satarupa22/MacromolecularLigandDB huggingface dataset:
MST3 in complex with HESPERADIN (PDB entry 4QMT)
Macromolecule: Serine/threonine-protein kinase 24
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 310 residues
Sequence: GPLGSEFMAHSPVQSGLPGMQNLKADPEELFTKLEKIGKGSFGEVFKGIDNRTQKVVAIKIIDLEEAEDEIEDIQQEITVLSQCDSPYVTKYYGSYLKDTKLWIIMEYLGGGSALDLLEPGPLDETQIATILREILKGLDYLHSEKKIHRDIKAANVLLSEHGEVKLADFGVAGQLTDTQIKRNTFVGTPFWMAPEVIKQSAYDSKADIWSLGITAIELARGEPPHSELHPMKVLFLIPKNNPPTLEGNYSKPLKEFVEACLNKEPSFRPTAKELLKHKFILRNAKKTSYLTELIDRYKRWKAEQSHDDS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.5
R work: 0.1505
R free: 0.1855
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 291
Crystal growth procedure: 12.5 mg/mL MST3, 1 mM HESPERADIN, 25 mM TRIS, PH 8.0, 50 MM HEPES pH 7.5, 125 mM SODIUM CHLORIDE, 100 mM MAGNESIUM CHLORIDE, 15% PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Matthews coefficient: 2.12
Solvent content (%): 42.03
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: 2015-07-01
HsNMT1 in complex with CoA and Myristoylated-GKSNSKLK octapeptide (PDB entry 5O9S)
Macromolecule: Glycylpeptide N-tetradecanoyltransferase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1.97
Sequence length: 402 residues
Sequence: GGSEFSVGQGPAKTMEEASKRSYQFWDTQPVPKLGEVVNTHGPVEPDKDNIRQEPYTLPQGFTWDALDLGDRGVLKELYTLLNENYVEDDDNMFRFDYSPEFLLWALRPPGWLPQWHCGVRVVSSRKLVGFISAIPANIHIYDTEKKMVEINFLCVHKKLRSKRVAPVLIREITRRVHLEGIFQAVYTAGVVLPKPVGTCRYWHRSLNPRKLIEVKFSHLSRNMTMQRTMKLYRLPETPKTAGLRPMETKDIPVVHQLLTRYLKQFHLTPVMSQEEVEHWFYPQENIIDTFVVENANGEVTDFLSFYTLPSTIMNHPTHKSLKAAYSFYNVHTQTPLLDLMSDALVLAKMKGFDVFNALDLMENKTFLEKLKFGIGDGNLQYYLYNWKCPSMGAEKVGLVLQ
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.7
R work: 0.1751
R free: 0.2274
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 22% PEG 6000, 0.1M sodium citrate pH 5.6, 0.1M magnesium chloride, 0.2M sodium chloride
Matthews coefficient: 2.18
Solvent content (%): 43.57
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: 2018-06-27
Crystal structure of TNKS2 in complex with 2-(3-aminophenyl)-3,4-dihydroquinazolin-4-one (PDB entry 5NT0)
Macromolecule: Tankyrase-2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.4.2.30
Sequence length: 49 residues
Sequence: KMAHSPPGHHSVTGRPSVNGLALAEYVIYRGEQAYPEYLITYQIMRPEG
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.75
R work: 0.16843
R free: 0.19425
Average B factor: 31.951
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.2 M LISO4, 0.1 M TRIS HCL, 24% PEG3350
Matthews coefficient: 2.41
Solvent content (%): 49
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: 2018-03-07
PanDDA analysis group deposition of models with modelled events (e.g. bound ligands) -- Crystal Structure of human PARP14 Macrodomain 3 in complex with FMOPL000385a (PDB entry 5QHZ)
