 0.2685
Average B factor: 25.7436
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 291
Crystal growth procedure: 0.1M MES pH 6.5, 30% PEG 4000
Matthews coefficient: 2.27
Solvent content (%): 45.9
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: 2016-07-13
Design and Synthesis of a pan-JAK Kinase Inhibitor Clinical Candidate (PF-06263276) Suitable for Inhaled and Topical Delivery for the Treatment of Inflammatory Diseases of the Lungs and Skin (PDB entry 5TQ4)
Macromolecule: Tyrosine-protein kinase JAK2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 298 residues
Sequence: GSEDRDPTQFEERHLKFLQQLGKGNFGSVEMCRYDPLQDNTGEVVAVKKLQHSTEEHLRDFEREIEILKSLQHDNIVKYKGVCYSAGRRNLKLIMEYLPYGSLRDYLQKHKERIDHIKLLQYTSQICKGMEYLGTKRYIHRDLATRNILVENENRVKIGDFGLTKVLPQDKEYYKVKEPGESPIFWYAPESLTESKFSVASDVWSFGVVLYELFTYIEKSKSPPAEFMRMIGNDKQGQSIVTHLIELLKNNGRLPRPDGCPDEIYMIMTECWNNNVNQRPSFRDLALRVDQIRDNMAG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.3
R work: 0.24734
R free: 0.2792
Average B factor: 23.727
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M Hepes, pH 7.5, 0.1 M sodium acetate, 30% PEG-3350
Matthews coefficient: 2.75
Solvent content (%): 55.35
Ligand: 6-(2-ethyl-4-hydroxyphenyl)-1H-indazole-3-carboxamide (7GY)
Ligand formula: C16 H15 N3 O2
Ligand molecular weight: 281.309
Ligand SMILES: CCc1cc(ccc1c2ccc3c(c2)[nH]nc3C(=O)N)O
Ligand InChI: InChI=1S/C16H15N3O2/c1-2-9-7-11(20)4-6-12(9)10-3-5-13-14(8-10)18-19-15(13)16(17)21/h3-8,20H,2H2,1H3,(H2,17,21)(H,18,19)
Release date: 2017-01-11
Crystal Structure of the Human vaccinia-related kinase bound to a N-propynyl-N-ethyl-dihydropteridine inhibitor (PDB entry 6CQH)
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): 2.15
R work: 0.20065
R free: 0.23885
Average B factor: 30.416
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6
Crystallization temperature (K): 293
Crystal growth procedure: 25% PEG3350, 300 mM LiSO4, 0.1M SBG, pH 6.0, 30% glycerol
Matthews coefficient: 2.62
Solvent content (%): 53.13
Ligand: (7R)-2-[(3,5-difluoro-4-hydroxyphenyl)amino]-8-ethyl-7-methyl-5-(prop-2-yn-1-yl)-7,8-dihydropteridin-6(5H)-one (F8Y)
Ligand formula: C18 H17 F2 N5 O2
Ligand molecular weight: 373.357
Ligand SMILES: CCN1c2c(cnc(n2)Nc3cc(c(c(c3)F)O)F)N(C(=O)C1C)CC#C
Ligand InChI: InChI=1S/C18H17F2N5O2/c1-4-6-25-14-9-21-18(22-11-7-12(19)15(26)13(20)8-11)23-16(14)24(5-2)10(3)17(25)27/h1,7-10,26H,5-6H2,2-3H3,(H,21,22,23)/t10-/m1/s1
Release date: 2018-03-28
Crystal structure of human ERK2 mutant (G37C) (PDB entry 7E75)
Macromolecule: Mitogen-activated protein kinase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.24
Sequence length: 363 residues
Sequence: GSHMAAAAAAGAGPEMVRGQVFDVGPRYTNLSYIGEGAYCMVCSAYDNVNKVRVAIKKISPFEHQTYCQRTLREIKILLRFRHENIIGINDIIRAPTIEQMKDVYIVQDLMETDLYKLLKTQHLSNDHICYFLYQILRGLKYIHSANVLHRDLKPSNLLLNTTCDLKICDFGLARVADPDHDHTGFLTEYVATRWYRAPEIMLNSKGYTKSIDIWSVGCILAEMLSNRPIFPGKHYLDQLNHILGILGSPSQEDLNCIINLKARNYLLSLPHKNKVPWNRLFPNADSKALDLLDKMLTFNPHKRIEVEQALAHPYLEQYYDPSDEPIAEAPFKFDMELDDLPKEKLKELIFEETARFQPGYRS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.481
R work: 0.1839
R free: 0.2656
Average B factor: 37.69
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 291
Crystal growth procedure: 0.1M HEPES/MOPS pH 7.5, 20% (v/v) PEGMME 550, 10% (w/v) PEG 20000, 20mM D-glycine, 20mM D-lysine
Matthews coefficient: 2.39
Solvent content (%): 48.5
Release date: 2022-03-02
ExoY Nucleotidyl Cyclase domain from Vibrio nigripulchritudo MARTX toxin, bound to ATP-Mg-actin, human profilin 1 and a sulfate ion (PDB entry 8BJJ)
Macromolecule: Actin, alpha skeletal muscle, intermediate form
Type: Protein, polypeptide(L)
