satarupa22/MacromolecularLigandDB huggingface dataset:
Crystal structure of BTK C481S kinase domain in complex with pirtobrutinib (PDB entry 8FLN)
Macromolecule: Tyrosine-protein kinase BTK
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 273 residues
Sequence: GMGLGYGSWEIDPKDLTFLKELGTGQFGVVKYGKWRGQYDVAIKMIKEGSMSEDEFIEEAKVMMNLSHEKLVQLYGVCTKQRPIFIITEYMANGSLLNYLREMRHRFQTQQLLEMCKDVCEAMEYLESKQFLHRDLAARNCLVNDQGVVKVSDFGLSRYVLDDEYTSSVGSKFPVRWSPPEVLMYSKFSSKSDIWAFGVLMWEIYSLGKMPYERFTNSETAEHIAQGLRLYRPHLASEKVYTIMYSCWHEKADERPTFKILLSNILDVMDEES
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.334
R work: 0.1931
R free: 0.1991
Average B factor: 28.29
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 293
Crystal growth procedure: 32% PEG3350, 0.3 M ammonium sulfate, 0.1 M Tis-Tris pH 5.5
Matthews coefficient: 1.99
Solvent content (%): 38.18
Ligand: pirtobrutinib (Y7W)
Ligand formula: C22 H21 F4 N5 O3
Ligand molecular weight: 479.427
Ligand SMILES: CC(C(F)(F)F)n1c(c(c(n1)c2ccc(cc2)CNC(=O)c3cc(ccc3OC)F)C(=O)N)N
Ligand InChI: InChI=1S/C22H21F4N5O3/c1-11(22(24,25)26)31-19(27)17(20(28)32)18(30-31)13-5-3-12(4-6-13)10-29-21(33)15-9-14(23)7-8-16(15)34-2/h3-9,11H,10,27H2,1-2H3,(H2,28,32)(H,29,33)/t11-/m0/s1
Release date: 2023-03-01
Nek2 bound to purine compound 51 (PDB entry 6SK9)
Macromolecule: Serine/threonine-protein kinase Nek2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 279 residues
Sequence: MPSRAEDYEVLYTIGTGSYGRCQKIRRKSDGKILVWKELDYGSMTEAEKQMLVSEVNLLRELKHPNIVRYYDRIIDRTNTTLYIVMEYCEGGDLASVITKGTKERQYLDEEFVLRVMTQLTLALKECHRRSDGGHTVLHRDLKPANVFLDGKQNVKLGDFGLARILNHDTSFAKTFVGTPYYMSPEQMNRMSYNEKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIREGKFRRIPYRYSDELNEIITRMLNLKDYHRPSVEEILENPLILEHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.0
R work: 0.187889564471
R free: 0.219599199899
Average B factor: 49.6367037345
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 279
Crystal growth procedure: 50 mM Hepes, pH 7.5, 300 mM sodium chloride, 10 mM sodium phosphate, 5 mM dithiothreitol and 5% glycerol
Matthews coefficient: 2.88
Solvent content (%): 57.33
Ligand: 3-[[6-(cyclohexylmethoxy)-7~{H}-purin-2-yl]amino]-~{N}-[3-(dimethylamino)propyl]benzenesulfonamide (F9N)
Ligand formula: C23 H33 N7 O3 S
Ligand molecular weight: 487.618
Ligand SMILES: CN(C)CCCNS(=O)(=O)c1cccc(c1)Nc2nc3c(c(n2)OCC4CCCCC4)[nH]cn3
Ligand InChI: InChI=1S/C23H33N7O3S/c1-30(2)13-7-12-26-34(31,32)19-11-6-10-18(14-19)27-23-28-21-20(24-16-25-21)22(29-23)33-15-17-8-4-3-5-9-17/h6,10-11,14,16-17,26H,3-5,7-9,12-13,15H2,1-2H3,(H2,24,25,27,28,29)
Release date: 2020-06-17
PanDDA analysis group deposition of ground-state model of PTP1B, using pre-clustering, cluster5 (PDB entry 7GTZ)
