satarupa22/MacromolecularLigandDB huggingface dataset:
DNA Polymerase Mu, dGTP:At Product State Ternary Complex, 50 mM Mn2+ (225min) (PDB entry 7KT2)
Macromolecule: DNA (5'-D(*CP*GP*TP*AP*G)-3')
Type: DNA, polydeoxyribonucleotide
Source organism: Homo sapiens
Sequence length: 5 residues
Sequence: CGTAG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.499
R work: 0.1679
R free: 0.189
Average B factor: 27.2252
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 85-90mM HEPES pH 7.5, 17-18% PEG 4000
Matthews coefficient: 2.5
Solvent content (%): 50.79
Ligand: SODIUM ION ()
Ligand formula: Na
Ligand molecular weight: 22.99
Ligand SMILES: [Na+]
Ligand InChI: InChI=1S/Na/q+1
Release date: 2022-01-19
Human Aldose Reductase complexed with a ligand with a new scaffold at 1.26 A (PDB entry 4QX4)
Macromolecule: Aldose reductase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.1.1.21
Sequence length: 316 residues
Sequence: MASRILLNNGAKMPILGLGTWKSPPGQVTEAVKVAIDVGYRHIDCAHVYQNENEVGVAIQEKLREQVVKREELFIVSKLWCTYHEKGLVKGACQKTLSDLKLDYLDLYLIHWPTGFKPGKEFFPLDESGNVVPSDTNILDTWAAMEELVDEGLVKAIGISNFNHLQVEMILNKPGLKYKPAVNQIECHPYLTQEKLIQYCQSKGIVVTAYSPLGSPDRPWAKPEDPSLLEDPRIKAIAAKHNKTTAQVLIRFPMQRNLVVIPKSVTPERIAENFKVFDFELSSQDMTTLLSYNRNWRVCALLSCTSHKDYPFHEEF
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.259
R work: 0.1325
R free: 0.1531
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8
Crystallization temperature (K): 291
Crystal growth procedure: 50 mM di-Ammoniumhydrogen citrate pH 5.0 PEG6000= 5 % (m/V) DTT= 5.15 g/L NADP+= 0.66 g/L and Human Aldose Reductase= 15 mg/ml. Afterwards the crystals were soaked into Tris 100 mM 25% (m/V) PEG6000 pH 8.0 saturated with the inhibitor. The well solution for crystallization was 120mM di-Ammonium hydrogen citrate with 20% PEG6000, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Matthews coefficient: 2.18
Solvent content (%): 43.67
Ligand: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE (NAP)
Ligand formula: C21 H28 N7 O17 P3
Ligand molecular weight: 743.405
Ligand SMILES: c1cc(c[n+](c1)C2C(C(C(O2)COP(=O)([O-])OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)OP(=O)(O)O)O)O)O)C(=O)N
Ligand InChI: InChI=1S/C21H28N7O17P3/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(44-46(33,34)35)14(30)11(43-21)6-41-48(38,39)45-47(36,37)40-5-10-13(29)15(31)20(42-10)27-3-1-2-9(4-27)18(23)32/h1-4,7-8,10-11,13-16,20-21,29-31H,5-6H2,(H7-,22,23,24,25,32,33,34,35,36,37,38,39)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
Release date: 2015-04-01
Crystal structure of the ILK ATP-binding deficient mutant (L207W)/alpha-parvin core complex (PDB entry 6MIB)
Macromolecule: Integrin-linked protein kinase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 271 residues
