satarupa22/MacromolecularLigandDB huggingface dataset:
Bruton's tyrosine kinase in complex with compound 65 (PDB entry 7N4S)
Macromolecule: Tyrosine-protein kinase BTK
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 269 residues
Sequence: GYGSWEIDPKDLTFLKELGTGQFGVVKYGKWRGQYDVAIKMIKEGSMSEDEFIEEAKVMMNLSHEKLVQLYGVCTKQRPIFIITEYMANGCLLNYLREMRHRFQTQQLLEMCKDVCEAMEYLESKQFLHRDLAARNCLVNDQGVVKVSDFGLSRYVLDDEYTSSVGSKFPVRWSPPEVLMYSKFSSKSDIWAFGVLMWEIYSLGKMPYERFTNSETAEHIAQGLRLYRPHLASEKVYTIMYSCWHEKADERPTFKILLSNILDVMDEES
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.05
R work: 0.2438
R free: 0.2763
Average B factor: 34.09
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 277
Crystal growth procedure: 0.1M BisTRIS pH 6.5, 0.2M Ammonium Acetate, 0.1M Guanidine HCl, 20% PEG2200 MME
Matthews coefficient: 2.28
Solvent content (%): 46.04
Ligand: (3R,3'R)-3-anilino-1'-(7H-pyrrolo[2,3-d]pyrimidin-4-yl)[1,3'-bipiperidin]-2-one (0B0)
Ligand formula: C22 H26 N6 O
Ligand molecular weight: 390.481
Ligand SMILES: c1ccc(cc1)NC2CCCN(C2=O)C3CCCN(C3)c4c5cc[nH]c5ncn4
Ligand InChI: InChI=1S/C22H26N6O/c29-22-19(26-16-6-2-1-3-7-16)9-5-13-28(22)17-8-4-12-27(14-17)21-18-10-11-23-20(18)24-15-25-21/h1-3,6-7,10-11,15,17,19,26H,4-5,8-9,12-14H2,(H,23,24,25)/t17-,19-/m1/s1
Release date: 2022-05-18
Human SIRT2 in complex with myristoylated peptide (H3K9myr) (PDB entry 4Y6L)
Macromolecule: NAD-dependent protein deacetylase sirtuin-2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.5.1
Sequence length: 293 residues
Sequence: GSQKERLLDELTLEGVARYMQSERCRRVICLVGAGISTSAGIPDFRSPSTGLYDNLEKYHLPYPEAIFEISYFKKHPEPFFALAKELYPGQFKPTICHYFMRLLKDKGLLLRCYTQNIDTLERIAGLEQEDLVEAHGTFYTSHCVSASCRHEYPLSWMKEKIFSEVTPKCEDCQSLVKPDIVFFGESLPARFFSCMQSDFLKVDLLLVMGTSLQVQPFASLISKAPLSTPRLLINKEKAGGGGMDFDSKKAYRDVAWLGECDQGCLALAELLGWKKELEDLVRREHASIDAQS
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.6
R work: 0.20712
R free: 0.23241
Average B factor: 16.193
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: PEG 3350
Matthews coefficient: 2.33
Solvent content (%): 47.23
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: 2016-01-06
Structure of human PARG complexed with JA2-9 (PDB entry 6OA0)
Macromolecule: Poly(ADP-ribose) glycohydrolase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.2.1.143
Sequence length: 533 residues
Sequence: GPHMSPDKKWLGTPIEEMRRMPRCGIRLPLLRPSANHTVTIRVDLLRAGEVPKPFPTHYKDLWDNKHVKMPCSEQNLYPVEDENGERTAGSRWELIQTALLNKFTRPQNLKDAILKYNVAYSKKWDFTALIDFWDKVLEEAEAQHLYQSILPDMVKIALCLPNICTQPIPLLAAAMNHSITMSQEQIASLLANAFFCTFPRRNAKMKSEYSSYPDINFNRLFEGRSSRKPEKLKTLFCYFRRVTAAAPTGLVTFTRQSLEDFPEWERCEKPLTRLHVTYEGTIEENGQGMLQVDFANRFVGGGVTSAGLVQEEIRFLINPELIISRLFTEVLDHNECLIITGTEQYSEYTGYAETYRWSRSHEDGSERDDWQRRCTEIVAIDALHFRRYLDQFVPEKMRRELNKAYCGFLRPGVSSENLSAVATGNWGCGAFGGDARLKALIQILAAAAAERDVVYFTFGDSELMRDIYSMHIFLTERKLTVGDVYKLLLRYYNEECRNCSTPGPDIKLYPFIYHAVESCAETADHSGQRTGT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2
R work: 0.17182
R free: 0.21849
Average B factor: 29.344