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): 1.6
R work: 0.2138
R free: 0.2406
Average B factor: 41.8709
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.3 M magnesium acetate, 0.1 M HEPES pH 7.5, 0.1% beta-mercaptoethanol, 13-14% PEG 8000, 2% ethanol
Matthews coefficient: 3.3
Solvent content (%): 62.68
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: 2024-01-31
Notum-Fragment 154 (PDB entry 7B8F)
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): 1.62
R work: 0.2058
R free: 0.2365
Average B factor: 27.2112
Crystallization method: EVAPORATION
Crystallization temperature (K): 296
Crystal growth procedure: 1.5 M Ammonium Sulphate
0.1 M Sodium Citrate, pH4.2
Matthews coefficient: 1.97
Solvent content (%): 37.47
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: 2022-01-12
Crystal structure of human KDR (VEGFR2) kinase domain in complex with AZD3229-analogue (compound 18) (PDB entry 6GQO)
Macromolecule: Vascular endothelial growth factor receptor 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 322 residues
Sequence: MDPDELPLDEHCERLPYDASKWEFPRDRLKLGKPLGRGAFGQVIEADAFGIDKTATCRTVAVKMLKEGATHSEHRALMSELKILIHIGHHLNVVNLLGACTKPGGPLMVIVEFCKFGNLSTYLRSKRNEFVPYKVAPEDLYKDFLTLEHLICYSFQVAKGMEFLASRKCIHRDLAARNILLSEKNVVKICDFGLARDIYKDPDYVRKGDARLPLKWMAPETIFDRVYTIQSDVWSFGVLLWEIFSLGASPYPGVKIDEEFCRRLKEGTRMRAPDYTTPEMYQTMLDCWHGEPSQRPTFSELVEHLGNLLQANAQQDENLYFQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.87
R work: 0.172
R free: 0.207
Average B factor: 47.98
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 293
Crystal growth procedure: 8 % PEG 8000, 0.1 M Tris pH 8.5
Matthews coefficient: 2.38
Solvent content (%): 48.36
Ligand: 2-[4-(6,7-dimethoxyquinazolin-4-yl)oxy-2-methoxy-phenyl]-~{N}-(1-propan-2-ylpyrazol-4-yl)ethanamide (F82)
Ligand formula: C25 H27 N5 O5
Ligand molecular weight: 477.512
Ligand SMILES: CC(C)n1cc(cn1)NC(=O)Cc2ccc(cc2OC)Oc3c4cc(c(cc4ncn3)OC)OC
Ligand InChI: InChI=1S/C25H27N5O5/c1-15(2)30-13-17(12-28-30)29-24(31)8-16-6-7-18(9-21(16)32-3)35-25-19-10-22(33-4)23(34-5)11-20(19)26-14-27-25/h6-7,9-15H,8H2,1-5H3,(H,29,31)
Release date: 2018-09-19
Protein Phosphatase 1 (PP1) T320E mutant (PDB entry 6ZK6)
Macromolecule: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.16
Sequence length: 331 residues
Sequence: GMSDSEKLNLDSIIGRLLEVQGSRPGKNVQLTENEIRGLCLKSREIFLSQPILLELEAPLKICGDIHGQYYDLLRLFEYGGFPPESNYLFLGDYVDRGKQSLETICLLLAYKIKYPENFFLLRGNHECASINRIYGFYDECKRRYNIKLWKTFTDCFNCLPIAAIVDEKIFCCHGGLSPDLQSMEQIRRIMRPTDVPDQGLLCDLLWSDPDKDVQGWGENDRGVSFTFGAEVVAKFLHKHDLDLICRAHQVVEDGYEFFAKRQLVTLFSAPNYCGEFDNAGAMMSVDETLMCSFQILKPADKNKGKYGQFSGLNPGGRPIEPPRNSAKAKK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.9
R work: 0.1594
R free: 0.1944
Average B factor: 43.57