Macromolecule: Poly [ADP-ribose] polymerase 14
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.4.2.30
Sequence length: 183 residues
Sequence: SMFYGTVSSPDSGVYEMKIGSIIFQVASGDITKEEADVIVNSTSNSFNLKAGVSKAILECAGQNVERECSQQAQQRKNDYIITGGGFLRCKNIIHVIGGNDVKSSVSSVLQECEKKNYSSICLPAIGTGNAKQHPDKVAEAIIDAIEDFVQKGSAQSVKKVKVVIFLPQVLDVFYANMKKREG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.15
R work: 0.1396
R free: 0.174
Average B factor: 15.11
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.4
Crystallization temperature (K): 277
Crystal growth procedure: 80 mM KBr, 30 % PEG2kMME
Matthews coefficient: 2.01
Solvent content (%): 38.83
Ligand: CHLORIDE ION (CL)
Ligand formula: Cl
Ligand molecular weight: 35.453
Ligand SMILES: [Cl-]
Ligand InChI: InChI=1S/ClH/h1H/p-1
Release date: 2019-04-10
Structure of DYRK1A in complex with compound 28 (PDB entry 7AJA)
Macromolecule: Dual specificity tyrosine-phosphorylation-regulated kinase 1A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.12.1
Sequence length: 359 residues
Sequence: MGSSHHHHHHSSGLVPRGSHMIVKNGEKWMDRYEIDSLIGKGSFGQVVKAYDRVEQEWVAIKIIKNKKAFLNQAQIEVRLLELMNKHDTEMKYYIVHLKRHFMFRNHLCLVFEMLSYNLYDLLRNTNFRGVSLNLTRKFAQQMCTALLFLATPELSIIHCDLKPENILLCNPKRSAIKIVDFGSSCQLGQRIYQYIQSRFYRSPEVLLGMPYDLAIDMWSLGCILVEMHTGEPLFSGANEVDQMNKIVEVLGIPPAHILDQAPKARKFFEKLPDGTWNLKKTKDGKREYKPPGTRKLHNILGVETGGPGGRRAGESGHTVADYLKFKDLILRMLDYDPKTRIQPYYALQHSFFKKTADE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.2
R work: 0.1681
R free: 0.206
Average B factor: 34.986
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 12% PEG3350, 0.1M MES buffer pH6.5, 0.2M MgCl2
Matthews coefficient: 2.49
Solvent content (%): 50.54
Ligand: 1-[4-(1-benzofuran-5-yl)pyridin-2-yl]piperazine (RJ2)
Ligand formula: C17 H17 N3 O
Ligand molecular weight: 279.336
Ligand SMILES: c1cc2c(cco2)cc1c3ccnc(c3)N4CCNCC4
Ligand InChI: InChI=1S/C17H17N3O/c1-2-16-15(4-10-21-16)11-13(1)14-3-5-19-17(12-14)20-8-6-18-7-9-20/h1-5,10-12,18H,6-9H2
Release date: 2021-05-26
Crystal structure of human Sirt5 in complex with the fluorogenic tetrapeptide substrate P15 (PDB entry 6LJN)
Macromolecule: NAD-dependent protein deacylase sirtuin-5, mitochondrial
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1
Sequence length: 272 residues
Sequence: QASARPSSSMADFRKFFAKAKHIVIISGAGVSAESGVPTFRGAGGYWRKWQAQDLATPLAFAHNPSRVWEFYHYRREVMGSKEPNAGHRAIAECETRLGKQGRRVVVITQNIDELHRKAGTKNLLEIHGSLFKTRCTSCGVVAENYKSPICPALSGKGAPEPGTQDASIPVEKLPRCEEAGCGGLLRPHVVWFGENLDPAILEEVDRELAHCDLCLVVGTSSVVYPAAMFAPQVAARGVPVAEFNTETTPATNRFRFHFQGPCGTTLPEALA
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.173
R free: 0.212
Average B factor: 23.76
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 289