Sequence: MNKHSGIDFKQLNFLTKLNENHSGEWWKGRWQGNDIVVKVLKVRDWSTRKSRDFNEECPRLRIFSHPNVLPVLGACQSPPAPHPTLITHWMPYGSLYNVLHEGTNFVVDQSQAVKFALDMARGMAFLHTLEPLIPRHALNSRSVMIDEDMTARISMADVKFSFQSPGRMYAPAWVAPEALQKKPEDTNRRSADMWSFAVLLWELVTREVPFADLSNMEIGMKVALEGLRPTIPPGISPHVSKLMKICMNEDPAKRPKFDMIVPILEKMQDK
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.16016
R free: 0.20778
Average B factor: 22.898
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.4
Crystallization temperature (K): 277
Crystal growth procedure: 16% PEG 3,350, 0.1 M Bis-Tris Propane, pH 7.4, 5% 1-Propanol
Matthews coefficient: 2.44
Solvent content (%): 49.49
Release date: 2018-11-07
Crystal structure of the Fyn SH3 domain A95S-D99T mutant in space group P21 (PDB entry 7A2N)
Macromolecule: Tyrosine-protein kinase Fyn
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 60 residues
Sequence: GVTLFVALYDYESRTETDLSFHKGEKFQILNSSEGDWWEARSLTTGETGYIPSNYVAPVD
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.4
R work: 0.1698
R free: 0.2035
Average B factor: 18.4293
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 4
Crystallization temperature (K): 298
Crystal growth procedure: 4.5 M sodium formate, 0.1 sodium acetate
Matthews coefficient: 2.68
Solvent content (%): 54.12
Ligand: FORMIC ACID (FMT)
Ligand formula: C H2 O2
Ligand molecular weight: 46.025
Ligand SMILES: C(=O)O
Ligand InChI: InChI=1S/CH2O2/c2-1-3/h1H,(H,2,3)
Release date: 2021-08-25
BRAF in complex with N-(4-methyl-3-(1-methyl-2-oxo-2,3-dihydro-1H-benzo[d]imidazol-5-yl)phenyl)-3-(trifluoromethyl)benzamide. (PDB entry 6N0Q)
Macromolecule: Serine/threonine-protein kinase B-raf
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 281 residues
Sequence: GSDSSDDWEIPDGQITVGQRIGSGSFGTVYKGKWHGDVAVKMLNVTAPTPQQLQAFKNEVGVLRKTRHVNILLFMGYSTKPQLAIVTQWCEGSSLYHHLHIIETKFEMIKLIDIARQTAQGMDYLHAKSIIHRDLKSNNIFLHEDLTVKIGDFGLATVKSRWSGSHQFEQLSGSILWMAPEVIRMQDKNPYSFQSDVYAFGIVLYELMTGQLPYSNINNRDQIIFMVGRGYLSPDLSKVRSNCPKAMKRLMAECLKKKRDERPLFPQILASIELLARSLPK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.04
R work: 0.181
R free: 0.213
Average B factor: 42.23
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 100 mM Tris pH 8.3, 15% PEG8000, and 25% glycerol
Matthews coefficient: 3.09
Solvent content (%): 60.17
Ligand: N-[4-methyl-3-(1-methyl-2-oxo-2,3-dihydro-1H-benzimidazol-5-yl)phenyl]-3-(trifluoromethyl)benzamide (K7S)
Ligand formula: C23 H18 F3 N3 O2
Ligand molecular weight: 425.403
Ligand SMILES: Cc1ccc(cc1c2ccc3c(c2)NC(=O)N3C)NC(=O)c4cccc(c4)C(F)(F)F
Ligand InChI: InChI=1S/C23H18F3N3O2/c1-13-6-8-17(27-21(30)15-4-3-5-16(10-15)23(24,25)26)12-18(13)14-7-9-20-19(11-14)28-22(31)29(20)2/h3-12H,1-2H3,(H,27,30)(H,28,31)
Release date: 2019-10-23
Crystal Structure of KRAS-Q61R (GMPPNP-bound) in complex with RAS-binding domain (RBD) and cysteine-rich domain (CRD) of RAF1/CRAF (PDB entry 6XGU)
Macromolecule: RAF proto-oncogene serine/threonine-protein kinase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 137 residues