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8
Crystallization temperature (K): 293
Crystal growth procedure: PEG 3350, TRIS , lithium chloride
Matthews coefficient: 2.25
Solvent content (%): 45.26
Ligand: FE (III) ION (FE)
Ligand formula: Fe
Ligand molecular weight: 55.845
Ligand SMILES: [Fe+3]
Ligand InChI: InChI=1S/Fe/q+3
Release date: 2020-11-18
Crystal structure of InhA:01 TCR in complex with HLA-E (Y84C) bound to InhA (53-61 GCG) (PDB entry 6ZKX)
Macromolecule: HLA class I histocompatibility antigen, alpha chain E
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 277 residues
Sequence: MGSHSLKYFHTSVSRPGRGEPRFISVGYVDDTQFVRFDNDAASPRMVPRAPWMEQEGSEYWDRETRSARDTAQIFRVNLRTLRGCYNQSEAGSHTLQWMHGCELGPDGRFLRGYEQFAYDGKDYLTLNEDLRSWTAVDTAAQISEQKSNDASEAEHQRAYLEDTCVEWLHKYLEKGKETLLHLEPPKTHVTHHPISDHEATLRCWALGFYPAEITLTWQQDGEGHTQDTELVETRPAGDGTFQKWAAVVVPSGEEQRYTCHVQHEGLPEPVTLRWKP
Oligomeric state: Hetero 5-mer
Stoichiometry: A1, B1, C1, D1, E1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.17
R work: 0.20908
R free: 0.24419
Average B factor: 45.68
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 293.15
Crystal growth procedure: 0.1 M Tris pH 8.5, 25% (w/v) PEG 4000, 15% Glycerol
Matthews coefficient: 2.46
Solvent content (%): 49.9
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: 2022-01-26
Crystal Structure of Human Hexokinase 2 with cmpd 30, a 2-amino-6-benzenesulfonamide glucosamine (PDB entry 5HEX)
Macromolecule: Hexokinase-2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.1.1
Sequence length: 923 residues
Sequence: MGSSHHHHHHSSGLENLYFQGSDQVQKVDQYLYHMRLSDETLLEISKRFRKEMEKGLGATTHPTAAVKMLPTFVRSTPDGTEHGEFLALDLGGTNFRVLWVKVTDNGLQKVEMENQIYAIPEDIMRGSGTQLFDHIAECLANFMDKLQIKDKKLPLGFTFSFPCHQTKLDESFLVSWTKGFKSSGVEGRDVVALIRKAIQRRGDFDIDIVAVVNDTVGTMMTCGYDDHNCEIGLIVGTGSNACYMEEMRHIDMVEGDEGRMCINMEWGAFGDDGSLNDIRTEFDQEIDMGSLNPGKQLFEKMISGMYMGELVRLILVKMAKEELLFGGKLSPELLNTGRFETKDISDIEGEKDGIRKAREVLMRLGLDPTQEDCVATHRICQIVSTRSASLCAATLAAVLQRIKENKGEERLRSTIGVDGSVYKKHPHFAKRLHKTVRRLVPGCDVRFLRSEDGSGKGAAMVTAVAYRLADQHRARQKTLEHLQLSHDQLLEVKRRMKVEMERGLSKETHASAPVKMLPTYVCATPDGTEKGDFLALDLGGTNFRVLLVRVRNGKWGGVEMHNKIYAIPQEVMHGTGDELFDHIVQCIADFLEYMGMKGVSLPLGFTFSFPCQQNSLDESILLKWTKGFKASGCEGEDVVTLLKEAIHRREEFDLDVVAVVNDTVGTMMTCGFEDPHCEVGLIVGTGSNACYMEEMRNVELVEGEEGRMCVNMEWGAFGDNGCLDDFRTEFDVAVDELSLNPGKQRFEKMISGMYLGEIVRNILIDFTKRGLLFRGRISERLKTRGIFETKFLSQIESDCLALLQVRAILQHLGLESTCDDSIIVKEVCTVVARRAAQLCGAGMAAVVDRIRENRGLDALKVTVGVDGTLYKLHPHFAKVMHETVKDLAPKCDVSFLQSEDGSGKGAALITAVACRIREAGQR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.734
R work: 0.1899
R free: 0.2517
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 5
Crystallization temperature (K): 296
