satarupa22/MacromolecularLigandDB huggingface dataset:
Human Casein Kinase 1 isoform delta (kinase domain) in complex with Epiblastin A (PDB entry 5IH5)
Macromolecule: Casein kinase I isoform delta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 294 residues
Sequence: MELRVGNRYRLGRKIGSGSFGDIYLGTDIAAGEEVAIKLECVKTKHPQLHIESKIYKMMQGGVGIPTIRWCGAEGDYNVMVMELLGPSLEDLFNFCSRKFSLKTVLLLADQMISRIEYIHSKNFIHRDVKPDNFLMGLGKKGNLVYIIDFGLAKKYRDARTHQHIPYRENKNLTGTARYASINTHLGIEQSRRDDLESLGYVLMYFNLGSLPWQGLKAATKRQKYERISEKKMSTPIEVLCKGYPSEFATYLNFCRSLRFDDKPDYSYLRQLFRNLFHRQGFSYDYVFDWNMLK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.25
R work: 0.24
R free: 0.26
Average B factor: 73.678
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 0.1 M Li2SO4, 0.7 - 0.8 M Na-K tartrate, 0.1 M CHES
Matthews coefficient: 2.71
Solvent content (%): 54.69
Ligand: 6-(3-chlorophenyl)pteridine-2,4,7-triamine (AUE)
Ligand formula: C12 H10 Cl N7
Ligand molecular weight: 287.708
Ligand SMILES: c1cc(cc(c1)Cl)c2c(nc3c(n2)c(nc(n3)N)N)N
Ligand InChI: InChI=1S/C12H10ClN7/c13-6-3-1-2-5(4-6)7-9(14)18-11-8(17-7)10(15)19-12(16)20-11/h1-4H,(H6,14,15,16,18,19,20)
Release date: 2016-04-13
Human kallikrein 7 with aromatic coumarinic ester compound 1 covalently bound to H57 (PDB entry 6SHH)
Macromolecule: Kallikrein-7
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.117
Sequence length: 224 residues
Sequence: IIDGAPCARGSHPWQVALLSGNQLHCGGVLVNERWVLTAAHCKMNEYTVHLGSDTLGDRRAQRIKASKSFRHPGYSTQTHVNDLMLVKLNSQARLSSMVKKVRLPSRCEPPGTTCTVSGWGTTTSPDVTFPSDLMCVDVKLISPQDCTKVYKDLLENSMLCAGIPDSKKNACNGDSGGPLVCRGTLQGLVSWGTFPCGQPNDPGVYTQVCKFTKWINDTMKKHR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2
R work: 0.189
R free: 0.226
Average B factor: 43.07
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 2.9 M ammonium sulphate, 0.1 M HEPES, pH 8.5, 0.5- 2 % PEG 3350
Matthews coefficient: 2.64
Solvent content (%): 53.37
Ligand: TRIETHYLENE GLYCOL (PGE)
Ligand formula: C6 H14 O4
Ligand molecular weight: 150.173
Ligand SMILES: C(COCCOCCO)O
Ligand InChI: InChI=1S/C6H14O4/c7-1-3-9-5-6-10-4-2-8/h7-8H,1-6H2
Release date: 2020-05-20
Crystal Structure of EGFR-T790M/C797S in Complex with Covalent Pyrrolopyrimidine 19h (PDB entry 6S8A)
Macromolecule: Epidermal growth factor receptor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 333 residues
Sequence: GSHMASGEAPNQALLRILKETEFKKIKVLGSGAFGTVYKGLWIPEGEKVKIPVAIKELREATSPKANKEILDEAYVMASVDNPHVCRLLGICLTSTVQLIMQLMPFGSLLDYVREHKDNIGSQYLLNWCVQIAKGMNYLEDRRLVHRDLAARNVLVKTPQHVKITDFGLAKLLGAAAAEYHAEGGKVPIKWMALESILHRIYTHQSDVWSYGVTVWELMTFGSKPYDGIPASEISSILEKGERLPQPPICTIDVYMIMVKCWMIDADSRPKFRELIIEFSKMARDPQRYLVIQGDERMHLPSPTDSNFYRALMDEEDMDDVVDADEYLIPQQG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.6
R work: 0.1855
R free: 0.2074
Average B factor: 84.1026