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 295
Crystal growth procedure: 20% PEG 3350, 0.05 M PCTP pH 7.5, 0.1 M NaCl, 0.15 M MgCl2
Matthews coefficient: 2.27
Solvent content (%): 45.73
Ligand: 4-(1,3-dimethyl-2,6-dioxo-1,2,3,6-tetrahydro-7H-purin-7-yl)butanoic acid (M1D)
Ligand formula: C11 H14 N4 O4
Ligand molecular weight: 266.253
Ligand SMILES: CN1c2c(n(cn2)CCCC(=O)O)C(=O)N(C1=O)C
Ligand InChI: InChI=1S/C11H14N4O4/c1-13-9-8(10(18)14(2)11(13)19)15(6-12-9)5-3-4-7(16)17/h6H,3-5H2,1-2H3,(H,16,17)
Release date: 2019-12-25
X-ray crystal structure of human TNKS in complex with a small molecule inhibitor (PDB entry 4UUH)
Macromolecule: TANKYRASE-1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.4.2.30
Sequence length: 258 residues
Sequence: MHHHHHHSSGVDLGTENLYFQSMQGTNPYLTFHCVNQGTILLDLAPEDKEYQSVEEEMQSTIREHRDGGNAGGIFNRYNVIRIQKVVNKKLRERFCHRQKEVSEENHNHHNERMLFHGSPFINAIIHKGFDERHAYIGGMFGAGIYFAENSSKSNQYVYGIGGGTGCPTHKDRSCYICHRQMLFCRVTLGKSFLQFSTIKMAHAPPGHHSVIGRPSVNGLAYAEYVIYRGEQAYPEYLITYQIMKPEAPSQTATAAEQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.52
R work: 0.1662
R free: 0.2176
Average B factor: 41.19
Crystallization pH: 6
Crystal growth procedure: 0.1 M MES PH 6.0, 0.1 M AMMONIUM TARTARATE, 12-16% W/V PEG 3350
Matthews coefficient: 2.34
Solvent content (%): 47.42
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: 2015-07-08
Covalent fragment group deposition -- Crystal Structure of OUTB2 in complex with PCM-0102954 (PDB entry 5QIY)
Macromolecule: Ubiquitin thioesterase OTUB2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.19.12
Sequence length: 225 residues
Sequence: FNLISEKCDILSILRDHPENRIYRRKIEELSKRFTAIRKTKGDRNCFYRALGYSYLESLLGKSREIFKFKERVLQTPNDLLAAGFEEHKFRNFFNAFYSVVELVEKDGSVSSLLKVFNDQSASDHIVQFLRLLTSAFIRNRADFFRHFIDEEMDIKDFCTHEVEPMATECDHIQITALSQALSIALQVEYVDEMDTALNHHVFPEAATPSVYLLYKTSHYNILYA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.58
R work: 0.1764
R free: 0.1933
Average B factor: 21.59
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 293
Crystal growth procedure: 16% PEG4K, 0.1M HEPES pH 7.0, 8% 2-propanol, 5 mM DTT
Matthews coefficient: 2.31
Solvent content (%): 46.78
Ligand: N'-acetyl-2-chlorobenzohydrazide (J61)
Ligand formula: C9 H9 Cl N2 O2
Ligand molecular weight: 212.633
Ligand SMILES: CC(=O)NNC(=O)c1ccccc1Cl
Ligand InChI: InChI=1S/C9H9ClN2O2/c1-6(13)11-12-9(14)7-4-2-3-5-8(7)10/h2-5H,1H3,(H,11,13)(H,12,14)
Release date: 2019-12-18
Crystal Structure of Ephrin A2 (EphA2) Receptor Protein Kinase with the NVP-BHG712 derivative ATDL14 (PDB entry 6Q7E)
Macromolecule: Ephrin type-A receptor 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 306 residues
Sequence: GDPNQAVLKFTTEIHPSCVTRQKVIGAGEFGEVYKGMLKTSSGKKEVPVAIKTLKAGYTEKQRVDFLGEAGIMGQFSHHNIIRLEGVISKYKPMMIITEYMENGALDKFLREKDGEFSVLQLVGMLRGIAAGMKYLANMNYVHRDLAARNILVNSNLVCKVSDFGLSRVLEDDPEATYTTSGGKIPIRWTAPEAISYRKFTSASDVWSFGIVMWEVMTYGERPYWELSNHEVMKAINDGFRLPTPMDCPSAIYQLMMQCWQQERARRPKFADIVSILDKLIRAPDSLKTLADFDPRVSIRLPSTSG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.059
