satarupa22/MacromolecularLigandDB huggingface dataset:
APE1 F266A exonuclease substrate complex with a C/T mismatch (PDB entry 5WN3)
Macromolecule: DNA (5'-D(P*TP*CP*GP*AP*CP*GP*GP*AP*TP*CP*C)-3')
Type: DNA, polydeoxyribonucleotide
Source organism: synthetic construct
Sequence length: 11 residues
Sequence: TCGACGGATCC
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2
R work: 0.21
R free: 0.258
Average B factor: 41.79
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5
Crystallization temperature (K): 291
Crystal growth procedure: 7% PEG20000, 100 mM sodium citrate, 15% glycerol, 5 mM calcium chloride
Matthews coefficient: 2.68
Solvent content (%): 54.13
Ligand: CALCIUM ION (CA)
Ligand formula: Ca
Ligand molecular weight: 40.078
Ligand SMILES: [Ca+2]
Ligand InChI: InChI=1S/Ca/q+2
Release date: 2018-02-28
X-ray structure of furin in complex with the canavanine-based inhibitor 4-aminomethyl-phenylacetyl-canavanine-Tle-Arg-Amba (PDB entry 6YD2)
Macromolecule: Furin
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.75
Sequence length: 482 residues
Sequence: DVYQEPTDPKFPQQWYLSGVTQRDLNVKAAWAQGYTGHGIVVSILDDGIEKNHPDLAGNYDPGASFDVNDQDPDPQPRYTQMNDNRHGTRCAGEVAAVANNGVCGVGVAYNARIGGVRMLDGEVTDAVEARSLGLNPNHIHIYSASWGPEDDGKTVDGPARLAEEAFFRGVSQGRGGLGSIFVWASGNGGREHDSCNCDGYTNSIYTLSISSATQFGNVPWYSEACSSTLATTYSSGNQNEKQIVTTDLRQKCTESHTGTSASAPLAAGIIALTLEANKNLTWRDMQHLVVQTSKPAHLNANDWATNGVGRKVSHSYGYGLLDAGAMVALAQNWTTVAPQRKCIIDILTEPKDIGKRLEVRKTVTACLGEPNHITRLEHAQARLTLSYNRRGDLAIHLVSPMGTRSTLLAARPHDYSADGFNDWAFMTTHSWDEDPSGEWVLEIENTSEANNYGTLTKFTLVLYGTASGSLVPRGSHHHHHH
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.1575
R free: 0.1771
Average B factor: 32.05
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293.15
Crystal growth procedure: CRYSTALLIZATION SOLUTION: 100MM MES, 200MM K/NAH2PO4, PH 5.5-6.0, 2 M NACL; RESERVOIR SOLUTION: 3-4M NACL
Matthews coefficient: 3.7
Solvent content (%): 66.74
Ligand: CALCIUM ION (CA)
Ligand formula: Ca
Ligand molecular weight: 40.078
Ligand SMILES: [Ca+2]
Ligand InChI: InChI=1S/Ca/q+2
Release date: 2021-02-17
Crystal structure of SMYD3 with diperodon R enantiomer bound to allosteric site (PDB entry 6YUH)
Macromolecule: Histone-lysine N-methyltransferase SMYD3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1.354
Sequence length: 425 residues
Sequence: PLKVEKFATANRGNGLRAVTPLRPGELLFRSDPLAYTVCKGSRGVVCDRCLLGKEKLMRCSQCRVAKYCSAKCQKKAWPDHKRECKCLKSCKPRYPPDSVRLLGRVVFKLMDGAPSESEKLYSFYDLESNINKLTEDRKEGLRQLVMTFQHFMREEIQDASQLPPAFDLFEAFAKVICNSFTICNAEMQEVGVGLYPSISLLNHSCDPNCSIVFNGPHLLLRAVRDIEVGEELTICYLDMLMTSEERRKQLRDQYCFECDCFRCQTQDKDADMLTGDEQVWKEVQESLKKIEELKAHWKWEQVLAMCQAIISSNSERLPDINIYQLKVLDCAMDACINLGLLEEALFYGTRTMEPYRIFFPGSHPVRGVQVMKVGKLQLHQGMFPQAMKNLRLAFDIMRVTHGREHSLIEDLILLLEECDANIRA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.93
R work: 0.1861
R free: 0.2295
Average B factor: 28.0359
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8.25
Crystallization temperature (K): 293