Crystal growth procedure: protein conditions: 10mgs/mL, 50mM TRIS HCL, pH 7.5, 250mM NaCl, 2mM DTT, 2mM MgCl2. and 1mM cmpd30
Reservoir: 0.1M Na Citrate pH=5, 14% PEG 3350, 10 % ethylene glycol 
Cryo protectant 20% ethylene glycol in mother liquor
Matthews coefficient: 2.83
Solvent content (%): 56.54
Ligand: 2-[(3-bromobenzene-1-carbonyl)amino]-6-{[(4-carboxy-5-methylfuran-2-yl)sulfonyl]amino}-2,6-dideoxy-alpha-D-glucopyranos
 e (604)
Ligand formula: C19 H21 Br N2 O10 S
Ligand molecular weight: 549.346
Ligand SMILES: Cc1c(cc(o1)S(=O)(=O)NCC2C(C(C(C(O2)O)NC(=O)c3cccc(c3)Br)O)O)C(=O)O
Ligand InChI: InChI=1S/C19H21BrN2O10S/c1-8-11(18(26)27)6-13(31-8)33(29,30)21-7-12-15(23)16(24)14(19(28)32-12)22-17(25)9-3-2-4-10(20)5-9/h2-6,12,14-16,19,21,23-24,28H,7H2,1H3,(H,22,25)(H,26,27)/t12-,14-,15-,16-,19+/m1/s1
Release date: 2016-03-30
X-ray structure of the complex between human alpha thrombin and a pseudo-cyclic thrombin binding aptamer (TBA-NNp/DDp) - Crystal form delta (PDB entry 7ZKO)
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 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.5
R work: 0.2459
R free: 0.2954
Average B factor: 77.887
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7
Crystallization temperature (K): 293
Crystal growth procedure: PEG 3350 30% w/v, 0.2 M sodium malonate, pH 7.0
Matthews coefficient: 2.62
Solvent content (%): 56.9
Ligand: D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide (0G6)
Ligand formula: C21 H34 Cl N6 O3
Ligand molecular weight: 453.986
Ligand SMILES: c1ccc(cc1)CC(C(=O)N2CCCC2C(=O)NC(CCCNC(=[NH2+])N)C(CCl)O)N
Ligand InChI: InChI=1S/C21H33ClN6O3/c22-13-18(29)16(8-4-10-26-21(24)25)27-19(30)17-9-5-11-28(17)20(31)15(23)12-14-6-2-1-3-7-14/h1-3,6-7,15-18,29H,4-5,8-13,23H2,(H,27,30)(H4,24,25,26)/p+1/t15-,16+,17+,18-/m1/s1
Release date: 2022-11-30
FACTOR XIA IN COMPLEX WITH THE INHIBITOR 1-{(1S)-1-[4-(3-amino-1H-indazol-6-yl)-5-chloro-1H-imidazol-2-yl]-2-phenylethyl}-3-[5-chloro-2-(1H-tetrazol-1-yl)benzyl]urea (PDB entry 4X6N)
Macromolecule: Coagulation factor XI, light chain
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.27
Sequence length: 244 residues
Sequence: IVGGTASVRGEWPWQVTLHTTSPTQRHLCGGSIIGNQWILTAAHCFYGVESPKILRVYSGILNQSEIKEDTSFFGVQEIIIHDQYKMAESGYDIALLKLETTVGYGDSQRPICLPSKGDRNVIYTDCWVTGWGYRKLRDKIQNTLQKAKIPLVTNEECQKRYRGHKITHKMICAGYREGGKDACKGDSGGPLSCKHNEVWHLVGITSWGEGCAQRERPGVYTNVVEYVDWILEKTQAVHHHHHH
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.1
R work: 0.1711
R free: 0.2101
Average B factor: 28.48
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 4.6
Crystallization temperature (K): 277
Crystal growth procedure: 100 MM SODIUM ACETATE, PH 4.6, 26%(w/v) MEPEG2000, 200 MM AMMONIUM SULFATE
Matthews coefficient: 3.47