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 1.15 K-Na-tartrate, 100 mM Na-MES (pH 6.5), 2 % 1,3-Propanediol, 5.3 mg/ml EGFR T790M/C797 (in 100 mM NaCl, 25mM Tris-HCl, 10 % Glycerol, 1mM TCEP, pH 8.0), 1 ul reservoir + 1 ul protein solution
Matthews coefficient: 3.35
Solvent content (%): 63.26
Ligand: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID (MES)
Ligand formula: C6 H13 N O4 S
Ligand molecular weight: 195.237
Ligand SMILES: C1COCC[NH+]1CCS(=O)(=O)[O-]
Ligand InChI: InChI=1S/C6H13NO4S/c8-12(9,10)6-3-7-1-4-11-5-2-7/h1-6H2,(H,8,9,10)
Release date: 2019-10-16
Crystal structure of human KDM4A in complex with compound 54j (PDB entry 5F3I)
Macromolecule: Lysine-specific demethylase 4A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11
Sequence length: 360 residues
Sequence: SMASESETLNPSARIMTFYPTMEEFRNFSRYIAYIESQGAHRAGLAKVVPPKEWKPRASYDDIDDLVIPAPIQQLVTGQSGLFTQYNIQKKAMTVREFRKIANSDKYCTPRYSEFEELERKYWKNLTFNPPIYGADVNGTLYEKHVDEWNIGRLRTILDLVEKESGITIEGVNTPYLYFGMWKTSFAWHTEDMDLYSINYLHFGEPKSWYSVPPEHGKRLERLAKGFFPGSAQSCEAFLRHKMTLISPLMLKKYGIPFDKVTQEAGEFMITFPYGYHAGFNHGFNCAESTNFATRRWIEYGKQAVLCSCRKDMVKISMDVFVRKFQPERYKLWKAGKDNTVIDHTLPTPEAAEFLKESEL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.24
R work: 0.1686
R free: 0.2129
Average B factor: 60.2
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 291
Crystal growth procedure: Crystallisation solution is 0.1M Bis-Tris-Propane pH7.5, 12-16% PEG-4000. Inhibitor is soaked in crystals by addition directly to the drops of DMSO dissolved compound
Matthews coefficient: 2.46
Solvent content (%): 50.03
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: 2016-01-20
Crystal structure of FGFR4 kinase domain in complex with compound 5 (PDB entry 6IUP)
Macromolecule: Fibroblast growth factor receptor 4
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 322 residues
Sequence: MGSSHHHHHHSSGLLAGLVSLDLPLDPLWEFPRDRLVLGKPLGEGCFGQVVRAEAFGMDPARPDQASTVAVKMLKDNASDKDLADLVSEMEVMKLIGRHKNIINLLGVCTQEGPLYVIVECAAKGNLREFLRARRPPGPDLSPDGPRSSEGPLSFPVLVSCAYQVARGMQYLESRKCIHRDLAARNVLVTEDNVMKIADFGLARGVHHIDYYKKTSNGRLPVKWMAPEALFDEVYTHQSDVWSFGILLWEIFTLGGSPYPGIPVEELFSLLREGHRMDRPPHCPPELYGLMRECWHAAPSQRPTFKQLVEALDKVLLAVSEE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2
R work: 0.1694
R free: 0.2277
Average B factor: 19.5483
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 0.1M MES pH5.5, 0.2M Li2SO4, 18% PEG3350
Matthews coefficient: 2.27
Solvent content (%): 45.77
Ligand: N-{4-[4-amino-3-(3,5-dimethyl-1-benzofuran-2-yl)-7-oxo-6,7-dihydro-2H-pyrazolo[3,4-d]pyridazin-2-yl]phenyl}prop-2-enamide (AX0)
Ligand formula: C24 H20 N6 O3
Ligand molecular weight: 440.454
Ligand SMILES: Cc1ccc2c(c1)c(c(o2)c3c4c(nn3c5ccc(cc5)NC(=O)C=C)C(=O)NN=C4N)C
Ligand InChI: InChI=1S/C24H20N6O3/c1-4-18(31)26-14-6-8-15(9-7-14)30-21(19-20(29-30)24(32)28-27-23(19)25)22-13(3)16-11-12(2)5-10-17(16)33-22/h4-11H,1H2,2-3H3,(H2,25,27)(H,26,31)(H,28,32)
Release date: 2019-11-06
CDK1/CyclinB1/CKS2 Apo (PDB entry 4YC3)
