satarupa22/MacromolecularLigandDB huggingface dataset:
Crystal Structure of p38alpha in Complex with Lipid Pocket Ligand 9m (PDB entry 5N68)
Macromolecule: Mitogen-activated protein kinase 14
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.24
Sequence length: 360 residues
Sequence: MSQERPTFYRQELNKTIWEVPERYQNLSPVGSGAYGSVCAAFDTKTGLRVAVKKLSRPFQSIIHAKRTYRELRLLKHMKHENVIGLLDVFTPARSLEEFNDVYLVTHLMGADLNNIVKCQKLTDDHVQFLIYQILRGLKYIHSADIIHRDLKPSNLAVNEDCELKILDFGLARHTDDEMTGYVATRWYRAPEIMLNWMHYNQTVDIWSVGCIMAELLTGRTLFPGTDHIDQLKLILRLVGTPGAELLKKISSESARNYIQSLTQMPKMNFANVFIGANPLAVDLLEKMLVLDSDKRITAAQALAHAYFAQYHDPDDEPVADPYDQSFESRDLLIDEWKSLTYDEVISFVPPPLDQEEMES
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.85
R work: 0.1977
R free: 0.2203
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293.15
Crystal growth procedure: 100 mM MES pH 5.6-6.2
20-30 % PEG4000
50 mM BOG
Matthews coefficient: 2.37
Solvent content (%): 48.16
Ligand: 2-(4-morpholin-4-ylphenyl)-~{N}4-(2-phenylethyl)quinazoline-4,7-diamine (8OK)
Ligand formula: C26 H27 N5 O
Ligand molecular weight: 425.525
Ligand SMILES: c1ccc(cc1)CCNc2c3ccc(cc3nc(n2)c4ccc(cc4)N5CCOCC5)N
Ligand InChI: InChI=1S/C26H27N5O/c27-21-8-11-23-24(18-21)29-25(30-26(23)28-13-12-19-4-2-1-3-5-19)20-6-9-22(10-7-20)31-14-16-32-17-15-31/h1-11,18H,12-17,27H2,(H,28,29,30)
Release date: 2017-09-20
The crystal structure of MLL1 (N3861I/Q3867L) in complex with RbBP5 and Ash2L (PDB entry 5F6L)
Macromolecule: Retinoblastoma-binding protein 5
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 27 residues
Sequence: SAFAPDFKELDENVEYEERESEFDIED
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.9
R work: 0.1663
R free: 0.2131
Average B factor: 21.4602
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.9
Crystallization temperature (K): 277
Crystal growth procedure: 200mM NaCl, 20% PEG 3350
Matthews coefficient: 2.24
Solvent content (%): 45.01
Ligand: S-ADENOSYL-L-HOMOCYSTEINE (SAH)
Ligand formula: C14 H20 N6 O5 S
Ligand molecular weight: 384.411
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)CSCCC(C(=O)O)N)O)O)N
Ligand InChI: InChI=1S/C14H20N6O5S/c15-6(14(23)24)1-2-26-3-7-9(21)10(22)13(25-7)20-5-19-8-11(16)17-4-18-12(8)20/h4-7,9-10,13,21-22H,1-3,15H2,(H,23,24)(H2,16,17,18)/t6-,7+,9+,10+,13+/m0/s1
Release date: 2016-02-24
MTH1 in complex with compound 15 (PDB entry 5ANU)
Macromolecule: 7,8-DIHYDRO-8-OXOGUANINE TRIPHOSPHATASE
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.1.55
Sequence length: 158 residues
Sequence: GAMGASRLYTLVLVLQPQRVLLGMKKRGFGAGRWNGFGGKVQEGETIEDGARRELQEESGLTVDALHKVGQIVFEFVGEPELMDVHVFCTDSIQGTPVESDEMRPCWFQLDQIPFKDMWPDDSYWFPLLLQKKKFHGYFKFQGQDTILDYTLREVDTV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.20668
R free: 0.25745
Average B factor: 27.525