Solvent content (%): 64.55
Ligand: 1-{(1S)-1-[4-(3-amino-1H-indazol-6-yl)-5-chloro-1H-imidazol-2-yl]-2-phenylethyl}-3-[5-chloro-2-(1H-tetrazol-1-yl)benzyl]urea (3Y5)
Ligand formula: C27 H23 Cl2 N11 O
Ligand molecular weight: 588.451
Ligand SMILES: c1ccc(cc1)CC(c2[nH]c(c(n2)c3ccc4c(c3)[nH]nc4N)Cl)NC(=O)NCc5cc(ccc5n6cnnn6)Cl
Ligand InChI: InChI=1S/C27H23Cl2N11O/c28-18-7-9-22(40-14-32-38-39-40)17(11-18)13-31-27(41)33-21(10-15-4-2-1-3-5-15)26-34-23(24(29)35-26)16-6-8-19-20(12-16)36-37-25(19)30/h1-9,11-12,14,21H,10,13H2,(H,34,35)(H3,30,36,37)(H2,31,33,41)/t21-/m0/s1
Release date: 2015-02-18
Crystal structure of Tdp1 catalytic domain in complex with compound XZ572 (PDB entry 6N0R)
Macromolecule: Tyrosyl-DNA phosphodiesterase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.4
Sequence length: 461 residues
Sequence: SGEGQDIWDMLDKGNPFQFYLTRVSGVKPKYNSGALHIKDILSPLFGTLVSSAQFNYCFDVDWLVKQYPPEFRKKPILLVHGDKREAKAHLHAQAKPYENISLCQAKLDIAFGTHHTKMMLLLYEEGLRVVIHTSNLIHADWHQKTQGIWLSPLYPRIADGTHKSGESPTHFKADLISYLMAYNAPSLKEWIDVIHKHDLSETNVYLIGSTPGRFQGSQKDNWGHFRLKKLLKDHASSMPNAESWPVVGQFSSVGSLGADESKWLCSEFKESMLTLGKESKTPGKSSVPLYLIYPSVENVRTSLEGYPAGGSLPYSIQTAEKQNWLHSYFHKWSAETSGRSNAMPHIKTYMRPSPDFSKIAWFLVTSANLSKAAWGALEKNGTQLMIRSYELGVLFLPSAFGLDSFKVKQKFFAGSQEPMATFPVPYDLPPELYGSKDRPWIWNIPYVKAPDTHGNMWVPS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.544
R work: 0.17
R free: 0.195
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 291
Crystal growth procedure: 0.1M MOPS/HEPES-Na pH 7.5, 10% (w/v) PEG 8000, 20% (v/v) ethylene glycol, 0.03 M sodium fluoride, 0.03 M sodium bromide, 0.03 M sodium iodide
Matthews coefficient: 2.45
Solvent content (%): 49.77
Ligand: 4-(methylamino)benzene-1,2-dicarboxylic acid (K8D)
Ligand formula: C9 H9 N O4
Ligand molecular weight: 195.172
Ligand SMILES: CNc1ccc(c(c1)C(=O)O)C(=O)O
Ligand InChI: InChI=1S/C9H9NO4/c1-10-5-2-3-6(8(11)12)7(4-5)9(13)14/h2-4,10H,1H3,(H,11,12)(H,13,14)
Release date: 2019-11-13
Crystal structure of human SMYD3 in complex with a MAP3K2 peptide (PDB entry 5EX0)
Macromolecule: Histone-lysine N-methyltransferase SMYD3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1.43
Sequence length: 431 residues
Sequence: SEFMEPLKVEKFATANRGNGLRAVTPLRPGELLFRSDPLAYTVCKGSRGVVCDRCLLGKEKLMRCSQCRVAKYCSAKCQKKAWPDHKRECKCLKSCKPRYPPDSVRLLGRVVFKLMDGAPSESEKLYSFYDLESNINKLTEDRKEGLRQLVMTFQHFMREEIQDASQLPPAFDLFEAFAKVICNSFTICNAEMQEVGVGLYPSISLLNHSCDPNCSIVFNGPHLLLRAVRDIEVGEELTICYLDMLMTSEERRKQLRDQYCFECDCFRCQTQDKDADMLTGDEQVWKEVQESLKKIEELKAHWKWEQVLAMCQAIISSNSERLPDINIYQLKVLDCAMDACINLGLLEEALFYGTRTMEPYRIFFPGSHPVRGVQVMKVGKLQLHQGMFPQAMKNLRLAFDIMRVTHGREHSLIEDLILLLEECDANIRAS
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.7
R work: 0.1779
R free: 0.2251
Average B factor: 36.4011