Crystal growth procedure: Tris buffer 0.1 M, pH 8.25
Magnesium acetate 0.1 M
PEG3350 16%
Matthews coefficient: 2.16
Solvent content (%): 43.12
Ligand: S-ADENOSYLMETHIONINE (SAM)
Ligand formula: C15 H22 N6 O5 S
Ligand molecular weight: 398.437
Ligand SMILES: C[S+](CCC(C(=O)[O-])N)CC1C(C(C(O1)n2cnc3c2ncnc3N)O)O
Ligand InChI: InChI=1S/C15H22N6O5S/c1-27(3-2-7(16)15(24)25)4-8-10(22)11(23)14(26-8)21-6-20-9-12(17)18-5-19-13(9)21/h5-8,10-11,14,22-23H,2-4,16H2,1H3,(H2-,17,18,19,24,25)/t7-,8+,10+,11+,14+,27-/m0/s1
Release date: 2021-01-13
ARHGEF2 PanDDA analysis group deposition -- ARHGEF2 and RhoA in complex with Z57899718 (PDB entry 7G97)
Macromolecule: Rho guanine nucleotide exchange factor 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 245 residues
Sequence: SMEMDEKDFAADSWSLAVDSSFLQQHKKEVMKQQDVIYELIQTELHHVRTLKIMTRLFRTGMLEELHLEPGVVQGLFPCVDELSDIHTRFLSQLLERRRQALCPGSTRNFVIHRLGDLLISQFSGPSAEQMCKTYSEFCSRHSKALKLYKELYARDKRFQQFIRKVTRPAVLKRHGVQECILLVTQRITKYPLLISRILQHSHGIEEERQDLTTALGLVKELLSNVDEGIYQLEKGARLQEIYNR
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.3
R work: 0.1898
R free: 0.249
Average B factor: 36.521
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 293
Crystal growth procedure: 100 mM Tris, 2.6M sodium formate
Matthews coefficient: 2.51
Solvent content (%): 50.96
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: 2023-07-12
Notum Fragment_274 [(4-fluorophenyl)amino]thiourea (PDB entry 7BO1)
Macromolecule: Palmitoleoyl-protein carboxylesterase NOTUM
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.1.98
Sequence length: 382 residues
Sequence: ETGSAQQLNEDLRLHLLLNTSVTCNDGSPAGYYLKESRGSRRWLLFLEGGWYCFNRENCDSRYDTMRRLMSSRDWPRTRTGTGILSSQPEENPYWWNANMVFIPYCSSDVWSGASSKSEKNEYAFMGALIIQEVVRELLGRGLSGAKVLLLAGSSAGGTGVLLNVDRVAEQLEKLGYPAIQVRGLADSGWFLDNKQYRHTDCVDTITCAPTEAIRRGIRYWNGVVPERCRRQFQEGEEWNCFFGYKVYPTLRSPVFVVQWLFDEAQLTVDNVHLTGQPVQEGLRLYIQNLGRELRHTLKDVPASFAPACLSHEIIIRSHWTDVQVKGTSLPRALHCWDRSLHDSHKASKTPLKGCPVHLVDSCPWPHCNPSCPTGTHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.4
R work: 0.1819
R free: 0.2159
Average B factor: 22.5012
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: 2
Solvent content (%): 38.49
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: 2022-03-02
ParkinS65N (PDB entry 6HUE)
Macromolecule: E3 ubiquitin-protein ligase parkin
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2.31
Sequence length: 405 residues
Sequence: MIVFVRFNSSHGFPVEVDSDTSIFQLKEVVAKRQGVPADQLRVIFAGKELRNDWTVQNCDLDQQNIVHIVQRPWRKGQEMNATNSFYVYCKGPCQRVQPGKLRVQCSTCRQATLTLTQGPSCWDDVLIPNRMSGECQSPHCPGTSAEFFFKCGAHPTSDKETSVALHLIATNSRNITCITCTDVRSPVLVFQCNSRHVICLDCFHLYCVTRLNDRQFVHDPQLGYSLPCVAGCPNSLIKELHHFRILGEEQYNRYQQYGAEECVLQMGGVLCPRPGCGAGLLPEPDQRKVTCEGGNGLGCGFAFCRECKEAYHEGECSAVFEASGTTTQAYRVDERAAEQARWEAASKETIKKTTKPCPRCHVPVEKNGGCMHMKCPQPQCRLEWCWNCGCEWNRVCMGDHWFDV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.85
R work: 0.22284
R free: 0.25486
Average B factor: 64.964
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 100mM BIS-TRIS pH 5.5, 200mM LiSO4 and 20% PEG3350