Crystallization pH: 4.5
Crystal growth procedure: PH 4.5
Matthews coefficient: 2.01
Solvent content (%): 38.68
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: 2016-03-02
Crystal structure of human STEP (PTPN5) at physiological temperature (310 K) and ambient pressure (0.1 MPa) (PDB entry 8SLT)
Macromolecule: Tyrosine-protein phosphatase non-receptor type 5
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 282 residues
Sequence: SMSRVLQAEELHEKALDPFLLQAEFFEIPMNFVDPKEYDIPGLVRKNRYKTILPNPHSRVCLTSPDPDDPLSSYINANYIRGYGGEEKVYIATQGPIVSTVADFWRMVWQEHTPIIVMITNIEEMNEKCTEYWPEEQVAYDGVEITVQKVIHTEDYRLRLISLKSGTEERGLKHYWFTSWPDQKTPDRAPPLLHLVREVEEAAQQEGPHCAPIIVHCSAGIGRTGCFIATSICCQQLRQEGVVDILKTTCQLRQDRGGMIQTCEQYQFVHHVMSLYEKQLSH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.96
R work: 0.1744
R free: 0.2057
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 293.15
Crystal growth procedure: 30% PEG 3350, 200 mM Li2SO4, 100 mM bis-tris pH 5.5
Matthews coefficient: 2.72
Solvent content (%): 54.77
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: 2023-06-21
Crystal structure of GSK-3B in complex with pyrazine inhibitor C22 (PDB entry 6HK4)
Macromolecule: Glycogen synthase kinase-3 beta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.26
Sequence length: 350 residues
Sequence: SKVTTVVATPGQGPDRPQEVSYTDTKVIGNGSFGVVYQAKLCDSGELVAIKKVLQDKRFKNRELQIMRKLDHCNIVRLRYFFYSSGEKKDEVYLNLVLDYVPETVYRVARHYSRAKQTLPVIYVKLYMYQLFRSLAYIHSFGICHRDIKPQNLLLDPDTAVLKLCDFGSAKQLVRGEPNVSYICSRYYRAPELIFGATDYTSSIDVWSAGCVLAELLLGQPIFPGDSGVDQLVEIIKVLGTPTREQIREMNPNYTEFKFPQIKAHPWTKVFRPRTPPEAIALCSRLLEYTPTARLTPLEACAHSFFDELRDPNVKLPNGRDTPALFNFTTQELSSNPPLATILIPPHARI
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.5
R work: 0.2098
R free: 0.2492
Average B factor: 62.4119
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 293
Crystal growth procedure: 0.2M potassium fluoride
22% PEG 3350
Matthews coefficient: 3.37
Solvent content (%): 63.54
Ligand: MALONATE ION (MLI)
Ligand formula: C3 H2 O4
Ligand molecular weight: 102.046
Ligand SMILES: C(C(=O)[O-])C(=O)[O-]
Ligand InChI: InChI=1S/C3H4O4/c4-2(5)1-3(6)7/h1H2,(H,4,5)(H,6,7)/p-2
Release date: 2019-07-17
Notum Inhibitor ARUK3004308 (PDB entry 8BTA)
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): 1.34
R work: 0.2105
R free: 0.2261
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 4.2
Crystallization temperature (K): 296
Crystal growth procedure: 1.5 M Ammonium Sulphate
0.1 M Sodium Citrate, pH4.2
Matthews coefficient: 1.94
Solvent content (%): 36.56
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: 2022-12-14
Prolyl isomerase Pin1 R14A mutant bound with Brd4 peptide (PDB entry 5UY9)
Macromolecule: Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 5.2.1.8