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 289
Crystal growth procedure: 3.4M NaAC
Matthews coefficient: 3.25
Solvent content (%): 62.2
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: 2016-03-09
The structure of NTMT1 in complex with compound BM-30 (PDB entry 6WH8)
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 4-mer
Stoichiometry: A2, B2
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.729
R work: 0.1799
R free: 0.1999
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M Na-HEPES, pH 7.5, 1.6 M ammonium sulfate, and 2% PEG 1000
Matthews coefficient: 3.04
Solvent content (%): 59.53
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: 2020-08-26
Crystal structure of LSD1 in complex with compound 4 (PDB entry 7VQS)
Macromolecule: Lysine-specific histone demethylase 1A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.99.66
Sequence length: 669 residues
Sequence: GPLGSHMSGVEGAAFQSRLPHDRMTSQEAACFPDIISGPQQTQKVFLFIRNRTLQLWLDNPKIQLTFEATLQQLEAPYNSDTVLVHRVHSYLERHGLINFGIYKRIKPLPTKKTGKVIIIGSGVSGLAAARQLQSFGMDVTLLEARDRVGGRVATFRKGNYVADLGAMVVTGLGGNPMAVVSKQVNMELAKIKQKCPLYEANGQAVPKEKDEMVEQEFNRLLEATSYLSHQLDFNVLNNKPVSLGQALEVVIQLQEKHVKDEQIEHWKKIVKTQEELKELLNKMVNLKEKIKELHQQYKEASEVKPPRDITAEFLVKSKHRDLTALCKEYDELAETQGKLEEKLQELEANPPSDVYLSSRDRQILDWHFANLEFANATPLSTLSLKHWDQDDDFEFTGSHLTVRNGYSCVPVALAEGLDIKLNTAVRQVRYTASGCEVIAVNTRSTSQTFIYKCDAVLCTLPLGVLKQQPPAVQFVPPLPEWKTSAVQRMGFGNLNKVVLCFDRVFWDPSVNLFGHVGSTTASRGELFLFWNLYKAPILLALVAGEAAGIMENISDDVIVGRCLAILKGIFGSSAVPQPKETVVSRWRADPWARGSYSYVAAGSSGNDYDLMAQPITPGPSIPGAPQPIPRLFFAGEHTIRNYPATVHGALLSGLREAGRIADQFLGAM
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.94
R work: 0.2126
R free: 0.2561
Average B factor: 98.99
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M MES (pH 6.2-6.3), 0.2M diammonium tartrate, 0.0005M TCEP, 10-12% PEG 3350
Matthews coefficient: 3.59
Solvent content (%): 65.72
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: 2022-06-01
Crystal structure of human Pim-1 kinase in complex with a quinazolinone-pyrrolopyrrolone inhibitor. (PDB entry 5IPJ)
Macromolecule: Serine/threonine-protein kinase pim-1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 286 residues
Sequence: MAHHHHHHDEVDGPLESQYQVGPLLGSGGFGSVYSGIRVSDNLPVAIKHVEKDRISDWGELPNGTRVPMEVVLLKKVSSGFSGVIRLLDWFERPDSFVLILERPEPVQDLFDFITERGALQEELARSFFWQVLEAVRHCHNCGVLHRDIKDENILIDLNRGELKLIDFGSGALLKDTVYTDFDGTRVYSPPEWIRYHRYHGRSAAVWSLGILLYDMVCGDIPFEHDEEIIRGQVFFRQRVSSECQHLIRWCLALRPSDRPTFEEIQNHPWMQDVLLPQETAEIHLH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.1
R work: 0.17926
R free: 0.22114
Average B factor: 42.691
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8
Crystallization temperature (K): 277