Macromolecule: Cyclin-dependent kinase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.22
Sequence length: 302 residues
Sequence: GPLGSMEDYTKIEKIGEGTYGVVYKGRHKTTGQVVAMKKIRLESEEEGVPSTAIREISLLKELRHPNIVSLQDVLMQDSRLYLIFEFLSMDLKKYLDSIPPGQYMDSSLVKSYLYQILQGIVFCHSRRVLHRDLKPQNLLIDDKGTIKLADFGLARAFGIPIRVYTHEVVTLWYRSPEVLLGSARYSTPVDIWSIGTIFAELATKKPLFHGDSEIDQLFRIFRALGTPNNEVWPEVESLQDYKNTFPKWKPGSLASHVKNLDENGLDLLSKMLIYDPAKRISGKMALNHPYFNDLDNQIKKM
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.7
R work: 0.2113
R free: 0.2595
Average B factor: 40.9313
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 6.7
Crystallization temperature (K): 277
Crystal growth procedure: 0.1M MES/imidazole buffer (pH6.7), 6.5% MPD, 5% PEG4K, 10% PEG1K
Protein at 10-12 mg/ml
Matthews coefficient: 2.49
Solvent content (%): 50.55
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: 2016-04-20
Human Aldose Reductase Mutant A299G/L300A in Complex with a Ligand with an IDD Structure (3-({[2-(carboxymethoxy)-4-fluorobenzoyl]amino}methyl)benzoic acid) (PDB entry 8P2R)
Macromolecule: Aldo-keto reductase family 1 member B1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.1.1.300
Sequence length: 316 residues
Sequence: MASRILLNNGAKMPILGLGTWKSPPGQVTEAVKVAIDVGYRHIDCAHVYQNENEVGVAIQEKLREQVVKREELFIVSKLWCTYHEKGLVKGACQKTLSDLKLDYLDLYLIHWPTGFKPGKEFFPLDESGNVVPSDTNILDTWAAMEELVDEGLVKAIGISNFNHLQVEMILNKPGLKYKPAVNQIECHPYLTQEKLIQYCQSKGIVVTAYSPLGSPDRPWAKPEDPSLLEDPRIKAIAAKHNKTTAQVLIRFPMQRNLVVIPKSVTPERIAENFKVFDFELSSQDMTTLLSYNRNWRVCGALSCTSHKDYPFHEEF
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.25
R work: 0.1068
R free: 0.1364
Average B factor: 13.53
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5
Crystallization temperature (K): 291
Crystal growth procedure: 50 mM Di-Ammoniumhydrogen citrate pH 5: 15 mg/mL hAR, 5.2 mg/mL DTT, 0.7 mg/mL NADP+, 12% (w/v) PEG 6000;
Reservoir: 120 mM Di-Ammoniumhydrogen citrate pH 5, 20% (w/v) PEG 6000;
Soaking: 120 mM di-ammonium hydrogen citrate pH 5.0, 25% PEG 6000, saturated ligand
Matthews coefficient: 2.17
Solvent content (%): 43.41
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: 2024-06-12
Native state mass spectrometry, surface plasmon resonance and X-ray crystallography correlate strongly as a fragment screening combination (PDB entry 5FNJ)
Macromolecule: CARBONIC ANHYDRASE 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 260 residues
Sequence: MSHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHAFNVEFDDSQDKAVLKGGPLDGTYRLIQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDFGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTKGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLLECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.67
R work: 0.13765
R free: 0.18286
Average B factor: 14.31
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystal growth procedure: 15 MG/ML PROTEIN WITH 2.7 M AMMONIUM SULFATE, 100 MM TRIS PH 8.5 AT 8 C IN SITTING DROPS.