Sequence length: 163 residues
Sequence: MADEEKLPPGWEKAMSRSSGRVYYFNHITNASQWERPSGNSSSGGKNGQGEPARVRCSHLLVKHSQSRRPSSWRQEKITRTKEEALELINGYIQKIKSGEEDFESLASQFSDCSSAKARGDLGAFSRGQMQKPFEDASFALRTGEMSGPVFTDSGIHIILRTE
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.85
R work: 0.23229
R free: 0.29078
Average B factor: 42.425
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 140 mM NaCl, 2.7 mM KCl, 10 mM Na2HPO4 , 1.8 mM KH2PO4, PH 7.3
Matthews coefficient: 2.76
Solvent content (%): 55.49
Ligand: 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL (PE4)
Ligand formula: C16 H34 O8
Ligand molecular weight: 354.436
Ligand SMILES: CCOCCOCCOCCOCCOCCOCCOCCO
Ligand InChI: InChI=1S/C16H34O8/c1-2-18-5-6-20-9-10-22-13-14-24-16-15-23-12-11-21-8-7-19-4-3-17/h17H,2-16H2,1H3
Release date: 2017-04-26
CK2 alpha bound to chemical probe SGC-CK2-1 (PDB entry 6Z83)
Macromolecule: Casein kinase II subunit alpha
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 359 residues
Sequence: MHHHHHHSSGVDLGTENLYFQSMSGPVPSRARVYTDVNTHRPREYWDYESHVVEWGNQDDYQLVRKLGRGKYSEVFEAINITNNEKVVVKILKPVKKKKIKREIKILENLRGGPNIITLADIVKDPVSRTPALVFEHVNNTDFKQLYQTLTDYDIRFYMYEILKALDYCHSMGIMHRDVKPHNVMIDHEHRKLRLIDWGLAEFYHPGQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRKEPFFHGHDNYDQLVRIAKVLGTEDLYDYIDKYNIELDPRFNDILGRHSRKRWERFVHSENQHLVSPEALDFLDKLLRYDHQSRLTAREAMEHPYFYTVVKDQARMGSS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.171
R work: 0.214
R free: 0.2446
Average B factor: 36.336
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.2 M ammonia sulphate
0.1 M bis-tris pH 5.5
23-26%  PEG 3350
Matthews coefficient: 2.93
Solvent content (%): 58.06
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: 2020-07-29
PanDDA analysis group deposition -- Crystal structure of PTP1B in complex with compound_XST00000599c (PDB entry 5QDY)
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: MEMEKEFEQIDKSGSWAAIYQDIRHEASDFPSRVAKLPKNKNRNRYRDVSPFDHSRIKLHQEDNDYINASLIKMEEAQRSYILTQGPLPNTVGHFWEMVWEQKSRGVVMLNRVMEKGSLKCAQYWPQKEEKEMIFEDTNLKLTLISEDIKSYYTVRQLELENLTTQETREILHFHYTTWPDFGVPESPASFLNFLFKVRESGSLSPEHGPVVVHCSAGIGRSGTFCLADTCLLLMDKRKDPSSVDIKKVLLEMRKFRMGLIQTADQLRFSYLAVIEGAKFIMGDSSVQDQWKELSHEDLEPPPEHIPPPPRPPKRILEPHN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.835
R work: 0.1983
R free: 0.2267
Average B factor: 46.0513
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: well solution: 0.3 M magnesium acetate, 0.1 M HEPES pH 7.5, 0.1% beta-mercaptoethanol, 13-14% PEG 8000, 2% ethanol
Matthews coefficient: 3.38
Solvent content (%): 63.57
Ligand: 1-methyl-3-(thiophen-2-yl)-1H-pyrazol-5-amine (MPV)
Ligand formula: C8 H9 N3 S
Ligand molecular weight: 179.242
Ligand SMILES: Cn1c(cc(n1)c2cccs2)N
Ligand InChI: InChI=1S/C8H9N3S/c1-11-8(9)5-6(10-11)7-3-2-4-12-7/h2-5H,9H2,1H3