Crystal growth procedure: 23%-27% (v/v) PEG 3350, 0.1 M MES, pH 5.5-6.0, 0.1-0.2 M NaCl
Matthews coefficient: 2.39
Solvent content (%): 48.59
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: 2020-10-28
Crystal Structure of human Legumain in complex with (2S)-N-[(1S)-3-amino-1-cyano-3-oxopropyl]-1-[1-[4-[(2,4-difluorophenyl)methoxy]phenyl]cyclopropanecarbonyl]pyrrolidine-2-carboxamide (PDB entry 7FQI)
Macromolecule: Legumain
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.22.34
Sequence length: 444 residues
Sequence: MKLCILLAVVAFVGLSLGVPIDDPEDGGKHWVVIVAGSNGWYNYRHQADACHAYQIIHRNGIPDEQIVVMMYDDIAYSEDNPTPGIVINRPNGTDVYQGVPKDYTGEDVTPQNFLAVLRGDAEAVKGIGSGKVLKSGPQDHVFIYFTNHGSTGILVFPNEDLHVKDLNETIHYMYKHKMYRKMVFYIEACESGSMMNHLPDNINVYATTAANPRESSYACYYDEKRSTYLGDWYSVNWMEDSDVEDLTKETLHKQYHLVKSHTNTSHVMQYGQKTISTMKVMQFQGMKRKASSPVPLPPVTHLDLTPSPDVPLTIMKRKLMNTNDLEESRQLTEEIQRHLDARHLIEKSVRKIVSLLAASEAEVEQLLSERAPLTGHSCYPEALLHFRTHCFNWHSPTYEYALRHLYVLVNLCEKPYPLHRIKLSMDHVCLGHYVDHHHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.45
R work: 0.1668
R free: 0.1891
Average B factor: 21.328
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 9
Crystallization temperature (K): 293
Crystal growth procedure: 23.4mg/mL deglycosylated protein in 25mM HEPES/NaOH pH7, 300 mM NaCl, 200mM Trehalose incubated with 10-fold excess of ligand, then mixed 50-70% with 50-30% reservoir consisting of 25% v/v PEG smear broad, 0.1M Bicine/NaOH pH 9.0, 10% v/v 2-Propanol, total volume 200nL
Matthews coefficient: 2.03
Solvent content (%): 39.45
Ligand: N-[(2R)-4-amino-1-imino-4-oxobutan-2-yl]-1-(1-{4-[(2,4-difluorophenyl)methoxy]phenyl}cyclopropane-1-carbonyl)-L-prolinamide (WSN)
Ligand formula: C26 H28 F2 N4 O4
Ligand molecular weight: 498.522
Ligand SMILES: c1cc(ccc1C2(CC2)C(=O)N3CCCC3C(=O)NC(CC(=O)N)C=N)OCc4ccc(cc4F)F
Ligand InChI: InChI=1S/C26H28F2N4O4/c27-18-6-3-16(21(28)12-18)15-36-20-7-4-17(5-8-20)26(9-10-26)25(35)32-11-1-2-22(32)24(34)31-19(14-29)13-23(30)33/h3-8,12,14,19,22,29H,1-2,9-11,13,15H2,(H2,30,33)(H,31,34)/b29-14-/t19-,22-/m0/s1
Release date: 2023-10-11
Crystal structure of the PTP1B YopH WPD loop Chimera 4 bound to vanadate (PDB entry 6XEF)
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: MEMEKEFEQIDKSGSWAAIYQDIRHEASDFPCRVAKLPKNKNRNRYRDVSPFDHSRIKLHQEDNDYINASLIKMEEAQRSYILTQGPLPNTCGHFWEMVWEQKSRGVVMLNRVMEKGSLKCAQYWPQKEEKEMIFEDTNLKLTLISEDIKSYYTVRQLELENLTTQETREILHFHYTNWPDQTAPESPASFLNFLFKVRESGSLSPEHGPVVVHCSAGIGRSGTFCLADTCLLLMDKRKDPSSVDIKKVLLEMRKFRMGLIQTADQLRFSYLAVIEGAKFIMGDSSVQDQWKELSHEDLEPPPEHIPPPPRPPKRILEPHN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.048
R work: 0.1814
R free: 0.2028
Average B factor: 49.3354
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.8