Sequence: SKTSNTIRVFLPNKQRTVVNVRNGMSLHDCLMKALKVRGLQPECCAVFRLLHEHKGKKARLDWNTDAASLIGEELQVDFLDHVPLTTHNFARKTFLKLAFCDICQKFLLNGFRCQTCGYKFHEHCSTKVPTMCVDWS
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.7
R work: 0.1873
R free: 0.2357
Average B factor: 94.6213
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.8
Crystallization temperature (K): 293
Crystal growth procedure: 100 mM Tris 7.8, 200 mM KBr, 200 mM KSCN, 3% PGA, 0.35 mM D-myo-phosphatidylinositol 3,4,5-triphosphate
Matthews coefficient: 3.21
Solvent content (%): 61.73
Ligand: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER (GNP)
Ligand formula: C10 H17 N6 O13 P3
Ligand molecular weight: 522.196
Ligand SMILES: c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(NP(=O)(O)O)O)O)O)N=C(NC2=O)N
Ligand InChI: InChI=1S/C10H17N6O13P3/c11-10-13-7-4(8(19)14-10)12-2-16(7)9-6(18)5(17)3(28-9)1-27-32(25,26)29-31(23,24)15-30(20,21)22/h2-3,5-6,9,17-18H,1H2,(H,25,26)(H3,11,13,14,19)(H4,15,20,21,22,23,24)/t3-,5-,6-,9-/m1/s1
Release date: 2021-01-13
thermostabilised 7TM domain of human mGlu5 receptor bound to photoswitchable ligand alloswitch-1 (PDB entry 7P2L)
Macromolecule: Metabotropic glutamate receptor 5,Endolysin,Metabotropic glutamate receptor 5
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.2.1.17
Sequence length: 464 residues
Sequence: MVSAIVLYVLLAAAAHSAFAAASPVQYLRWGDPAPIAAVVFACLGLLATLFVTVVFIIYRDTPVVKSSSRELCYIILAGICLGYLCTFCLIAKPKQIYCYLQRIGIGLSPAMSYSALVTKTYRAARILAMSKKNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDAYKICTKKPRFMSACAQLVIAFILICIQLGIIVALFIMEPPDIMHDYPSIREVYLICNTTNLGVVAPLGYNGLLILACTFYAFKTRNVPANFNEAKYIAFTMYTTCIIWLAFVPIYFGSNYKIITMCFSVSLSATVALGCMFVPKVYIILAKPERNVRSAAAAHHHHHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.54
R work: 0.2267
R free: 0.2853
Average B factor: 69.807
Crystallization method: LIPIDIC CUBIC PHASE
Crystallization temperature (K): 295
Crystal growth procedure: 0.15-0.25 M ammonium phosphate dibasic, 22-24 % polyethylene glycol 400, either with 0.10 M 2-(N-morpholino)ethanesulfonic acid (MES) pH 6.7-6.8 or 0.1 M HEPES pH 6.8
Matthews coefficient: 2.72
Solvent content (%): 54.83
Ligand: 2-chloranyl-~{N}-[2-methoxy-4-[(~{E})-pyridin-2-yldiazenyl]phenyl]benzamide (4YI)
Ligand formula: C19 H15 Cl N4 O2
Ligand molecular weight: 366.801
Ligand SMILES: COc1cc(ccc1NC(=O)c2ccccc2Cl)N=Nc3ccccn3
Ligand InChI: InChI=1S/C19H15ClN4O2/c1-26-17-12-13(23-24-18-8-4-5-11-21-18)9-10-16(17)22-19(25)14-6-2-3-7-15(14)20/h2-12H,1H3,(H,22,25)/b24-23+
Release date: 2021-09-08
Crystal structure of kinase (PDB entry 5Y86)
Macromolecule: Dual specificity tyrosine-phosphorylation-regulated kinase 3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.12.1
Sequence length: 588 residues