R work: 0.1922
R free: 0.2115
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 291
Crystal growth procedure: 37.5% MPD_PEG1000_PEG3350, 100 mM Alanine, 100 mM Morpheus Buffer System 3  (Tris/Bicine)
Matthews coefficient: 1.97
Solvent content (%): 37.47
Ligand: 3-[[4-imidazol-1-yl-6-[(3~{R})-3-oxidanylpyrrolidin-1-yl]-1,3,5-triazin-2-yl]amino]-4-methyl-~{N}-[3-(trifluoromethyl)phenyl]benzamide (HMW)
Ligand formula: C25 H23 F3 N8 O2
Ligand molecular weight: 524.498
Ligand SMILES: Cc1ccc(cc1Nc2nc(nc(n2)N3CCC(C3)O)n4ccnc4)C(=O)Nc5cccc(c5)C(F)(F)F
Ligand InChI: InChI=1S/C25H23F3N8O2/c1-15-5-6-16(21(38)30-18-4-2-3-17(12-18)25(26,27)28)11-20(15)31-22-32-23(35-9-7-19(37)13-35)34-24(33-22)36-10-8-29-14-36/h2-6,8,10-12,14,19,37H,7,9,13H2,1H3,(H,30,38)(H,31,32,33,34)/t19-/m1/s1
Release date: 2020-01-15
COMPLEX CRYSTAL STRUCTURE OF MUTANT HUMAN MONOGLYCERIDE LIPASE WITH COMPOUND 5l (PDB entry 8PTQ)
Macromolecule: Monoglyceride lipase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.1.23
Sequence length: 323 residues
Sequence: MGSSHHHHHHSSGENLYFQGMPEESSPRRTPQSIPYQDLPHLVNADGQYLFCRYWAPTGTPKALIFVSHGAGEHSGRYEELARMLMGLDLLVFAHDHVGHGQSEGERMVVSDFHVFVRDVLQHVDSMQKDYPGLPVFLLGHSMGGAIAILTAAERPGHFAGMVLISPLVLANPESATTFKVLAAKVLNSVLPNLSSGPIDSSVLSRNKTEVDIYNSDPLICRAGLKVCFGIQLLNAVSRVERALPKLTVPFLLLQGSADRLCDSKGAYLLMELAKSQDKTLKIYEGAYHVLHKELPEVTNSVFHEINMWVSQRTATAGTASPP
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.55
R work: 0.1946
R free: 0.2257
Average B factor: 35.23
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M MES pH 6.5, 6 to 13% PEG MME 5K, 12% isopropanol
Matthews coefficient: 2.44
Solvent content (%): 49.66
Ligand: methyl 4-[(2~{S},3~{R})-3-(4-fluorophenyl)-1-(1-methanoylpiperidin-4-yl)-4-oxidanylidene-azetidin-2-yl]benzoate (EJI)
Ligand formula: C23 H23 F N2 O4
Ligand molecular weight: 410.438
Ligand SMILES: COC(=O)c1ccc(cc1)C2C(C(=O)N2C3CCN(CC3)C=O)c4ccc(cc4)F
Ligand InChI: InChI=1S/C23H23FN2O4/c1-30-23(29)17-4-2-16(3-5-17)21-20(15-6-8-18(24)9-7-15)22(28)26(21)19-10-12-25(14-27)13-11-19/h2-9,14,19-21H,10-13H2,1H3/t20-,21+/m1/s1
Release date: 2024-01-31
DYRK1A IN COMPLEX WITH FLUORO BENZOTHIAZOLE FRAGMENT (PDB entry 5A4L)
Macromolecule: DUAL SPECIFICITY TYROSINE-PHOSPHORYLATION- REGULATED KINASE 1A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.12.1
Sequence length: 368 residues
Sequence: GASDSSHKKERKVYNDGYDDDNYDYIVKNGEKWMDRYEIDSLIGKGSFGQVVKAYDRVEQEWVAIKIIKNKKAFLNQAQIEVRLLELMNKHDTEMKYYIVHLKRHFMFRNHLCLVFEMLSYNLYDLLRNTNFRGVSLNLTRKFAQQMCTALLFLATPELSIIHCDLKPENILLCNPKRSAIKIVDFGSSCQLGQRIYQYIQSRFYRSPEVLLGMPYDLAIDMWSLGCILVEMHTGEPLFSGANEVDQMNKIVEVLGIPPAHILDQAPKARKFFEKLPDGTWNLKKTKDGKREYKPPGTRKLHNILGVETGGPGGRRAGESGHTVADYLKFKDLILRMLDYDPKTRIQPYYALQHSFFKKTADEGTNTS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.73
R work: 0.22141
R free: 0.26716
Average B factor: 20.446
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.8
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M KSCN; 0.05M LICL; 10% PEG 3350, PH 6.8, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K