Matthews coefficient: 2.1
Solvent content (%): 41.4
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: 2016-03-02
DISCOVERY OF NOVEL 7-AZAINDOLES AS PDK1 INHIBITORS (PDB entry 5HKM)
Macromolecule: 3-phosphoinositide-dependent protein kinase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 309 residues
Sequence: MDGTAAEPRPGAGSLQHAQPPPQPRKKRPEDFKFGKILGEGSFSTVVLARELATSREYAIKILEKRHIIKENKVPYVTRERDVMSRLDHPFFVKLYFTFQDDEKLYFGLSYAKNGELLKYIRKIGSFDETCTRFYTAEIVSALEYLHGKGIIHRDLKPENILLNEDMHIQITDFGTAKVLSPESKQARANSFVGTAQYVSPELLTEKSACKSSDLWALGCIIYQLVAGLPPFRAGNEYLIFQKIIKLEYDFPEKFFPKARDLVEKLLVLDATKRLGCEEMEGYGPLKAHPFFESVTWENLHQQTPPKLT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.1
R work: 0.19
R free: 0.273
Average B factor: 34.68
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8.6
Crystallization temperature (K): 298
Crystal growth procedure: 100 mM TRIS-HCl, 1.8 M NH4-sulfate
Matthews coefficient: 3.35
Solvent content (%): 63.33
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: 2016-06-08
NaI--Interactions between Hofmeister Anions and the Binding Pocket of a Protein (PDB entry 4YGN)
Macromolecule: Carbonic anhydrase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 258 residues
Sequence: HHWGYGGHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHAFNVEFDDSQDKAVLKGGPLDGTYRLIQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDFGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTKGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLLECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.23
R work: 0.17525
R free: 0.20937
Average B factor: 14.768
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.8
Crystallization temperature (K): 277
Crystal growth procedure: 100 mM Tris-Cl, 1.15 M sodium citrate, pH 7.8
Matthews coefficient: 2.13
Solvent content (%): 42.32
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: 2015-03-25
Crystal structure of the PCTAIRE1 kinase in complex with inhibitor (PDB entry 5G6V)
Macromolecule: CYCLIN-DEPENDENT KINASE 16
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.22
Sequence length: 324 residues
Sequence: METYIKLDKLGEGTYATVYKGKSKLTDNLVALKEIRLEHEEGAPCTAIREVSLLKDLKHANIVTLHDIIHTEKSLTLVFEYLDKDLKQYLDDCGNIINMHNVKLFLFQLLRGLAYCHRQKVLHRDLKPQNLLINERGELKLADFGLARAKSIPTKTYDNEVVTLWYRPPDILLGSTDYSTQIDMWGVGCIFYEMATGRPLFPGSTVEEQLHFIFRILGTPTEETWPGILSNEEFKTYNYPKYRAEALLSHAPRLDSDGADLLTKLLQFEGRNRISAEDAMKHPFFLSLGERIHKLPDTTSIFALKEIQLQKEASLRSAHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.2
R work: 0.20785
R free: 0.2711
Average B factor: 40.421
Crystallization pH: 5.5
Crystal growth procedure: 25% PEG MEDIUM SMEAR (PEG 2000, PEG 3350, PEG 4000, PEG 5000MME) AND 0.1 M CITRATE PH 5.5
Matthews coefficient: 2.44
Solvent content (%): 49.51
Ligand: 4-[4-({[3-tert-butyl-1-(quinolin-6-yl)-1H-pyrazol-5-yl]carbamoyl}amino)-3-fluorophenoxy]-N-methylpyridine-2-carboxamide (919)
Ligand formula: C30 H28 F N7 O3
Ligand molecular weight: 553.587
Ligand SMILES: CC(C)(C)c1cc(n(n1)c2ccc3c(c2)cccn3)NC(=O)Nc4ccc(cc4F)Oc5ccnc(c5)C(=O)NC