Sequence: MGGTARGPGRKDAGPPGAGLPPQQRRLGDGVYDTFMMIDETKCPPCSNVLCNPSEPPPPRRLNMTTEQFTGDHTQHFLDGGEMKVEQLFQEFGNRKSNTIQSDGISDSEKCSPTVSQGKSSDCLNTVKSNSSSKAPKVVPLTPEQALKQYKHHLTAYEKLEIINYPEIYFVGPNAKKRHGVIGGPNNGGYDDADGAYIHVPRDHLAYRYEVLKIIGKGSFGQVARVYDHKLRQYVALKMVRNEKRFHRQAAEEIRILEHLKKQDKTGSMNVIHMLESFTFRNHVCMAFELLSIDLYELIKKNKFQGFSVQLVRKFAQSILQSLDALHKNKIIHCDLKPENILLKHHGRSSTKVIDFGSSCFEYQKLYTYIQSRFYRAPEIILGSRYSTPIDIWSFGCILAELLTGQPLFPGEDEGDQLACMMELLGMPPPKLLEQSKRAKYFINSKGIPRYCSVTTQADGRVVLVGGRSRRGKKRGPPGSKDWGTALKGCDDYLFIEFLKRCLHWDPSARLTPAQALRHPWISKSVPRPLTTIDKVSGKRVVNPASAFQGLGSKLPPVVGIANKLKANLMSETNGSIPLCSVLPKLIS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.9
R work: 0.16685
R free: 0.19642
Average B factor: 21.25
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.2
Crystallization temperature (K): 290.15
Crystal growth procedure: 1M NaH2PO4 and K2HPO4 (pH8.2)
Matthews coefficient: 1.85
Solvent content (%): 33.4
Ligand: 7-METHOXY-1-METHYL-9H-BETA-CARBOLINE (HRM)
Ligand formula: C13 H12 N2 O
Ligand molecular weight: 212.247
Ligand SMILES: Cc1c2c(ccn1)c3ccc(cc3[nH]2)OC
Ligand InChI: InChI=1S/C13H12N2O/c1-8-13-11(5-6-14-8)10-4-3-9(16-2)7-12(10)15-13/h3-7,15H,1-2H3
Release date: 2018-05-02
Crystal structure of human BRM in complex with compound 15 (PDB entry 6EG3)
Macromolecule: Maltose/maltodextrin-binding periplasmic protein,Probable global transcription activator SNF2L2
Type: Protein, polypeptide(L)
Source organism: Escherichia coli O157:H7
EC number: 3.6.4
Sequence length: 621 residues
Sequence: KIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGPDIIFWAHDRFGGYAQSGLLAEITPAAAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYNKDLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYAAGKYDIKDVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNIDTSAVNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNKDKPLGAVALKSYEEELAKDPRIAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTVDEALKDAQTNAAAAHAISERVEKQSALLINGTLKHYQLQGLEWMVSLYNNNLNGILADEMGLGKTIQTIALITYLMEHKRLNGPYLIIVPLSTLSNWTYEFDKWAPSVVKISYKGTPAMRRSLVPQLRSGKFNVLLTTYEYIIKDKHILAKIRWKYMIVDEGHRMKNHHCKLTQVLNTHYVAPRRILLTGTPLQNKLPELWALLNFLLPTIFKSCSTFEQWFNAPFAMTGERVDLNEEETILIIRRLHKVLRPFLLRRLKKEVE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.84
R work: 0.2287
R free: 0.2668
Average B factor: 78.03
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 277
Crystal growth procedure: 100mM Tris pH7, 14% Ethanol
Matthews coefficient: 4.06
Solvent content (%): 69.68
Ligand: 3-[(4-{[(2-chloropyridin-4-yl)carbamoyl]amino}pyridin-2-yl)ethynyl]benzoic acid (J7G)
Ligand formula: C20 H13 Cl N4 O3
Ligand molecular weight: 392.795
Ligand SMILES: c1cc(cc(c1)C(=O)O)C#Cc2cc(ccn2)NC(=O)Nc3ccnc(c3)Cl
Ligand InChI: InChI=1S/C20H13ClN4O3/c21-18-12-17(7-9-23-18)25-20(28)24-16-6-8-22-15(11-16)5-4-13-2-1-3-14(10-13)19(26)27/h1-3,6-12H,(H,26,27)(H2,22,23,24,25,28)
Release date: 2018-10-31