Crystallization temperature (K): 277.15
Crystal growth procedure: tris hydrochloride pH 7.8, magnesium acetate tetrahydrate, PEG 8000 and benzamidine
Matthews coefficient: 3.27
Solvent content (%): 61.12
Ligand: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL (TRS)
Ligand formula: C4 H12 N O3
Ligand molecular weight: 122.143
Ligand SMILES: C(C(CO)(CO)[NH3+])O
Ligand InChI: InChI=1S/C4H11NO3/c5-4(1-6,2-7)3-8/h6-8H,1-3,5H2/p+1
Release date: 2021-12-15
Crystal structure of FGF401 in complex of FGFR4 (PDB entry 6JPJ)
Macromolecule: Fibroblast growth factor receptor 4
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 311 residues
Sequence: GPLLAGLVSLDLPLDPLWEFPRDRLVLGKPLGEGAFGQVVRAEAFGMDPARPDQASTVAVKMLKDNASDKDLADLVSEMEVMKLIGRHKNIINLLGVCTQEGPLYVIVECAAKGNLREFLRARRPPGPDLSPDGPRSSEGPLSFPVLVSCAYQVARGMQYLESRKCIHRDLAARNVLVTEDNVMKIADFGLARGVHHIDYYKKTSNGRLPVKWMAPEALFDEVYTHQSDVWSFGILLWEIFTLGGSPYPGIPVEELFSLLREGHRMDRPPHCPPELYGLMRECWHAAPSQRPTFKQLVEALDKVLLAVSEE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.638
R work: 0.1953
R free: 0.2433
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 0.1M MES pH 5.5, 20% PEG 4000, 0.15M (NH4)2SO4, 4% (v/v) formamide
Matthews coefficient: 2.25
Solvent content (%): 45.26
Ligand: N-[5-cyano-4-(2-methoxyethylamino)pyridin-2-yl]-7-methanoyl-6-[(4-methyl-2-oxidanylidene-piperazin-1-yl)methyl]-3,4-dihydro-2H-1,8-naphthyridine-1-carboxamide (FGF)
Ligand formula: C25 H30 N8 O4
Ligand molecular weight: 506.557
Ligand SMILES: CN1CCN(C(=O)C1)Cc2cc3c(nc2C=O)N(CCC3)C(=O)Nc4cc(c(cn4)C#N)NCCOC
Ligand InChI: InChI=1S/C25H30N8O4/c1-31-7-8-32(23(35)15-31)14-18-10-17-4-3-6-33(24(17)29-21(18)16-34)25(36)30-22-11-20(27-5-9-37-2)19(12-26)13-28-22/h10-11,13,16H,3-9,14-15H2,1-2H3,(H2,27,28,30,36)
Release date: 2019-05-15
The structure of the polo-box domain (PBD) of polo-like kinase 1 (Plk1) in complex with LHSpTA peptide (PDB entry 5NFU)
Macromolecule: Serine/threonine-protein kinase PLK1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.21
Sequence length: 236 residues
Sequence: GAHMDCHLSDMLQQLHSVNASKPSERGLVRQEEAEDPACIPIFWVSKWVDYSDKYGLGYQLCDNSVGVLFNDSTRLILYNDGDSLQYIERDGTESYLTVSSHPNSLMKKITLLKYFRNYMSEHLLKAGANITPREGDELARLPYLRTWFRTRSAIILHLSNGSVQINFFQDHTKLILCPLMAAVTYIDEKRDFRTYRLSLLEEYGCCKELASRLRYARTMVDKLLSSRSASNRLKA
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.809
R work: 0.1681
R free: 0.202
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 7
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M HEPES 7
30% Jeffamine ED-2001
Matthews coefficient: 2.15
Solvent content (%): 42.74
Release date: 2018-05-16
Crystal structure of GDP-bound human M-RAS protein in crystal form II (PDB entry 9C1B)
Macromolecule: Ras-related protein M-Ras