Ligand InChI: InChI=1S/C30H28FN7O3/c1-30(2,3)26-17-27(38(37-26)19-7-9-23-18(14-19)6-5-12-33-23)36-29(40)35-24-10-8-20(15-22(24)31)41-21-11-13-34-25(16-21)28(39)32-4/h5-17H,1-4H3,(H,32,39)(H2,35,36,40)
Release date: 2016-11-23
The structure of NTMT1 in complex with compound C2A (PDB entry 6WJ7)
Macromolecule: N-terminal Xaa-Pro-Lys N-methyltransferase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1.244
Sequence length: 241 residues
Sequence: MGSSHHHHHHSSGLVPRGSTSEVIEDEKQFYSKAKTYWKQIPPTVDGMLGGYGHISSIDINSSRKFLQRFLREGPNKTGTSCALDCGAGIGRITKRLLLPLFREVDMVDITEDFLVQAKTYLGEEGKRVRNYFCCGLQDFTPEPDSYDVIWIQWVIGHLTDQHLAEFLRRCKGSLRPNGIIVIKDNMAQEGVILDDVDSSVCRDLDVVRRIICSAGLSLLAEERQENLPDEIYHVYSFALR
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.42
R work: 0.165
R free: 0.188
Average B factor: 23.95
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.8 M Lithium Chloride 0.1 M Tris: HCl, pH 8.5 32 % (w/v) PEG 4000
Matthews coefficient: 2.17
Solvent content (%): 43.2
Ligand: 5'-{[(3S)-3-amino-3-carboxypropyl](ethyl)amino}-5'-deoxyadenosine (AN6)
Ligand formula: C16 H25 N7 O5
Ligand molecular weight: 395.414
Ligand SMILES: CCN(CCC(C(=O)O)N)CC1C(C(C(O1)n2cnc3c2ncnc3N)O)O
Ligand InChI: InChI=1S/C16H25N7O5/c1-2-22(4-3-8(17)16(26)27)5-9-11(24)12(25)15(28-9)23-7-21-10-13(18)19-6-20-14(10)23/h6-9,11-12,15,24-25H,2-5,17H2,1H3,(H,26,27)(H2,18,19,20)/t8-,9+,11+,12+,15+/m0/s1
Release date: 2020-08-19
Crystal structure of human KDM4A in complex with compound 16a (PDB entry 6H4P)
Macromolecule: Lysine-specific demethylase 4A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11
Sequence length: 360 residues
Sequence: SMASESETLNPSARIMTFYPTMEEFRNFSRYIAYIESQGAHRAGLAKVVPPKEWKPRASYDDIDDLVIPAPIQQLVTGQSGLFTQYNIQKKAMTVREFRKIANSDKYCTPRYSEFEELERKYWKNLTFNPPIYGADVNGTLYEKHVDEWNIGRLRTILDLVEKESGITIEGVNTPYLYFGMWKTSFAWHTEDMDLYSINYLHFGEPKSWYSVPPEHGKRLERLAKGFFPGSAQSCEAFLRHKMTLISPLMLKKYGIPFDKVTQEAGEFMITFPYGYHAGFNHGFNCAESTNFATRRWIEYGKQAVLCSCRKDMVKISMDVFVRKFQPERYKLWKAGKDNTVIDHTLPTPEAAEFLKESEL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.19
R work: 0.17
R free: 0.207
Average B factor: 61.35
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: Crystallisation solution is 0.1M Bis-Tris-Propane pH7.5, 12-16% PEG-4000. Inhibitor is soaked in crystals by addition directly to the drops of DMSO dissolved compound
Matthews coefficient: 2.49
Solvent content (%): 50.67
Ligand: ZINC ION (ZN)
Ligand formula: Zn
Ligand molecular weight: 65.409
Ligand SMILES: [Zn+2]
Ligand InChI: InChI=1S/Zn/q+2
Release date: 2019-06-12
Thrombin Mutant A190S in complex with (S) -1 - ((R) -2-amino-3,3-diphenylpropanoyl) -N- (3-chlorobenzyl) pyrrolidine-2-carboxamide (PDB entry 5MJT)
Macromolecule: Thrombin light chain
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): 1.4
R work: 0.1479
R free: 0.1722
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 20 mM Sodium dihydrogen phosphate ph 7.5, 350 mM NaCl, 27% PEG 8000
Matthews coefficient: 2.5
Solvent content (%): 50
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: 2017-12-20
Unbound BACE2 mutant structure (PDB entry 6UJ0)