CDK2 in complex with AZD5438 (PDB entry 6GUH)
Macromolecule: Cyclin-dependent kinase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.22
Sequence length: 306 residues
Sequence: GPLGSPEFMENFQKVEKIGEGTYGVVYKARNKLTGEVVALKKIRLDTETEGVPSTAIREISLLKELNHPNIVKLLDVIHTENKLYLVFEFLHQDLKKFMDASALTGIPLPLIKSYLFQLLQGLAFCHSHRVLHRDLKPQNLLINTEGAIKLADFGLARAFGVPVRTYTHEVVTLWYRAPEILLGCKYYSTAVDIWSLGCIFAEMVTRRALFPGDSEIDQLFRIFRTLGTPDEVVWPGVTSMPDYKPSFPKWARQDFSKVVPPLDEDGRSLLSQMLHYDPNKRISAKAALAHPFFQDVTKPVPHLRL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.5
R work: 0.19893
R free: 0.2433
Average B factor: 33.24
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 10MG/ML CDK2 10% V/V PEG3350, 50 MM HEPES/NAOH, 50 MM NA/K PHOSPHATE, PH 7.5
Matthews coefficient: 1.97
Solvent content (%): 37.62
Ligand: 4-(2-methyl-3-propan-2-yl-imidazol-4-yl)-~{N}-(4-methylsulfonylphenyl)pyrimidin-2-amine (FB8)
Ligand formula: C18 H21 N5 O2 S
Ligand molecular weight: 371.457
Ligand SMILES: Cc1ncc(n1C(C)C)c2ccnc(n2)Nc3ccc(cc3)S(=O)(=O)C
Ligand InChI: InChI=1S/C18H21N5O2S/c1-12(2)23-13(3)20-11-17(23)16-9-10-19-18(22-16)21-14-5-7-15(8-6-14)26(4,24)25/h5-12H,1-4H3,(H,19,21,22)
Release date: 2018-12-05
Crystal Structure of human phosphodiesterase 10 in complex with 1-[2-[2-(5,8-dimethyl-[1,2,4]triazolo[1,5-c]pyrimidin-2-yl)ethyl]-1-methylimidazol-4-yl]pyrrolidin-2-one (PDB entry 5SJG)
Macromolecule: cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.4.17
Sequence length: 343 residues
Sequence: GSSICTSEEWQGLMQFTLPVRLCKEIELFHFDIGPFENMWPGIFVYMVHRSCGTSCFELEKLCRFIMSVKKNYRRVPYHNWKHAVTVAHCMYAILQNNHTLFTDLERKGLLIACLCHDLDHRGFSNSYLQKFDHPLAALYSTSTMEQHHFSQTVSILQLEGHNIFSTLSSSEYEQVLEIIRKAIIATDLALYFGNRKQLEEMYQTGSLNLNNQSHRDRVIGLMMTACDLCSVTKLWPVTKLTANDIYAEFWAEGDEMKKLGIQPIPMMDRDKKDEVPQGQLGFYNAVAIPCYTTLTQILPPTEPLLKACRDNLSQWEKVIRGEETATWISSPSVAQKAAASED
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.97
R work: 0.1761
R free: 0.2242
Average B factor: 35.422
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 295
Crystal growth procedure: 5-20 mg/mL protein in 25mM HEPES/NaOH pH7.5, 150mM NaCl, 50mM BME mixed 1:1 with reservoir 0.1M HEPES/NaOH pH7.5, 30% PEG550MME, 50mM MgCl2
Matthews coefficient: 2.64
Solvent content (%): 53.33
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: 2022-10-12
Crystal structure of MTH1 in complex with compound 32 (PDB entry 7N13)
Macromolecule: 7,8-dihydro-8-oxoguanine triphosphatase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.1.55
Sequence length: 158 residues
Sequence: GSMGASRLYTLVLVLQPQRVLLGMKKRGFGAGRWNGFGGKVQEGETIEDGARRELQEESGLTVDALHKVGQIVFEFVGEPELMDVHVFCTDSIQGTPVESDEMRPCWFQLDQIPFKDMWPDDSYWFPLLLQKKKFHGYFKFQGQDTILDYTLREVDTV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.59
R work: 0.2116
R free: 0.254
Average B factor: 17.759
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 3.5