Release date: 2018-10-10
Tsetse thrombin inhibitor in complex with human alpha-thrombin - orthorhombic form at 12keV (PDB entry 6TKG)
Macromolecule: Prothrombin
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.5
Sequence length: 36 residues
Sequence: TFGSGEADCGLRPLFEKKSLEDKTERELLESYIDGR
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.35
R work: 0.1641
R free: 0.195
Average B factor: 27.88
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M HEPES pH 7.5, 0.2 M ammonium acetate, 25 % (w/v) PEG 3350
Matthews coefficient: 2.23
Solvent content (%): 44.8
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: 2020-11-04
Crystal Structure of Thrombin in complex with compound51 (PDB entry 6ZV8)
Macromolecule: Prothrombin
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.5
Sequence length: 36 residues
Sequence: TFGSGEADCGLRPLFEKKSLEDKTERELLESYIDGR
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.7
R work: 0.203
R free: 0.2473
Average B factor: 18.885
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 283
Crystal growth procedure: 0.02 M phosphate buffer pH 7.5, 
27% PEG 8000, 100 mM NaCl
Matthews coefficient: 2.42
Solvent content (%): 49.17
Ligand: [2-[[(1~{S})-1-(3-chlorophenyl)-2-fluoranyl-ethyl]amino]-7-methoxy-1,3-benzoxazol-5-yl]-[(2~{S},5~{S})-5-(2-hydroxyethyl)-2-methyl-morpholin-4-yl]methanone (QQT)
Ligand formula: C24 H27 Cl F N3 O5
Ligand molecular weight: 491.94
Ligand SMILES: CC1CN(C(CO1)CCO)C(=O)c2cc3c(c(c2)OC)oc(n3)NC(CF)c4cccc(c4)Cl
Ligand InChI: InChI=1S/C24H27ClFN3O5/c1-14-12-29(18(6-7-30)13-33-14)23(31)16-9-19-22(21(10-16)32-2)34-24(27-19)28-20(11-26)15-4-3-5-17(25)8-15/h3-5,8-10,14,18,20,30H,6-7,11-13H2,1-2H3,(H,27,28)/t14-,18-,20+/m0/s1
Release date: 2020-08-26
Crystal Structure of human cyclic GMP-AMP synthase in complex with (Z)-N-(4-acetylphenyl)-2-cyano-3-hydroxy-3-(5-methyl-1,2-oxazol-4-yl)prop-2-enamide (PDB entry 7FTR)
Macromolecule: Cyclic GMP-AMP synthase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.86
Sequence length: 362 residues
Sequence: GASKLRAVLEKLKLSRDDISTAAGMVKGVVDHLLLRLKCDSAFRGVGLLNTGSYYEHVKISAPNEFDVMFKLEVPRIQLEEYSNTRAYYFVKFKRNPKENPLSQFLEGEILSASKMLSKFRKIIKEEINDIKDTDVIMKRKRGGSPAVTLLISEKISVDITLALESKSSWPASTQEGLRIQNWLSAKVRKQLRLKPFYLVPKHAKEGNGFQEETWRLSFSHIEKEILNNHGKSKTCCENKEEKCCRKDCLKLMKYLLEQLKERFKDKKHLDKFSSYHVKTAFFHVCTQNPQDSQWDRKDLGLCFDNCVTYFLQCLRTEKLENYFIPEFNLFSSNLIDKRSKEFLTKQIEYERNNEFPVFDEF
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.64
R work: 0.217
R free: 0.252
Average B factor: 50.02
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 293