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.5.2
Sequence length: 219 residues
Sequence: MGHHHHHHENLYFQGMATSAVPSDNLPTYKLVVVGDGGVGKSALTIQFFQKIFVPDYDPTIEDSYLKHTEIDNQWAILDVLDTAGQEEFSAMREQYMRTGDGFLIVYSVTDKASFEHVDRFHQLILRVKDRESFPMILVANKVDLMHLRKITREQGKEMATKHNIPYIETSAKDPPLNVDKAFHDLVRVIRQQIPEKSQKKKKKTKWRGDRATGTHKLQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.27
R work: 0.1992
R free: 0.2469
Average B factor: 38.65
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 295
Crystal growth procedure: 20% PEG3350
Matthews coefficient: 1.94
Solvent content (%): 36.5
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: 2024-09-11
Human PARP1 (ARTD1) - Catalytic domain in complex with inhibitor ME0527 (PDB entry 6GHK)
Macromolecule: Poly [ADP-ribose] polymerase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.4.2.30
Sequence length: 358 residues
Sequence: MKSKLPKPVQDLIKMIFDVESMKKAMVEYEIDLQKMPLGKLSKRQIQAAYSILSEVQQAVSQGSSDSQILDLSNRFYTLIPHDFGMKKPPLLNNADSVQAKAEMLDNLLDIEVAYSLLRGGSDDSSKDPIDVNYEKLKTDIKVVDRDSEEAEIIRKYVKNTHATTHNAYDLEVIDIFKIEREGECQRYKPFKQLHNRRLLWHGSRTTNFAGILSQGLRIAPPEAPVTGYMFGKGIYFADMVSKSANYCHTSQGDPIGLILLGEVALGNMYELKHASHISKLPKGKHSVKGLGKTTPDPSANISLDGVDVPLGTGISSGVNDTSLLYNEYIVYDIAQVNLKYLLKLKFNFKTAHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.28
R work: 0.1869
R free: 0.2265
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 277
Crystal growth procedure: 22.5% PEG 3350, 0.18M ammonium sulfate,  0.09M Bis-Tris
Matthews coefficient: 2.73
Solvent content (%): 54.87
Ligand: ~{N}-[(1~{R})-1-(4-imidazol-1-ylphenyl)ethyl]-3-(4-oxidanylidene-1~{H}-quinazolin-2-yl)propanamide (EZ2)
Ligand formula: C22 H21 N5 O2
Ligand molecular weight: 387.434
Ligand SMILES: CC(c1ccc(cc1)n2ccnc2)NC(=O)CCC3=NC(=O)c4ccccc4N3
Ligand InChI: InChI=1S/C22H21N5O2/c1-15(16-6-8-17(9-7-16)27-13-12-23-14-27)24-21(28)11-10-20-25-19-5-3-2-4-18(19)22(29)26-20/h2-9,12-15H,10-11H2,1H3,(H,24,28)(H,25,26,29)/t15-/m1/s1
Release date: 2019-05-22
DDR1 bound to Dasatinib (PDB entry 6BSD)
Macromolecule: Epithelial discoidin domain-containing receptor 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 351 residues
Sequence: QNSVPHYAEADIVTLQGVTGGNTYAVPALPPGAVGDGPPRVDFPRSRLRFKEKLGEGQFGEVHLCEVDSPQDLVSLDFPLNVRKGHPLLVAVKILRPDATKNARNDFLKEVKIMSRLKDPNIIRLLGVCVQDDPLCMITDYMENGDLNQFLSAHQLEDKAAEGAPGDGQAAQGPTISYPMLLHVAAQIASGMRYLATLNFVHRDLATRNCLVGENFTIKIADFGMSRNLYAGDYYRVQGRAVLPIRWMAWECILMGKFTTASDVWAFGVTLWEVLMLCRAQPFGQLTDEQVIENAGEFFRDQGRQVYLSRPPACPQGLYELMLRCWSRESEQRPPFSQLHRFLAEDALNTV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.606
R work: 0.1781
R free: 0.2552
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 298
Crystal growth procedure: 18% PEG 3350 and 0.1 M Bis-Tris pH 5.5
Matthews coefficient: 2.12