Macromolecule: Beta-secretase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.23.45
Sequence length: 460 residues
Sequence: MGALARALLLPLLAQWLLRAAPELAPAPFTLPLRVAAATNRVVAPTPGPGTPAERHADGLALALEPALASPAGAANFLAMVDNLQGDSGRGYYLEMLIGTPPQKLQILVDTGSSNFAVAGTPHSYIDTYFDTERSSTYRSKGFDVTVKYTQGSWTGFVGEDLVTIPKGFNTSFLVNIATIFESENFFLPGIKWNGILGLAYATLAKPSSSLETFFDSLVTQANIPNVFSMQMCGAGLPVAGSGTNGGSLVLGGIEPSLYKGDIWYTPIKEEWYYQIEILKLEIGGQSLNLDCREYNADKAIVDSGTTLLRLPQKVFDAVVEAVARASLIPAFSDGFWTGSQLACWTNSETPWSYFPKISIYLRDENSSRSFRITILPQLYIQPMMGAGLNYECYRFGISPSTNALVIGATVMEGFYVIFDRAQKRVGFAASPCAEIAGAAVSEISGPFSTEDVASNCVPA
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.15
R work: 0.2198
R free: 0.2578
Average B factor: 46
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6
Crystallization temperature (K): 298
Crystal growth procedure: 0.1 M MES, pH = 6
1.26 M (NH4)2SO4
Matthews coefficient: 2.11
Solvent content (%): 41.63
Release date: 2020-10-07
Crystal Structure of human phosphodiesterase 10 in complex with 7-[(4-ethoxy-5-methylpyridin-2-yl)methylsulfanyl]-6H-imidazo[4,5-g][1,3]benzothiazole (PDB entry 5SKA)
Macromolecule: cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.4.17
Sequence length: 343 residues
Sequence: GSSICTSEEWQGLMQFTLPVRLCKEIELFHFDIGPFENMWPGIFVYMVHRSCGTSCFELEKLCRFIMSVKKNYRRVPYHNWKHAVTVAHCMYAILQNNHTLFTDLERKGLLIACLCHDLDHRGFSNSYLQKFDHPLAALYSTSTMEQHHFSQTVSILQLEGHNIFSTLSSSEYEQVLEIIRKAIIATDLALYFGNRKQLEEMYQTGSLNLNNQSHRDRVIGLMMTACDLCSVTKLWPVTKLTANDIYAEFWAEGDEMKKLGIQPIPMMDRDKKDEVPQGQLGFYNAVAIPCYTTLTQILPPTEPLLKACRDNLSQWEKVIRGEETATWISSPSVAQKAAASED
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.21
R work: 0.1913
R free: 0.2418
Average B factor: 37.704
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 295
Crystal growth procedure: 5-20 mg/mL protein in 25mM HEPES/NaOH pH7.5, 150mM NaCl, 50mM BME mixed 1:1 with reservoir 0.1M HEPES/NaOH pH7.5, 30% PEG550MME, 50mM MgCl2
Matthews coefficient: 2.62
Solvent content (%): 53.06
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: 2022-10-12
Crystal structure of BACE complex with BMC026 (PDB entry 5QCR)
Macromolecule: Beta-secretase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.23.46
Sequence length: 402 residues
Sequence: GPDEEPEEPGRRGSFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHPFLHRYYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTVRANIAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTHVPNLFSLQLCGAGFPLNQSEVLASVGGSMIIGGIDHSLYTGSLWYTPIRREWYYEVIIVRVEINGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVKSIKAASSTEKFPDGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRITILPQQYLRPVEDVATSQDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSACHVHDEFRTAAVEGPFVTLDMEDCGYNI
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.2
R work: 0.173
R free: 0.205
Average B factor: 51
Crystallization method: hanging drop
Crystallization temperature (K): 292
Crystal growth procedure: CRYSTALS WERE GROWN AT 19C BY VAPOUR DIFFUSION IN HANGING DROPS USING 1.0M UNBUFFERED AMMONIUM SULFATE AS PRECIPITANT.