Crystal growth procedure: 10-12 mg/mL protein in 25 mM Tris/HCl pH7.5, 500mM NaCl, 2mM TCEP, supplemented with 10x molar excess of ligand and, if needed, with 10 mM MgCl2 and 5mM ATP, then mixed 1:1 with reservoir of the Procomplex screen. Several conditions resulted in crystals
Matthews coefficient: 2.27
Solvent content (%): 45.82
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: 2024-02-21
Crystal structure analysis of human USP28 complex with a compound (PDB entry 7TUO)
Macromolecule: Ubiquitin carboxyl-terminal hydrolase 28
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.19.12
Sequence length: 385 residues
Sequence: SPNPNDWRRVDGWPVGLKNVGNTCWFSAVIQSLFQLPEFRRLVLSYSLPQNVLENCRSHTEKRNIMFMQELQYLFALMMGSNRKFVDPSAALDLLKGAFRSSEEQQQDVSEFTHKLLDWLEDAFQLAVNVNSPRNKSENPMVQLFYGTFLTEGVREGKPFCNNETFGQYPLQVNGYRNLDECLEGAMVEGDVELLPSDHSVKYGQERWFTKLPPVLTFELSRFEFNQSLGQPEKIHNKLEFPQIIYMDRYMYGSGSGSRQVPYRLHAVLVHEGQANAGHYWAYIYNQPRQSWLKYNDISVTESSWEEVERDSYGGLRNVSAYCLMYINDKLPYFNAEAAPTESDQMSEVEALSVELKHYIQEDNWRFEQEVEEWEEEQSCKIQLN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.96
R work: 0.1777
R free: 0.2031
Average B factor: 47.6014
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 1.4M Sodium maleic acid, pH 8.0
Matthews coefficient: 2.79
Solvent content (%): 55.94
Ligand: 7-amino-N-(2-{4-[(1R,3s,5S)-8-azabicyclo[3.2.1]octan-3-yl]phenyl}ethyl)-3-methylthieno[2,3-b]pyrazine-6-carboxamide (KL9)
Ligand formula: C23 H27 N5 O S
Ligand molecular weight: 421.558
Ligand SMILES: Cc1cnc2c(c(sc2n1)C(=O)NCCc3ccc(cc3)C4CC5CCC(C4)N5)N
Ligand InChI: InChI=1S/C23H27N5OS/c1-13-12-26-20-19(24)21(30-23(20)27-13)22(29)25-9-8-14-2-4-15(5-3-14)16-10-17-6-7-18(11-16)28-17/h2-5,12,16-18,28H,6-11,24H2,1H3,(H,25,29)/t16-,17-,18+
Release date: 2023-02-15
Joint X-ray/neutron structure of PKG II CNB-B domain in complex with 8-pCPT-cGMP (PDB entry 6BQ8)
Macromolecule: cGMP-dependent protein kinase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.12
Sequence length: 152 residues
Sequence: GSTAQARDEQYRNFLRSVSLLKNLPEDKLTKIIDCLEVEYYDKGDYIIREGEEGSTFFILAKGKVKVTQSTEGHDQPQLIKTLQKGEYFGEKALISDDVRSANIIAEENDVACLVIDRETFNQTVGTFEELQKYLEGYVANLNRDDEKRHAK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION, NEUTRON DIFFRACTION
Refinement resolution (Å): 2, 2.2
R work: 0.199
R free: 0.245
Average B factor: 38.16
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 4.6
Crystallization temperature (K): 277
Crystal growth procedure: 30% MPD, 20 mM SrCl2, 100 mM NaOAc pH 4.6
Matthews coefficient: 2.19
Solvent content (%): 43.96
Ligand: 2-(~2~H_2_)amino-8-[(4-chlorophenyl)sulfanyl]-9-[(2S,4aR,6R,7R,7aS)-2-hydroxy-7-(~2~H)hydroxy-2-oxotetrahydro-2H,4H-2lambda~5~-furo[3,2-d][1,3,2]dioxaphosphinin-6-yl](~2~H)-1,9-dihydro-6H-purin-6-one (WNU)
Ligand formula: C16 H15 Cl N5 O7 P S
Ligand molecular weight: 487.811
Ligand SMILES: c1cc(ccc1Sc2nc3c(n2C4C(C5C(O4)COP(=O)(O5)O)O)N=C(NC3=O)N)Cl