Crystal growth procedure: 1.0M LiCl, 0.1M TRIS pH8.0, 20% PEG6K
Matthews coefficient: 3.34
Solvent content (%): 63.19
Ligand: 2-(tert-butylamino)-3-methyl-8-[(6R)-6-methyl-4-oxo-1,4,5,6-tetrahydropyrrolo[3,4-b]pyrrol-2-yl]quinazolin-4(3H)-one (6CD)
Ligand formula: C20 H23 N5 O2
Ligand molecular weight: 365.429
Ligand SMILES: CC1c2c(cc([nH]2)c3cccc4c3N=C(N(C4=O)C)NC(C)(C)C)C(=O)N1
Ligand InChI: InChI=1S/C20H23N5O2/c1-10-15-13(17(26)21-10)9-14(22-15)11-7-6-8-12-16(11)23-19(24-20(2,3)4)25(5)18(12)27/h6-10,22H,1-5H3,(H,21,26)(H,23,24)/t10-/m1/s1
Release date: 2016-06-22
Human Gcn5 bound to butyryl-CoA (PDB entry 5H86)
Macromolecule: Histone acetyltransferase KAT2A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1.48
Sequence length: 168 residues
Sequence: GSGIIEFHVIGNSLTPKANRRVLLWLVGLQNVFSHQLPRMPKEYIARLVFDPKHKTLALIKDGRVIGGICFRMFPTQGFTEIVFCAVTSNEQVKGYGTHLMNHLKEYHIKHNILYFLTYADEYAIGYFKKQGFSKDIKVPKSRYLGYIKDYEGATLMECELNPRIPYT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.08
R work: 0.15642
R free: 0.19421
Average B factor: 20.113
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.8
Crystallization temperature (K): 293
Crystal growth procedure: 10% (v/v) 2-propanol, 3% glycerol, 100 mM HEPES, pH 7.8, and 11% (w/v) PEG 4,000
Matthews coefficient: 2.03
Solvent content (%): 39.53
Ligand: Butyryl Coenzyme A (BCO)
Ligand formula: C25 H42 N7 O17 P3 S
Ligand molecular weight: 837.624
Ligand SMILES: CCCC(=O)SCCNC(=O)CCNC(=O)C(C(C)(C)COP(=O)(O)OP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)O
Ligand InChI: InChI=1S/C25H42N7O17P3S/c1-4-5-16(34)53-9-8-27-15(33)6-7-28-23(37)20(36)25(2,3)11-46-52(43,44)49-51(41,42)45-10-14-19(48-50(38,39)40)18(35)24(47-14)32-13-31-17-21(26)29-12-30-22(17)32/h12-14,18-20,24,35-36H,4-11H2,1-3H3,(H,27,33)(H,28,37)(H,41,42)(H,43,44)(H2,26,29,30)(H2,38,39,40)/t14-,18-,19-,20+,24-/m1/s1
Release date: 2016-03-23
Sirt2 in complex with a myristoyl peptide (PDB entry 4X3P)
Macromolecule: NAD-dependent protein deacetylase sirtuin-2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.5.1
Sequence length: 304 residues
Sequence: GSQKERLLDELTLEGVARYMQSERCRRVICLVGAGISTSAGIPDFRSPSTGLYDNLEKYHLPYPEAIFEISYFKKHPEPFFALAKELYPGQFKPTICHYFMRLLKDKGLLLRCYTQNIDTLERIAGLEQEDLVEAHGTFYTSHCVSASCRHEYPLSWMKEKIFSEVTPKCEDCQSLVKPDIVFFGESLPARFFSCMQSDFLKVDLLLVMGTSLQVQPFASLISKAPLSTPRLLINKEKAGQSDPFLGMIMGLGGGMDFDSKKAYRDVAWLGECDQGCLALAELLGWKKELEDLVRREHASIDAQ
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.154
R free: 0.1732
Average B factor: 22.59
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 300
Crystal growth procedure: 25% PEG 3350, 0.1M HEPES, 5% Glycerol
Matthews coefficient: 2.38
Solvent content (%): 48.39
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: 2016-01-13