Matthews coefficient: 2.6
Solvent content (%): 53
Ligand: N-(5-FLUORANYL-1,3-BENZOTHIAZOL-2-YL)ETHANAMIDE (ZC3)
Ligand formula: C9 H7 F N2 O S
Ligand molecular weight: 210.228
Ligand SMILES: CC(=O)Nc1nc2cc(ccc2s1)F
Ligand InChI: InChI=1S/C9H7FN2OS/c1-5(13)11-9-12-7-4-6(10)2-3-8(7)14-9/h2-4H,1H3,(H,11,12,13)
Release date: 2016-06-29
PB3 Domain of Human PLK4 in Complex with Coiled-Coil Domain of STIL (PDB entry 5LHZ)
Macromolecule: Serine/threonine-protein kinase PLK4
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.21
Sequence length: 91 residues
Sequence: GPMGSAQLLKSVFVKNVGWATQLTSGAVWVQFNDGSQLVVQAGVSSISYTSPNGQTTRYGENEKLPDYIKQKLQCLSSILLMFSNPTPNFH
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.51
R work: 0.2496
R free: 0.2821
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6
Crystallization temperature (K): 292
Crystal growth procedure: 150nl Protein solution (41.87 mg/ml protein in 20 mM Tris pH 7.5, 150 mM NaCl, 2 mM DTT) and 50 nl mother liquor (100mM MES pH 6.0, 191.7 mM Zn acetate, 10% Isopropanol)
Matthews coefficient: 2.36
Solvent content (%): 47.78
Release date: 2017-03-01
The novel SUV4-20 inhibitor A-196 verifies a role for epigenetics in genomic integrity (PDB entry 5CPR)
Macromolecule: Histone-lysine N-methyltransferase SUV420H1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1.43
Sequence length: 268 residues
Sequence: GSSGMSAKELCENDDLATSLVLDPYLGFQTHKMNTSAFPSRSSRHFSKSDSFSHNNPVRFRPIKGRQEELKEVIERFKKDEHLEKAFKCLTSGEWARHYFLNKNKMQEKLFKEHVFIYLRMFATDSGFEILPCNRYSSEQNGAKIVATKEWKRNDKIELLVGCIAELSEIEENMLLRHGENDFSVMYSTRKNCAQLWLGPAAFINHDCRPNCKFVSTGRDTACVKALRDIEPGEEISCYYGDGFFGENNEFCECYTCERRGTGAFKSR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.22
R work: 0.1901
R free: 0.2486
Average B factor: 37.52
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 298
Crystal growth procedure: The purified protein was concentrated to 10 mg/mL and with 1 mM SAM. SAM bound protein crystals were obtained by hanging drop vapor diffusion method at 17C using 10% (w/v) ethanol, 5% (w/v) glycerol, 0.1 M tris pH 8.5 as the well solution. A-196 was soaked into the crystals
Matthews coefficient: 2.11
Solvent content (%): 41.71
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: 2017-01-25
Crystal Structure of Human Kallikrein 6 in complex with GSK3205388B (PDB entry 6QHA)
Macromolecule: Kallikrein-6
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21
Sequence length: 223 residues
Sequence: LVHGGPCDKTSHPYQAALYTSGHLLCGGVLIHPLWVLTAAHCKKPNLQVFLGKHNLGQQESSQEQSSVVRAVIHPDYDAASHDQDIMLLRLARPAKLSELIQPLPLERDCSAQTTSCHILGWGKTADGDFPDTIQCAYIHLVSREECEHAYPGQITQNMLCAGDEKYGKDSCQGDSGGPLVCGDHLRGLVSWGNIPCGSKEKPGVYTNVCRYTNWIQKTIQAK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.82
R work: 0.213
R free: 0.248
Average B factor: 28.37
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.6
Crystallization temperature (K): 293
Crystal growth procedure: 100mM Tris-HCl pH 8.6, PEG 4000 18-28%
Matthews coefficient: 2.47