Ligand InChI: InChI=1S/C16H15ClN5O7PS/c17-6-1-3-7(4-2-6)31-16-19-9-12(20-15(18)21-13(9)24)22(16)14-10(23)11-8(28-14)5-27-30(25,26)29-11/h1-4,8,10-11,14,23H,5H2,(H,25,26)(H3,18,20,21,24)/t8-,10-,11-,14-/m1/s1
Release date: 2018-03-21
IRAK4 IN COMPLEX WITH inhibitor (PDB entry 6TIA)
Macromolecule: Interleukin-1 receptor-associated kinase 4
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 308 residues
Sequence: GENKSLEVSDTRFHSFSFYELKNVTNNFDERPISVGGNKMGEGGFGVVYKGYVNNTTVAVKKLAAMVDITTEELKQQFDQEIKVMAKCQHENLVELLGFSSDGDDLCLVYVYMPNGSLLDRLSCLDGTPPLSWHMRCKIAQGAANGINFLHENHHIHRDIKSANILLDEAFTAKISDFGLARASEKFAQTVMTSRIVGTTAYMAPEALRGEITPKSDIYSFGVVLLEIITGLPAVDEHREPQLLLDIKEEIEDEEKTIEDYIDKKMNDADSTSVEAMYSVASQCLHEKKNKRPDIKKVQQLLQEMTAS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.52
R work: 0.216
R free: 0.261
Average B factor: 75.5
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 298
Crystal growth procedure: 2.7 M AMS 0.1 M Hepes pH 7.1-7.7  
Protein Buffer:  50mM HEPES pH 7.5, 300 mM NaCl, 0,02% OG, 1 mM TCEP, 10% Glycerol
Matthews coefficient: 2.58
Solvent content (%): 52.39
Ligand: 4-(1-methylcyclopropyl)oxy-~{N}-[1-(1-methylpiperidin-4-yl)pyrazol-4-yl]-6-(1-methylpyrazol-4-yl)pyrido[3,2-d]pyrimidin-2-amine (ND2)
Ligand formula: C24 H29 N9 O
Ligand molecular weight: 459.547
Ligand SMILES: CC1(CC1)Oc2c3c(ccc(n3)c4cnn(c4)C)nc(n2)Nc5cnn(c5)C6CCN(CC6)C
Ligand InChI: InChI=1S/C24H29N9O/c1-24(8-9-24)34-22-21-20(5-4-19(28-21)16-12-25-32(3)14-16)29-23(30-22)27-17-13-26-33(15-17)18-6-10-31(2)11-7-18/h4-5,12-15,18H,6-11H2,1-3H3,(H,27,29,30)
Release date: 2020-10-28
Human Sirt6 in complex with activator UBCS039 (PDB entry 5MF6)
Macromolecule: NAD-dependent protein deacetylase sirtuin-6
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.5.1
Sequence length: 302 residues
Sequence: GIDPFTADKGKCGLPEIFDPPEELERKVWELARLVWQSSSVVFHTGAGISTASGIPDFRGPHGVWTMEERGLAPKFDTTFESARPTQTHMALVQLERVGLLRFLVSQNVDGLHVRSGFPRDKLAELHGNMFVEECAKCKTQYVRDTVVGTMGLKATGRLCTVAKARGLRACRGELRDTILDWEDSLPDRDLALADEASRNADLSITLGTSLQIRPSGNLPLATKRRGGRLVIVNLQPTKHDRHADLRIHGYVDEVMTRLMKHLGLEIPAWDGPRVLERALPPLPRPPTPKLEPKEESPTRIN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.87
R work: 0.18988
R free: 0.21957
Average B factor: 32.836
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, Bis-Tris buffer pH 5.7
Matthews coefficient: 2.59
Solvent content (%): 52.45
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: 2016-12-28
Selection of fragments for kinase inhibitor design: decoration is key (PDB entry 4X2G)
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): 1.51
R work: 0.1648
R free: 0.1853
Average B factor: 18.26
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: 2.12
Solvent content (%): 41.96