Solvent content (%): 42.02
Ligand: N-(2-CHLORO-6-METHYLPHENYL)-2-({6-[4-(2-HYDROXYETHYL)PIPERAZIN-1-YL]-2-METHYLPYRIMIDIN-4-YL}AMINO)-1,3-THIAZOLE-5-CARBOXAMIDE (1N1)
Ligand formula: C22 H26 Cl N7 O2 S
Ligand molecular weight: 488.006
Ligand SMILES: Cc1cccc(c1NC(=O)c2cnc(s2)Nc3cc(nc(n3)C)N4CCN(CC4)CCO)Cl
Ligand InChI: InChI=1S/C22H26ClN7O2S/c1-14-4-3-5-16(23)20(14)28-21(32)17-13-24-22(33-17)27-18-12-19(26-15(2)25-18)30-8-6-29(7-9-30)10-11-31/h3-5,12-13,31H,6-11H2,1-2H3,(H,28,32)(H,24,25,26,27)
Release date: 2018-12-05
Crystal structure of human KDM4A in complex with compound 16 (PDB entry 5F2W)
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): 2.6
R work: 0.1791
R free: 0.2256
Average B factor: 54.06
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: 2.45
Solvent content (%): 49.81
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
Human PDK1 Kinase Domain in Complex with Compound PS653 Bound to the ATP-Binding Site (PDB entry 5LVL)
Macromolecule: 3-phosphoinositide-dependent protein kinase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 311 residues
Sequence: GAMDGTAAEPRPGAGSLQHAQPPPQPRKKRPEDFKFGKILGEGSFSTVVLARELATSREYAIKILEKRHIIKENKVPYVTRERDVMSRLDHPFFVKLYFTFQDDEKLYFGLSYAKNGELLKYIRKIGSFDETCTRFYTAEIVSALEYLHGKGIIHRDLKPENILLNEDMHIQITDFGTAKVLSPESKQARANSFVGTAQYVSPELLTEKSACKSSDLWALGCIIYQLVAGLPPFRAGNEGLIFAKIIKLEYDFPEKFFPKARDLVEKLLVLDATKRLGCEEMEGYGPLKAHPFFESVTWENLHQQTPPKLT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.4
R work: 0.1529
R free: 0.178
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: 1.2 M NA CITRATE, 0.1 M HEPES PH 7.5, 0.01 M DTT
Matthews coefficient: 2.16
Solvent content (%): 43.12
Ligand: 2,6-DIHYDROANTHRA/1,9-CD/PYRAZOL-6-ONE (537)
Ligand formula: C14 H8 N2 O
Ligand molecular weight: 220.226
Ligand SMILES: c1ccc2c(c1)-c3c4c(cccc4[nH]n3)C2=O
Ligand InChI: InChI=1S/C14H8N2O/c17-14-9-5-2-1-4-8(9)13-12-10(14)6-3-7-11(12)15-16-13/h1-7H,(H,15,16)
Release date: 2016-10-19
Crystal Structure of kinase (PDB entry 5C03)
Macromolecule: Non-receptor tyrosine-protein kinase TYK2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 342 residues
Sequence: MSYYHHHHHHDYDIPTTENLYFQGAMGETSNLIIMRGARASPRTLNLSQLSFHRVDQKEITQLSHLGQGTRTNVYEGRLRVEGSGDPEEGKMDDEDPLVPGRDRGQELRVVLKVLDPSHHDIALAFYETASLMSQVSHTHLAFVHGVCVRGPENIMVTEYVEHGPLDVWLRRERGHVPMAWKMVVAQQLASALSYLENKNLVHGNVCGRNILLARLGLAEGTSPFIKLSDPGVGLGALSREERVERIPWLAPECLPGGANSLSTAMDKWGFGATLLEICFDGEAPLQSRSPSEKEHFYQRQHRLPEPSCPQLATLTSQCLTYEPTQRPSFRTILRDLTRLQP
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.9
R work: 0.1815
R free: 0.2185
Average B factor: 25.981
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 293
Crystal growth procedure: 18-22% PEG 4000, 0.1 M Tris, pH 8.5, 200 mM CaCl2
Matthews coefficient: 2.12