Solvent content (%): 50.24
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: 2019-02-06
Crystal structure of the p97 D2 domain in a helical split-washer conformation (PDB entry 6G2V)
Macromolecule: Transitional endoplasmic reticulum ATPase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.4.6
Sequence length: 275 residues
Sequence: GPGSALRETVVEVPQVTWEDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANECQANFISIKGPELLTSEANVREIFDKARQAAPCVLFFDELDSIAKAADRVINQILTEMDGMSTKKNVFIIGATNRPDIIDPAILRPGRLDQLIYIPLPDEKSRVAILKANLRKSPVAKDVDLEFLAKMTNGFSGADLTEICQRACKLAIRESIESEIRREREVPEIRRDHFEEAMRFARRSVSDNDIRKYEMFAQTLQQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.903
R work: 0.1966
R free: 0.2367
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.08M L-Na-Glutamate; 0.08M Alanine (racemic); 0.08M Glycine; 0.08M Lysine HCl (racemic); 0.08M Serine (racemic), 0.08M Tris, 0.08M BICINE, 10% v/v MPD; 10% PEG 1000; 10% w/v PEG 3350 at pH 8.5
Matthews coefficient: 2.47
Solvent content (%): 50.2
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: 2019-04-10
Complement factor D in complex with the inhibitor (1R,3S,5R)-2-Aza-bicyclo[3.1.0]hexane-2,3-dicarboxylic acid 2-[(1-carbamoyl-1H-indol-3-yl)-amide] 3-[(3-trifluoromethoxy-phenyl)-amide] (PDB entry 5NAW)
Macromolecule: Complement factor D
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.46
Sequence length: 232 residues
Sequence: ILGGREAEAHARPYMASVQLNGAHLCGGVLVAEQWVLSAAHCLEDAADGKVQVLLGAHSLSQPEPSKRLYDVLRAVPHPDSQPDTIDHDLLLLQLSEKATLGPAVRPLPWQRVDRDVAPGTLCDVAGWGIVNHAGRRPDSLQHVLLPVLDRATCNRRTHHDGAITERLMCAESNRRDSCKGDSGGPLVCGGVLEGVVTSGSRVCGNRKKPGIYTRVASYAAWIDSVLASAAA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.25
R work: 0.12789
R free: 0.17791
Average B factor: 18.891
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 298
Crystal growth procedure: 27% PEG 3350
100 mM HEPES pH 7.5
Matthews coefficient: 2.1
Solvent content (%): 41.43
Ligand: (1~{R},3~{S},5~{R})-~{N}2-(1-aminocarbonylindol-3-yl)-~{N}3-[3-(trifluoromethyloxy)phenyl]-2-azabicyclo[3.1.0]hexane-2,3-dicarboxamide (8RZ)
Ligand formula: C23 H20 F3 N5 O4
Ligand molecular weight: 487.431
Ligand SMILES: c1ccc2c(c1)c(cn2C(=O)N)NC(=O)N3C4CC4CC3C(=O)Nc5cccc(c5)OC(F)(F)F
Ligand InChI: InChI=1S/C23H20F3N5O4/c24-23(25,26)35-14-5-3-4-13(10-14)28-20(32)19-9-12-8-18(12)31(19)22(34)29-16-11-30(21(27)33)17-7-2-1-6-15(16)17/h1-7,10-12,18-19H,8-9H2,(H2,27,33)(H,28,32)(H,29,34)/t12-,18-,19+/m1/s1
Release date: 2017-06-28
Crystal Structure of SIRT3 in complex with H4K16bhb peptide (PDB entry 5ZGC)
Macromolecule: NAD-dependent protein deacetylase sirtuin-3, mitochondrial
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.5.1
Sequence length: 274 residues
Sequence: GKLSLQDVAELIRARACQRVVVMVGAGISTPSGIPDFRSPGSGLYSNLQQYDLPYPEAIFELPFFFHNPKPFFTLAKELYPGNYKPNVTHYFLRLLHDKGLLLRLYTQNIDGLERVSGIPASKLVEAHGTFASATCTVCQRPFPGEDIRADVMADRVPRCPVCTGVVKPDIVFFGEPLPQRFLLHVVDFPMADLLLILGTSLEVEPFASLTEAVRSSVPRLLINRDLVGPLAWHPRSRDVAQLGDVVHGVESLVELLGWTEEMRDLVQRETGKL