Ligand: 4-[(4-aminophenyl)amino]pyrido[2,3-d]pyrimidin-5(6H)-one (3WK)
Ligand formula: C13 H11 N5 O
Ligand molecular weight: 253.259
Ligand SMILES: c1cc(ccc1N)Nc2c3c(ncn2)N=CCC3=O
Ligand InChI: InChI=1S/C13H11N5O/c14-8-1-3-9(4-2-8)18-13-11-10(19)5-6-15-12(11)16-7-17-13/h1-4,6-7H,5,14H2,(H,16,17,18)
Release date: 2015-08-12
Crystal structures of AKR1C3 ternary complex with NADP+ and the chromene derivative 2j (PDB entry 7C7G)
Macromolecule: Aldo-keto reductase family 1 member C3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.3.1.20
Sequence length: 325 residues
Sequence: GSMDSKHQCVKLNDGHFMPVLGFGTYAPPEVPRSKALEVTKLAIEAGFRHIDSAHLYNNEEQVGLAIRSKIADGSVKREDIFYTSKLWSTFHRPELVRPALENSLKKAQLDYVDLYLIHSPMSLKPGEELSPTDENGKVIFDIVDLCTTWEAMEKCKDAGLAKSIGVSNFNRRQLEMILNKPGLKYKPVCNQVECHPYFNRSKLLDFCKSKDIVLVAYSALGSQRDKRWVDPNSPVLLEDPVLCALAKKHKRTPALIALRYQLQRGVVVLAKSYNEQRIRQNVQVFEFQLTAEDMKAIDGLDRNLHYFNSDSFASHPNYPYSDEY
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.86
R work: 0.2192
R free: 0.265
Average B factor: 42.74
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 25-30% (w/v) polyethylene glycol 3350 (PEG3350), 200 mM sodium acetate and 100 mM cacodylate, pH 6.6
Matthews coefficient: 2.07
Solvent content (%): 40.55
Ligand: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE (NAP)
Ligand formula: C21 H28 N7 O17 P3
Ligand molecular weight: 743.405
Ligand SMILES: c1cc(c[n+](c1)C2C(C(C(O2)COP(=O)([O-])OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)OP(=O)(O)O)O)O)O)C(=O)N
Ligand InChI: InChI=1S/C21H28N7O17P3/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(44-46(33,34)35)14(30)11(43-21)6-41-48(38,39)45-47(36,37)40-5-10-13(29)15(31)20(42-10)27-3-1-2-9(4-27)18(23)32/h1-4,7-8,10-11,13-16,20-21,29-31H,5-6H2,(H7-,22,23,24,25,32,33,34,35,36,37,38,39)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
Release date: 2020-09-23
Human Pin1 with cysteine sulfonic acid 113 (PDB entry 4U86)
Macromolecule: Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 5.2.1.8
Sequence length: 181 residues
Sequence: HHHHHHHHGGLVPRGSHGMADEEKLPPGWEKAMSRSSGRVYYFNHITNASQWERPSGNSSSGGKNGQGEPARVRCSHLLVKHSQSRRPSSWRQEKITRTKEEALELINGYIQKIKSGEEDFESLASQFSDCSSAKARGDLGAFSRGQMQKPFEDASFALRTGEMSGPVFTDSGIHIILRTE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.6
R work: 0.19627
R free: 0.23073
Average B factor: 26.896
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 50mM HEPES7.5
1% PEG400
1.2-1.5M Ammonium Sulfate
Matthews coefficient: 2.71
Solvent content (%): 54.62
Ligand: 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL (1PG)
Ligand formula: C11 H24 O6
Ligand molecular weight: 252.305
Ligand SMILES: COCCOCCOCCOCCOCCO
Ligand InChI: InChI=1S/C11H24O6/c1-13-4-5-15-8-9-17-11-10-16-7-6-14-3-2-12/h12H,2-11H2,1H3
Release date: 2015-04-08