PROTEIN STOCK WAS BACE MUT46B BATCH IX 8.1MG/ML IN 10MM TRIS-HCL PH 7.4, 25MM NACL WITH A 4-FOLD EXCESS OF BMC026 ADDED
FROM A 100MM STOCK SOLUTION IN DMSO. CRYO-PROTECTANT WAS 2.0M LI2SO4, 2%(V/V) PEG 400, 0.1M CITRATE PH 5.5, 0.5MM
BMC026, 1% DMSO.
Matthews coefficient: 3.04
Solvent content (%): 59.56
Ligand: 2-(butylamino)-N-[(2S,3S,5R)-6-(butylamino)-3-hydroxy-5-methyl-6-oxo-1-phenylhexan-2-yl]-6-methoxypyridine-4-carboxamide (E4J)
Ligand formula: C28 H42 N4 O4
Ligand molecular weight: 498.657
Ligand SMILES: CCCCNc1cc(cc(n1)OC)C(=O)NC(Cc2ccccc2)C(CC(C)C(=O)NCCCC)O
Ligand InChI: InChI=1S/C28H42N4O4/c1-5-7-14-29-25-18-22(19-26(32-25)36-4)28(35)31-23(17-21-12-10-9-11-13-21)24(33)16-20(3)27(34)30-15-8-6-2/h9-13,18-20,23-24,33H,5-8,14-17H2,1-4H3,(H,29,32)(H,30,34)(H,31,35)/t20-,23+,24+/m1/s1
Release date: 2020-06-03
Rapid Discovery of Pyrido[3,4-d]pyrimidine Inhibitors of Monopolar Spindle kinase 1 (MPS1) Using a Structure-Based Hydridization Approach (PDB entry 5EI6)
Macromolecule: Dual specificity protein kinase TTK
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.12.1
Sequence length: 313 residues
Sequence: MHHHHHHSSGVDLGTENLYFQSMSVKGRIYSILKQIGSGGSSKVFQVLNEKKQIYAIKYVNLEEADNQTLDSYRNEIAYLNKLQQHSDKIIRLYDYEITDQYIYMVMECGNIDLNSWLKKKKSIDPWERKSYWKNMLEAVHTIHQHGIVHSDLKPANFLIVDGMLKLIDFGIANQMQPDTTSVVKDSQVGTVNYMPPEAIKDMSSSRENGKSKSKISPKSDVWSLGCILYYMTYGKTPFQQIINQISKLHAIIDPNHEIEFPDIPEKDLQDVLKCCLKRDPKQRISIPELLAHPYVQIQTHPVNQMAKGTTEE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.01
R work: 0.1967
R free: 0.2205
Average B factor: 52.83
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 291.15
Crystal growth procedure: 0.1 M BIS-TRIS Propane, 0.2 M MgCl2, 0.2 M Sodium formate, 20% PEG 3350
Matthews coefficient: 2.84
Solvent content (%): 56.65
Ligand: ~{N}-(2,4-dimethoxyphenyl)-5-(1-methylpyrazol-4-yl)isoquinolin-3-amine (5OQ)
Ligand formula: C21 H20 N4 O2
Ligand molecular weight: 360.409
Ligand SMILES: Cn1cc(cn1)c2cccc3c2cc(nc3)Nc4ccc(cc4OC)OC
Ligand InChI: InChI=1S/C21H20N4O2/c1-25-13-15(12-23-25)17-6-4-5-14-11-22-21(10-18(14)17)24-19-8-7-16(26-2)9-20(19)27-3/h4-13H,1-3H3,(H,22,24)
Release date: 2016-04-20