Matthews coefficient: 2.51
Solvent content (%): 51.07
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: 2018-10-17
Metalloproteinase (PDB entry 6QIG)
Macromolecule: Antibody Light Chain
Type: Protein, polypeptide(L)
Source organism: Rattus norvegicus
Sequence length: 213 residues
Sequence: DIELTQAPATLSVTPGDRVSLSCRASQSLSNYLAWYQQKSGEGPRLLINYVSQSISGIPSRFSGSGSGTDYTLSINSVETEDFGMYFCQQYSRLPFTFGAGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNE
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.8
R work: 0.2055
R free: 0.24715
Average B factor: 54.621
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 35% (v/v) pentaerythritol ethoxylate, 200 mM CaCl2, 100 mM HEPES, pH 6.5
Matthews coefficient: 3.96
Solvent content (%): 68.97
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: 2019-09-04
Crystal structure of human tankyrase 2 in complex with 3-(4- chlorophenyl)-5-methyl-1,2-dihydroisoquinolin-1-one (PDB entry 4UVV)
Macromolecule: TANKYRASE-2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.4.2.30
Sequence length: 240 residues
Sequence: MHHHHHHSSGVDLGTENLYFQSMLNTSGSGTILIDLSPDDKEFQSVEEEMQSTVREHRDGGHAGGIFNRYNILKIQKVCNKKLWERYTHRRKEVSEENHNHANERMLFHGSPFVNAIIHKGFDERHAYIGGMFGAGIYFAENSSKSNQYVYGIGGGTGCPVHKDRSCYICHRQLLFCRVTLGKSFLQFSAMKMAHSPPGHHSVTGRPSVNGLALAEYVIYRGEQAYPEYLITYQIMRPEG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.9
R work: 0.16623
R free: 0.19803
Average B factor: 35.195
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, 22% PEG3350, PH 8.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K
Matthews coefficient: 2.4
Solvent content (%): 49
Ligand: 3-(4-chlorophenyl)-5-methylisoquinolin-1(2H)-one (W8L)
Ligand formula: C16 H12 Cl N O
Ligand molecular weight: 269.726
Ligand SMILES: Cc1cccc2c1C=C(NC2=O)c3ccc(cc3)Cl
Ligand InChI: InChI=1S/C16H12ClNO/c1-10-3-2-4-13-14(10)9-15(18-16(13)19)11-5-7-12(17)8-6-11/h2-9H,1H3,(H,18,19)
Release date: 2015-07-29
Crystal structure of full-length HPV31 E6 oncoprotein in complex with LXXLL peptide of ubiquitin ligase E6AP (PDB entry 6SLM)
Macromolecule: Maltose/maltodextrin-binding periplasmic protein,Protein E6,Ubiquitin-protein ligase E3A
Type: Protein, polypeptide(L)
Source organism: Escherichia coli K-12
EC number: 2.3.2.26
Sequence length: 551 residues
Sequence: MKIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGPDIIFWAHDRFGGYAQSGLLAEITPAAAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYNKDLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYENGKYDIKDVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNIDTSAVNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNKDKPLGAVALKSYEEELAKDPRIAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTVDAALAAAQTNAAAMFKNPAERPRKLHELSSALEIPYDELRLNCVYCKGQLTETEVLDFAFTDLTIVYRDDTPHGVCTKCLRFYSKVSEFRWYRYSVYGTTLEKLTNKGISDLLIRCITCQRPLSPEEKQRHLDKKKRFHNIGGRWTGRCIACWRRPRTETQVGSSGSGSGSGSGSAAAESSELTLQELLGEER
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.8