Solvent content (%): 42
Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER (AGS)
Ligand formula: C10 H16 N5 O12 P3 S
Ligand molecular weight: 523.247
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=S)(O)O)O)O)N
Ligand InChI: InChI=1S/C10H16N5O12P3S/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(25-10)1-24-28(18,19)26-29(20,21)27-30(22,23)31/h2-4,6-7,10,16-17H,1H2,(H,18,19)(H,20,21)(H2,11,12,13)(H2,22,23,31)/t4-,6-,7-,10-/m1/s1
Release date: 2015-09-16
Crystal structure of TRIM7 B30.2 domain at 1.8 angstrom resolution (PDB entry 6UMB)
Macromolecule: E3 ubiquitin-protein ligase TRIM7
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2.27
Sequence length: 177 residues
Sequence: SHMKEEKVELTLDPDTANPRLILSLDLKGVRLGERAQDLPNHPCRFDTNTRVLASCGFSSGRHHWEVEVGSKDGWAFGVARESVRRKGLTPFTPEEGVWALQLNGGQYWAVTSPERSPLSCGHLSRVRVALDLEVGAVSFYAVEDMRHLYTFRVNFQERVFPLFSVCSTGTYLRIWP
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.1841
R free: 0.2234
Average B factor: 24.54
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6
Crystallization temperature (K): 283
Crystal growth procedure: Sodium malonate pH 6.0
Matthews coefficient: 2.29
Solvent content (%): 46.25
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: 2021-04-14
Crystal structure of human protein kinase CK2alpha' (CSNK2A2 gene product) in complex with the ATP-competitive inhibitor 5,6-dibromo-1H-triazolo[4,5-b]pyridine (PDB entry 7A1B)
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): 1.287
R work: 0.1573
R free: 0.1925
Average B factor: 18.92
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 293
Crystal growth procedure: Reservoir composition: 28 % (w/v) PEG6000, 0.9 M LiCl, 0.1 M, Tris/HCl, pH 8.5; drop composition prior to equilibration: 0.01 ml reservoir solution + 0.02 ml CK2alpha' (mutant Cys336Ser)/inhibitor MB002 mixture (0.180 ml 6 mg/ml CK2alpha'Cys336Ser, 0.5 M NaCl, 25 mM Tris/HCl, pH 8.5, mixed and pre-equilibrated with 0.02 ml 10 mM MB002 in dimethyl sulfoxide); the initial inhibitor MB002 was replaced by the inhibitor 5,6-dibromo-1H-triazolo[4,5-b]pyridine by extensive crystal soaking.
Matthews coefficient: 2.62
Solvent content (%): 52.97
Ligand:  5,6-dibromo-1H-triazolo[4,5-b]pyridine (QXW)
Ligand formula: C5 H2 Br2 N4
Ligand molecular weight: 277.904
Ligand SMILES: c1c2c(nc(c1Br)Br)nn[nH]2
Ligand InChI: InChI=1S/C5H2Br2N4/c6-2-1-3-5(8-4(2)7)10-11-9-3/h1H,(H,8,9,10,11)
Release date: 2020-12-09
Notum Cotinine (PDB entry 7BNF)
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): 1.45
R work: 0.1561
R free: 0.1804
Average B factor: 22.1774
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: 1.95
Solvent content (%): 36.79
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: 2022-03-02