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.9
R work: 0.2244
R free: 0.2798
Average B factor: 72.3898
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 9
Crystallization temperature (K): 291
Crystal growth procedure: 0.1M Bicine pH 9.0, 10% PEG 6000
Matthews coefficient: 3.09
Solvent content (%): 60.23
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: 2019-04-03
Crystal Structure of NRAS Q61K bound to GTP (PDB entry 8VM2)
Macromolecule: GTPase NRas
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.5.2
Sequence length: 190 residues
Sequence: MHHHHHHSSGRENLYFQGMTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGKEEYSAMRDQYMRTGEGFLCVFAINNSKSFADINLYREQIKRVKDSDDVPMVLVGNKCDLPTRTVDTKQAHELAKSYGIPFIETSAKTRQGVEDAFYTLVREIRQYRMKKLN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.74
R work: 0.1721
R free: 0.2026
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 4.1
Crystallization temperature (K): 298
Crystal growth procedure: PEG/Ion (containing 0.06 M Citric acid, 0.04 M BIS-TRIS propane)/pH 4.1, 16% w/v Polyethylene glycol 3350
Matthews coefficient: 2.61
Solvent content (%): 52.8
Ligand: GUANOSINE-5'-TRIPHOSPHATE (GTP)
Ligand formula: C10 H16 N5 O14 P3
Ligand molecular weight: 523.18
Ligand SMILES: c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
Ligand InChI: InChI=1S/C10H16N5O14P3/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(27-9)1-26-31(22,23)29-32(24,25)28-30(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H,24,25)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1
Release date: 2024-05-01
Rational drug design of phenazopyridine derivatives as novel inhibitors of Rev1-CT (PDB entry 6WS5)
Macromolecule: DNA repair protein REV1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7
Sequence length: 95 residues
Sequence: GNLAGAVEFNDVKTLLREWITTISDPMEEDILQVVKYCTDLIEEKDLEKLDLVIKYMKRLMQQSVESVWNMAFDFILDNVQVVLQQTYGSTLKVT
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.472
R work: 0.2014
R free: 0.2375
Average B factor: 70
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 162 mM triammonium citrate and 18% w/v PEG 3350
Ligand: 3-[(Z)-(2,3-difluorophenyl)diazenyl]pyridine-2,6-diamine (U8M)
Ligand formula: C11 H9 F2 N5
Ligand molecular weight: 249.219
Ligand SMILES: c1cc(c(c(c1)F)F)N=Nc2ccc(nc2N)N
Ligand InChI: InChI=1S/C11H9F2N5/c12-6-2-1-3-7(10(6)13)17-18-8-4-5-9(14)16-11(8)15/h1-5H,(H4,14,15,16)
Release date: 2020-12-23
CRYSTAL STRUCTURE OF HUMAN SOLUBLE ADENYLYL CYCLASE IN COMPLEX WITH THE INHIBITOR TDI-011861 (PDB entry 8B75)
Macromolecule: Adenylate cyclase type 10
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.6.1.1
Sequence length: 475 residues
Sequence: MNTPKEEFQDWPIVRIAAHLPDLIVYGHFSPERPFMDYFDGVLMFVDISGFTAMTEKFSSAMYMDRGAEQLVEILNYHISAIVEKVLIFGGDILKFAGDALLALWRVERKQLKNIITVVIKCSLEIHGLFETQEWEEGLDIRVKIGLAAGHISMLVFGDETHSHFLVIGQAVDDVRLAQNMAQMNDVILSPNCWQLCDRSMIEIESVPDQRAVKVNFLKPPPNFNFDEFFTKCTTFMHYYPSGEHKNLLRLACTLKPDPELEMSLQKYVMESILKQIDNKQLQGYLSELRPVTIVFVNLMFEDQDKAEEIGPAIQDAYMHITSVLKIFQGQINKVFMFDKGCSFLCVFGFPGEKVPDELTHALECAMDIFDFCSQVHKIQTVSIGVASGIVFCGIVGHTVRHEYTVIGQKVNLAARMMMYYPGIVTCDSVTYNGSNLPAYFFKELPKKVMKGVADSGPLYQYWGRTEKVHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.82