Source organism: Oryctolagus cuniculus
Sequence length: 375 residues
Sequence: DEDETTALVCDNGSGLVKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYPIEHGIITNWDDMEKIWHHTFYNELRVAPEEHPTLLTEAPLNPKANREKMTQIMFETFNVPAMYVAIQAVLSLYASGRTTGIVLDSGDGVTHNVPIYEGYALPHAIMRLDLAGRDLTDYLMKILTERGYSFVTTAEREIVRDIKEKLCYVALDFENEMATAASSSSLEKSYELPDGQVITIGNERFRCPETLFQPSFIGMESAGIHETTYNSIMKCDIDIRKDLYANNVMSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWITKQEYDEAGPSIVHRKCF
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.699
R work: 0.1751
R free: 0.1949
Average B factor: 33.36
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 291
Crystal growth procedure: 30% peg3000
0.3M LiSO4
0.1M Tris pH8.5
3% Dioxane
Matthews coefficient: 2.36
Solvent content (%): 47.88
Ligand: MAGNESIUM ION (MG)
Ligand formula: Mg
Ligand molecular weight: 24.305
Ligand SMILES: [Mg+2]
Ligand InChI: InChI=1S/Mg/q+2
Release date: 2023-09-20
Human pancreatic alpha-amylase in complex with montbretin A (PDB entry 4W93)
Macromolecule: Pancreatic alpha-amylase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.2.1.1
Sequence length: 496 residues
Sequence: QYSPNTQQGRTSIVHLFEWRWVDIALECERYLAPKGFGGVQVSPPNENVAIYNPFRPWWERYQPVSYKLCTRSGNEDEFRNMVTRCNNVGVRIYVDAVINHMCGNAVSAGTSSTCGSYFNPGSRDFPAVPYSGWDFNDGKCKTGSGDIENYNDATQVRDCRLTGLLDLALEKDYVRSKIAEYMNHLIDIGVAGFRLDASKHMWPGDIKAILDKLHNLNSNWFPAGSKPFIYQEVIDLGGEPIKSSDYFGNGRVTEFKYGAKLGTVIRKWNGEKMSYLKNWGEGWGFVPSDRALVFVDNHDNQRGHGAGGASILTFWDARLYKMAVGFMLAHPYGFTRVMSSYRWPRQFQNGNDVNDWVGPPNNNGVIKEVTINPDTTCGNDWVCEHRWRQIRNMVIFRNVVDGQPFTNWYDNGSNQVAFGRGNRGFIVFNNDDWSFSLTLQTGLPAGTYCDVISGDKINGNCTGIKIYVSDDGKAHFSISNSAEDPFIAIHAESKL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.352
R work: 0.1976
R free: 0.2113
Average B factor: 18.5
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 300
Crystal growth procedure: 58% MPD, 100 mM sodium cacodylate
Matthews coefficient: 2.36
Solvent content (%): 47.81
Ligand: CALCIUM ION (CA)
Ligand formula: Ca
Ligand molecular weight: 40.078
Ligand SMILES: [Ca+2]
Ligand InChI: InChI=1S/Ca/q+2
Release date: 2015-07-15
Crystal structure of the catalytic domain of human diphosphoinositol pentakisphosphate kinase 2 (PPIP5K2) in complex with AMP-PNP and 5-(PCF2P)-IP5, an analog of 5-IP7 (PDB entry 8G9E)
Macromolecule: Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.4.21
Sequence length: 330 residues
Sequence: GSFTERQIVVGICSMAKKSKSKPMKEILERISLFKYITVVVFEEEVILNEPVENWPLCDCLISFHSKGFPLDKAVAYAKLRNPFVINDLNMQYLIQDRREVYSILQAEGILLPRYAILNRDPNNPKECNLIEGEDHVEVNGEVFQKPFVEKPVSAEDHNVYIYYPTSAGGGSQRLFRKIGSRSSVYSPESNVRKTGSYIYEEFMPTDGTDVKVYTVGPDYAHAEARKSPALDGKVERDSEGKEVRYPVILNAREKLIAWKVCLAFKQTVCGFDLLRANGQSYVCDVNGFSFVKNSMKYYDDCAKILGNIVMRELAPQFHIPWSIPLEAED
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.75
R work: 0.1241
R free: 0.1752
Average B factor: 21.625
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7
Crystallization temperature (K): 277
Crystal growth procedure: 14% (w/v) PEG 3350, 20 mM MgCl2, 0.1 M HEPES, pH 7.0, 1 mM AMPPNP, 2 mM CdCl2, Soaking with 2mM 5-PCF2P-InsP5 under pH 5.2 for 3 days , VAPOR DIFFUSION, HANGING DROP, temperature 277K
Matthews coefficient: 2.65
Solvent content (%): 53.53
Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER (ANP)
Ligand formula: C10 H17 N6 O12 P3
Ligand molecular weight: 506.196
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(NP(=O)(O)O)O)O)O)N
Ligand InChI: InChI=1S/C10H17N6O12P3/c11-8-5-9(13-2-12-8)16(3-14-5)10-7(18)6(17)4(27-10)1-26-31(24,25)28-30(22,23)15-29(19,20)21/h2-4,6-7,10,17-18H,1H2,(H,24,25)(H2,11,12,13)(H4,15,19,20,21,22,23)/t4-,6-,7-,10-/m1/s1
Release date: 2024-01-03