R work: 0.23
R free: 0.2682
Average B factor: 85.21
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 200mM tri-lithium citrate, 20% PEG 33350
protein concentration: 30mg/ml
cryo condition: 35% glycerol
Matthews coefficient: 2.89
Solvent content (%): 57.46
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: 2020-09-09
Ube2T in complex with fragment EM04 (PDB entry 5NGZ)
Macromolecule: Ubiquitin-conjugating enzyme E2 T
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2.23
Sequence length: 197 residues
Sequence: MQRASRLKRELHMLATEPPPGITCWQDKDQMDDLRAQILGGANTPYEKGVFKLEVIIPERYPFEPPQIRFLTPIYHPNIDSAGRICLDVLKLPPKGAWRPSLNIATVLTSIQLLMSEPNPDDPLMADISSEFKYNKPAFLKNARQWTEKHARQKQKADEEEMLDNLPEAGDSRVHNSTQKRKASQLVGIEKKFHPDV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.4
R work: 0.20986
R free: 0.24734
Average B factor: 64.201
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: potassium acetate, Tris-HCl pH 8.5
Matthews coefficient: 3.2
Solvent content (%): 61.55
Ligand: 1-(1,3-benzothiazol-2-yl)methanamine (2BG)
Ligand formula: C8 H8 N2 S
Ligand molecular weight: 164.228
Ligand SMILES: c1ccc2c(c1)nc(s2)CN
Ligand InChI: InChI=1S/C8H8N2S/c9-5-8-10-6-3-1-2-4-7(6)11-8/h1-4H,5,9H2
Release date: 2017-05-03
Structure of RPA70N in complex with PrimPol (fragment 514-525) (PDB entry 5N85)
Macromolecule: Replication protein A 70 kDa DNA-binding subunit
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 123 residues
Sequence: GSHMVGQLSRGAIAAIMQKGDTNIKPILQVINIRPITTGNSPPRYRLLMSDGLNTLSSFMLATQLNPLVEEEQLSSNCVCQIHRFIVNTLKDGRRVVILMELEVLKSAEAVGVKIGNPVPYNE
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2
R work: 0.187
R free: 0.2275
Average B factor: 26.2015
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 4.5
Crystallization temperature (K): 293.15
Crystal growth procedure: 0.2 M Ammonium acetate 0.1 M Sodium acetate 4.5 20 % w/v PEG 3350
Matthews coefficient: 1.81
Solvent content (%): 31.96
Release date: 2017-06-07
Human protein kinase CK2 alpha in complex with 2-cyano-2-propenamide compound 1 (PDB entry 6RB1)
Macromolecule: Casein kinase II subunit alpha
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 336 residues
Sequence: MSGPVPSRARVYTDVNTHRPREYWDYESHVVEWGNQDDYQLVRKLGRGKYSEVFEAINITNNEKVVVKILKPVKKKKIKREIKILENLRGGPNIITLADIVKDPVSRTPALVFEHVNNTDFKQLYQTLTDYDIRFYMYEILKALDYCHSMGIMHRDVKPHNVMIDHEHRKLRLIDWGLAEFYHPGQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRKEPFFHGHDNYDQLVRIAKVLGTEDLYDYIDKYNIELDPRFNDILGRHSRKRWERFVHSENQHLVSPEALDFLDKLLRYDHQSRLTAREAMEHPYFYTVVKDQARMGS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.5
R work: 0.1652
R free: 0.1902
Average B factor: 24.5243
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 293
Crystal growth procedure: 32% PEG4000, 0.2 M Lithium Sulfate
Matthews coefficient: 2
Solvent content (%): 38.54
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: 2020-04-08
Thrombin in Complex with a D-Phe-Pro-p-aminopyridine derivative (PDB entry 6T4A)
Macromolecule: Prothrombin