Crystallization temperature (K): 277
Crystal growth procedure: 23% (w/v) PEG 6k, 200 mM lithium sulfate, 100 mM sodium acetate pH 3.5
Matthews coefficient: 2.21
Solvent content (%): 44
Ligand: 4-anilino-6-[4-(butylcarbamoyl)-3-fluorophenyl]-N-cyclopropyl-7-fluoroquinoline-3-carboxamide (ZRV)
Ligand formula: C30 H28 F2 N4 O2
Ligand molecular weight: 514.566
Ligand SMILES: CCCCNC(=O)c1ccc(cc1F)c2cc3c(cc2F)ncc(c3Nc4ccccc4)C(=O)NC5CC5
Ligand InChI: InChI=1S/C30H28F2N4O2/c1-2-3-13-33-29(37)21-12-9-18(14-25(21)31)22-15-23-27(16-26(22)32)34-17-24(30(38)36-20-10-11-20)28(23)35-19-7-5-4-6-8-19/h4-9,12,14-17,20H,2-3,10-11,13H2,1H3,(H,33,37)(H,34,35)(H,36,38)
Release date: 2021-11-03
TGF-BETA RECEPTOR TYPE 1 KINASE DOMAIN (T204D) IN COMPLEX WITH 6-[1-(2,2-DIFLUOROETHYL)-4-(6-METHYLPYRIDIN-2-YL)-1H-IMIDAZOL-5-YL]IMIDAZO[1,2-A]PYRIDINE (PDB entry 5QTZ)
Macromolecule: TGF-beta receptor type-1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.30
Sequence length: 307 residues
Sequence: GHMTIARDIVLQESIGKGRFGEVWRGKWRGEEVAVKIFSSREERSWFREAEIYQTVMLRHENILGFIAADNKDNGTWTQLWLVSDYHEHGSLFDYLNRYTVTVEGMIKLALSTASGLAHLHMEIVGTQGKPAIAHRDLKSKNILVKKNGTCCIADLGLAVRHDSATDTIDIAPNHRVGTKRYMAPEVLDDSINMKHFESFKRADIYAMGLVFWEIARRCSIGGIHEDYQLPYYDLVPSDPSVEEMRKVVCEQKLRPNIPNRWQSCEALRVMAKIMRECWYANGAARLTALRIKKTLSQLSQQEGIKM
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.83
R work: 0.169
R free: 0.1999
Average B factor: 24.26
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.6
Crystallization temperature (K): 277
Crystal growth procedure: 23%(w/v) PEG3350, 3%(v/v) glcyerol
Matthews coefficient: 2.08
Solvent content (%): 40.75
Ligand: 6-[1-(2,2-difluoroethyl)-4-(6-methylpyridin-2-yl)-1H-imidazol-5-yl]imidazo[1,2-a]pyridine (QMY)
Ligand formula: C18 H15 F2 N5
Ligand molecular weight: 339.342
Ligand SMILES: Cc1cccc(n1)c2c(n(cn2)CC(F)F)c3ccc4nccn4c3
Ligand InChI: InChI=1S/C18H15F2N5/c1-12-3-2-4-14(23-12)17-18(25(11-22-17)10-15(19)20)13-5-6-16-21-7-8-24(16)9-13/h2-9,11,15H,10H2,1H3
Release date: 2020-02-05
Crystal structure of DAPK1 in the presence of bromide ions. (PDB entry 5AV1)
Macromolecule: Death-associated protein kinase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 293 residues
Sequence: MTVFRQENVDDYYDTGEELGSGQFAVVKKCREKSTGLQYAAKFIKKRRTKSSRRGVSREDIEREVSILKEIQHPNVITLHEVYENKTDVILILELVAGGELFDFLAEKESLTEEEATEFLKQILNGVYYLHSLQIAHFDLKPENIMLLDRNVPKPRIKIIDFGLAHKIDFGNEFKNIFGTPEFVAPEIVNYEPLGLEADMWSIGVITYILLSGASPFLGDTKQETLANVSAVNYEFEDEYFSNTSALAKDFIRRLLVKDPKKRMTIQDSLQHPWIKPKDTQQALSLEHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.5
R work: 0.186
R free: 0.2147
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 2 M ammonium sulfate, 0.1 M MES
Matthews coefficient: 1.91
Solvent content (%): 35.53
Ligand: BROMIDE ION (BR)
Ligand formula: Br
Ligand molecular weight: 79.904
Ligand SMILES: [Br-]