R work: 0.2027
R free: 0.2457
Average B factor: 32.338
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 0.1 M sodiumacetate, 0.2 M trisodiumcitrate, 15% PEG4000, 10% Glycerol, 277 K
Matthews coefficient: 2.61
Solvent content (%): 52.88
Ligand: [(3~{R})-4-[2-[2-[[3-(2-azanyl-6-chloranyl-pyrimidin-4-yl)-1-[bis(fluoranyl)methyl]pyrazol-4-yl]methyl]phenoxy]ethyl]morpholin-3-yl]methanol (PJU)
Ligand formula: C22 H25 Cl F2 N6 O3
Ligand molecular weight: 494.922
Ligand SMILES: c1ccc(c(c1)Cc2cn(nc2c3cc(nc(n3)N)Cl)C(F)F)OCCN4CCOCC4CO
Ligand InChI: InChI=1S/C22H25ClF2N6O3/c23-19-10-17(27-22(26)28-19)20-15(11-31(29-20)21(24)25)9-14-3-1-2-4-18(14)34-8-6-30-5-7-33-13-16(30)12-32/h1-4,10-11,16,21,32H,5-9,12-13H2,(H2,26,27,28)/t16-/m1/s1
Release date: 2023-03-29
Naturally Occurring Mutations in the MPS1 Gene Predispose Cells to Kinase Inhibitor Drug Resistance. (PDB entry 5AP1)
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): 2.05
R work: 0.1945
R free: 0.2107
Average B factor: 69.04
Crystallization pH: 6.5
Crystal growth procedure: 0.1M MES PH 6.5, 0.2M MGCL2, 10% (W/V) PEG4000, CO-CRYSTALLISED WITH 1MM INHIBITOR
Matthews coefficient: 3.04
Solvent content (%): 59.49
Ligand: 6-{[3-(cyanomethoxy)-4-(1-methyl-1H-pyrazol-4-yl)phenyl]amino}-2-(cyclohexylamino)pyridine-3-carbonitrile (O38)
Ligand formula: C24 H25 N7 O
Ligand molecular weight: 427.502
Ligand SMILES: Cn1cc(cn1)c2ccc(cc2OCC#N)Nc3ccc(c(n3)NC4CCCCC4)C#N
Ligand InChI: InChI=1S/C24H25N7O/c1-31-16-18(15-27-31)21-9-8-20(13-22(21)32-12-11-25)28-23-10-7-17(14-26)24(30-23)29-19-5-3-2-4-6-19/h7-10,13,15-16,19H,2-6,12H2,1H3,(H2,28,29,30)
Release date: 2015-09-23
Caspase-3 Mutant- D9A,D28A,T245D (PDB entry 6BFL)
Macromolecule: Caspase-3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.22.56
Sequence length: 175 residues
Sequence: MENTENSVASKSIKNLEPKIIHGSESMASGISLDNSYKMDYPEMGLCIIINNKNFHKSTGMTSRSGTDVDAANLRETFRNLKYEVRNKNDLTREEIVELMRDVSKEDHSKRSSFVCVLLSHGEEGIIFGTNGPVDLKKITNFFRGDRCRSLTGKPKLFIIQACRGTELDCGIETD
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.87
R work: 0.1541
R free: 0.1897
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 291
Crystal growth procedure: Crystals were obtained at 18 C by the hanging drop vapor diffusion method using 4 mL drops that contained equal volumes of protein and reservoir solutions over a 0.5 mL solution of 100 mM sodium citrate, pH 4.9-5.2, 8-18 % PEG 6000 (w/v), 10 mM DTT, and 3 mM NaN3. Crystals appeared within 3-5 days and were briefly immersed in a cryogenic solution containing 10% MPD (2-methylpentane-2,4-diol) and 90% reservoir solution.
Matthews coefficient: 2.17
Solvent content (%): 43.3
Ligand: AZIDE ION (AZI)
Ligand formula: N3
Ligand molecular weight: 42.02
Ligand SMILES: [N-]=[N+]=[N-]
Ligand InChI: InChI=1S/N3/c1-3-2/q-1
Release date: 2018-02-21