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.5
Sequence length: 36 residues
Sequence: TFGSGEADCGLRPLFEKKSLEDKTERELLESYIDGR
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.31
R work: 0.1271
R free: 0.148
Average B factor: 17.44
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 20 mM NaH2PO4 (pH 7.5), 350 mM NaCl, 27% (w/v) PEG8000
Matthews coefficient: 2.5
Solvent content (%): 50.89
Ligand: (2~{S})-1-[(2~{R})-2-azanyl-3-phenyl-propanoyl]-~{N}-[(6-azanylpyridin-3-yl)methyl]pyrrolidine-2-carboxamide (J5K)
Ligand formula: C20 H25 N5 O2
Ligand molecular weight: 367.445
Ligand SMILES: c1ccc(cc1)CC(C(=O)N2CCCC2C(=O)NCc3ccc(nc3)N)N
Ligand InChI: InChI=1S/C20H25N5O2/c21-16(11-14-5-2-1-3-6-14)20(27)25-10-4-7-17(25)19(26)24-13-15-8-9-18(22)23-12-15/h1-3,5-6,8-9,12,16-17H,4,7,10-11,13,21H2,(H2,22,23)(H,24,26)/t16-,17+/m1/s1
Release date: 2020-05-13
MTH1 in complex with TH013350 (PDB entry 8A0S)
Macromolecule: 7,8-dihydro-8-oxoguanine triphosphatase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.1.55
Sequence length: 159 residues
Sequence: GSHMGASRLYTLVLVLQPQRVLLGMKKRGFGAGRWNGFGGKVQEGETIEDGARRELQEESGLTVDALHKVGQIVFEFVGEPELMDVHVFCTDSIQGTPVESDEMRPCWFQLDQIPFKDMWPDDSYWFPLLLQKKKFHGYFKFQGQDTILDYTLREVDTV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.4
R work: 0.18001
R free: 0.21188
Average B factor: 15.728
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 292
Crystal growth procedure: 30% PEG6000, 0.1M Sodium Acetate pH4.0, 0.2 M Lithium Sulfate
Matthews coefficient: 2.02
Solvent content (%): 39.21
Ligand: 4-[(2-chlorophenyl)methylsulfanyl]-5~{H}-pyrimidin-2-one (KOX)
Ligand formula: C11 H9 Cl N2 O S
Ligand molecular weight: 252.72
Ligand SMILES: c1ccc(c(c1)CSC2=NC(=O)N=CC2)Cl
Ligand InChI: InChI=1S/C11H9ClN2OS/c12-9-4-2-1-3-8(9)7-16-10-5-6-13-11(15)14-10/h1-4,6H,5,7H2
Release date: 2023-09-20
Fragment-Based Discovery of a Small Molecule Reversible Inhibitor of Bruton's Tyrosine Kinase (PDB entry 4Z3V)
Macromolecule: Tyrosine-protein kinase BTK
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 283 residues
Sequence: GPLPGKNAPSTAGLGYGSWEIDPKDLTFLKELGTGQFGVVKYGKWRGQYDVAIKMIKEGSMSEDEFIEEAKVMMNLSHEKLVQLYGVCTKQRPIFIITEYMANGCLLNYLREMRHRFQTQQLLEMCKDVCEAMEYLESKQFLHRDLAARNCLVNDQGVVKVSDFGLSRYVLDDEYTSSVGSKFPVRWSPPEVLMYSKFSSKSDIWAFGVLMWEIYSLGKMPYERFTNSETAEHIAQGLRLYRPHLASEKVYTIMYSCWHEKADERPTFKILLSNILDVMDEES
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.6
R work: 0.1646
R free: 0.1975
Average B factor: 17.847
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 277
Crystal growth procedure: 10% polyethylene glycol 4000, 20% glycerol, 0.1M imidazole/MES, pH 6.5, 0.12M alcohol mixture
Matthews coefficient: 2.29
Solvent content (%): 46.34
Ligand: IMIDAZOLE (IMD)
Ligand formula: C3 H5 N2
Ligand molecular weight: 69.085
Ligand SMILES: c1c[nH+]c[nH]1
Ligand InChI: InChI=1S/C3H4N2/c1-2-5-3-4-1/h1-3H,(H,4,5)/p+1
Release date: 2015-07-01
KRAS 1-169 G12C Mutant at 313k (PDB entry 8TY9)
Macromolecule: Isoform 2B of GTPase KRas
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.5.2
Sequence length: 169 residues
Sequence: MTEYKLVVVGACGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKCDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQGVDDAFYTLVREIRKHKEK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.43
R work: 0.1919
R free: 0.213
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 200mM Na Acetate pH 3.6
100mM Tris pH 8.5
20% PEG 3350
1mM DTT
Matthews coefficient: 1.96
Solvent content (%): 37.32
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: 2024-08-28
STRUCTURE OF THE WNT DEACYLASE NOTUM - CRYSTAL FORM IV - 2.1A (PDB entry 4UZ5)
Macromolecule: NOTUM
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.1.1
Sequence length: 383 residues
Sequence: ETGSAQQLNEDLRLHLLLNTSVTCNDGSPAGYYLKESRGSRRWLLFLEGGWYCFNRENCDSRYDTMRRLMSSRDWPRTRTGTGILSSQPEENPYWWNANMVFIPYCSSDVWSGASSKSEKNEYAFMGALIIQEVVRELLGRGLSGAKVLLLAGSSAGGTGVLLNVDRVAEQLEKLGYPAIQVRGLADSGWFLDNKQYRHTDCVDTITCAPTEAIRRGIRYWNGVVPERCRRQFQEGEEWNCFFGYKVYPTLRSPVFVVQWLFDEAQLTVDNVHLTGQPVQEGLRLYIQNLGRELRHTLKDVPASFAPACLSHEIIIRSHWTDVQVKGTSLPRALHCWDRSLHDSHKASKTPLKGCPVHLVDSCPWPHCNPSCPTGTKHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.1
R work: 0.18746
R free: 0.2371
Average B factor: 43.492
Crystallization pH: 6
Crystal growth procedure: 10 %W/V PEG4000, 0.01 M CACL2, 0.05 M NACACOD PH 6.0, 0.20 M KCL, 1 MM HEPARIN HEXAMER
Matthews coefficient: 2.5
Solvent content (%): 52
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: 2015-02-25
Human beta-tryptase co-crystal structure with 5-{4-[3-(aminomethyl)phenyl]piperidine-1-carbonyl}-2-(3'-{4-[3-(aminomethyl)phenyl]piperidine-1-carbonyl}-[1,1'-biphenyl]-3-yl)-2-hydroxy-2H-1,3,2-benzodioxaborol-2-uide (PDB entry 6P0P)
Macromolecule: Tryptase alpha/beta-1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.59
Sequence length: 275 residues
Sequence: MLNLLLLALPVLASRAYAAPAPGQALQRVGIVGGQEAPRSKWPWQVSLRVHGPYWMHFCGGSLIHPQWVLTAAHCVGPDVKDLAALRVQLREQHLYYQDQLLPVSRIIVHPQFYTAQIGADIALLELEEPVKVSSHVHTVTLPPASETFPPGMPCWVTGWGDVDNDERLPPPFPLKQVKVPIMENHICDAKYHLGAYTGDDVRIVRDDMLCAGNTRRDSCQGDSGGPLVCKVNGTWLQAGVVSWGEGCAQPNRPGIYTRVTYYLDWIHHYVPKKP
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.55
R work: 0.18037
R free: 0.24889
Average B factor: 33.433
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 4.6
Crystallization temperature (K): 298
Crystal growth procedure: 1.9 mg/mL protein incubated with compound for 30 minutes on ice prior to setup with 30% PEG1500, 0.1 M sodium acetate, pH 4.6, 0.2 M ammonium sulfate
Matthews coefficient: 2.38
Solvent content (%): 48.3
Ligand: (3'-{4-[3-(aminomethyl)phenyl]piperidine-1-carbonyl}[1,1'-biphenyl]-3-yl){4-[3-(aminomethyl)phenyl]piperidin-1-yl}[3,4-di(hydroxy-kappaO)phenyl]methanonato(2-)hydroxyborate(1-) (Y35)
Ligand formula: C44 H46 B N4 O5
Ligand molecular weight: 721.671
Ligand SMILES: [B-]1(Oc2ccc(cc2O1)C(=O)N3CCC(CC3)c4cccc(c4)CN)(c5cccc(c5)c6cccc(c6)C(=O)N7CCC(CC7)c8cccc(c8)CN)O
Ligand InChI: InChI=1S/C44H46BN4O5/c46-28-30-5-1-7-34(23-30)32-15-19-48(20-16-32)43(50)38-11-3-9-36(25-38)37-10-4-12-40(26-37)45(52)53-41-14-13-39(27-42(41)54-45)44(51)49-21-17-33(18-22-49)35-8-2-6-31(24-35)29-47/h1-14,23-27,32-33,52H,15-22,28-29,46-47H2/q-1/t45-/m1/s1
Release date: 2020-03-25
EGFR kinase domain (L858R/V948R) in complex with 2-(6,7-dihydro-5H-pyrrolo[1,2-c]imidazol-1-yl)-2-[6-[2-[4-[[4-(hydroxymethyl)-1-piperidyl]methyl]phenyl]ethynyl]-1-oxo-4-(trifluoromethyl)isoindolin-2-yl]-N-thiazol-2-yl-acetamide (PDB entry 8A2B)
Macromolecule: Epidermal growth factor receptor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 326 residues
Sequence: GSMNQALLRILKETEFKKIKVLGSGAFGTVYKGLWIPEGEKVKIPVAIKELREATSPKANKEILDEAYVMASVDNPHVCRLLGICLTSTVQLITQLMPFGCLLDYVREHKDNIGSQYLLNWCVQIAKGMNYLEDRRLVHRDLAARNVLVKTPQHVKITDFGRAKLLGAEEKEYHAEGGKVPIKWMALESILHRIYTHQSDVWSYGVTVWELMTFGSKPYDGIPASEISSILEKGERLPQPPICTIDVYMIMRKCWMIDADSRPKFRELIIEFSKMARDPQRYLVIQGDERMHLPSPTDSNFYRALMDEEDMDDVVDADEYLIPQQG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.69
R work: 0.2098
R free: 0.2576
Average B factor: 32.128
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8
Crystallization temperature (K): 293
Crystal growth procedure: 25% PEG Smear High, 0.1M Tris, 0.2M magnesium chloride, 10% glycerole
Matthews coefficient: 2.36
Solvent content (%): 47.92
Ligand: (2R)-2-(6,7-dihydro-5H-pyrrolo[1,2-c]imidazol-1-yl)-2-[5-[2-[4-[[4-(hydroxymethyl)piperidin-1-yl]methyl]phenyl]ethynyl]-3-oxidanylidene-7-(trifluoromethyl)-1H-isoindol-2-yl]-N-(1,3-thiazol-2-yl)ethanamide (KY9)
Ligand formula: C35 H33 F3 N6 O3 S
Ligand molecular weight: 674.735
Ligand SMILES: c1cc(ccc1CN2CCC(CC2)CO)C#Cc3cc4c(c(c3)C(F)(F)F)CN(C4=O)C(c5c6n(cn5)CCC6)C(=O)Nc7nccs7
Ligand InChI: InChI=1S/C35H33F3N6O3S/c36-35(37,38)28-17-25(8-5-22-3-6-23(7-4-22)18-42-13-9-24(20-45)10-14-42)16-26-27(28)19-44(33(26)47)31(32(46)41-34-39-11-15-48-34)30-29-2-1-12-43(29)21-40-30/h3-4,6-7,11,15-17,21,24,31,45H,1-2,9-10,12-14,18-20H2,(H,39,41,46)/t31-/m1/s1
Release date: 2022-10-19
human STK19 dimer (PDB entry 7XRB)
Macromolecule: Isoform 2 of Serine/threonine-protein kinase 19
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 232 residues
Sequence: GMESDPLRGEPGSARAAVSELMQLFPRGLFEDALPPIVLRSQVYSLVPDRTVADRQLKELQEQGEIRIVQLGFDLDAHGIIFTEDYRTRVLKACDGRPYAGAVQKFLASVLPACGDLSFQQDQMTQTFGFRDSEITHLVNAGVLTVRDAGSWWLAVPGAGRFIKYFVKGRQAVLSMVRKAKYRELLLSELLGRRAPVVVRLGLTYHVHDLIGAQLVDCISTTSGTLLRLPET
Oligomeric state: Homo 2-mer
Stoichiometry: A2
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.65
R work: 0.1488
R free: 0.1938
Average B factor: 36.494
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 2 M ammonium sulfate, 0.1 M MES pH 6.5, 0.2 M NaCl
Matthews coefficient: 2.53
Solvent content (%): 51.3
Ligand: SULFATE ION (SO4)
Ligand formula: O4 S
Ligand molecular weight: 96.063
Ligand SMILES: [O-]S(=O)(=O)[O-]
Ligand InChI: InChI=1S/H2O4S/c1-5(2,3)4/h(H2,1,2,3,4)/p-2
Release date: 2023-06-07