Ligand InChI: InChI=1S/BrH/h1H/p-1
Release date: 2015-10-07
Death-associated Protein Kinase 1 (DAPK1) catalytic and auto-regulatory domains with S289E and S308A mutations (PDB entry 6QMO)
Macromolecule: Death-associated protein kinase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 313 residues
Sequence: GPMATVFRQENVDDYYDTGEELGSGQFAVVKKCREKSTGLQYAAKFIKKRRTKSSRRGVSREDIEREVSILKEIQHPNVITLHEVYENKTDVILILELVAGGELFDFLAEKESLTEEEATEFLKQILNGVYYLHSLQIAHFDLKPENIMLLDRNVPKPRIKIIDFGLAHKIDFGNEFKNIFGTPEFVAPEIVNYEPLGLEADMWSIGVITYILLSGASPFLGDTKQETLANVSAVNYEFEDEYFSNTSALAKDFIRRLLVKDPKKRMTIQDSLQHPWIKPKDTQQALSRKAEAVNMEKFKKFAARKKWKQAVR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.87
R work: 0.1859
R free: 0.2236
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 292.15
Crystal growth procedure: 20% PEG 3350, 0.2M magnesium formate
Matthews coefficient: 2.32
Solvent content (%): 47.01
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: 2019-08-28
human purine nucleoside phosphorylase in complex with JS-379 (PDB entry 7ZSN)
Macromolecule: Purine nucleoside phosphorylase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.4.2.1
Sequence length: 289 residues
Sequence: MENGYTYEDYKNTAEWLLSHTKHRPQVAIICGSGLGGLTDKLTQAQIFDYGEIPNFPRSTVPGHAGRLVFGFLNGRACVMMQGRFHMYEGYPLWKVTFPVRVFHLLGVDTLVVTNAAGGLNPKFEVGDIMLIRDHINLPGFSGQNPLRGPNDERFGDRFPAMSDAYDRTMRQRALSTWKQMGEQRELQEGTYVMVAGPSFETVAECRVLQKLGADAVGMSTVPEVIVARHCGLRVFGFSLITNKVIMDYESLEKANHEEVLAAGKQAAQKLEQFVSILMASIPLPDKAS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.36
R work: 0.2204
R free: 0.2587
Average B factor: 66.426
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291.15
Crystal growth procedure: 15.00 % w/v Polyethylene glycol 8,000; 500 mM Lithium sulfate; 100 mM Sodium acetate; pH 4.6; 1 mM TEW
Solvent content (%): 74.8
Ligand: 6-tungstotellurate(VI) (TEW)
Ligand formula: O24 Te W6
Ligand molecular weight: 1614.626
Ligand SMILES: [O-]=[W]123(O[W]45(=O)(O1[Te]6789O2[W]1(=O)(O3)(O6[W]2(=O)(O1)(O7[W]1(=O)(O2)(O8[W](=O)(O94)(O5)(O1)[O-])[O-])[O-])[O-])[O-])[O]
Ligand InChI: InChI=1S/O6Te.H2O.17O.6W/c1-7(2,3,4,5)6;;;;;;;;;;;;;;;;;;;;;;;;/h;1H2;;;;;;;;;;;;;;;;;;;;;;;/q;;;;;;;;;;;;;6*-1;;;;;;+1/p-1
Release date: 2023-05-17
Crystal structure of the bromodomain of ATAD2 with AZ13824374 (PDB entry 7Q6T)
Macromolecule: ATPase family AAA domain-containing protein 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.1.3
Sequence length: 130 residues
Sequence: SMQEEDTFRELRIFLRNVTHRLAIDKRFRVFTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLRDIDLICSNALEYNPDRDPGDRLIRHRACALRDTAYAIIKEELDEDFEQLCEEIQESR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.05
R work: 0.1971
R free: 0.2155
Average B factor: 33.26
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 6.25
Crystallization temperature (K): 293
Crystal growth procedure: ATAD2 (981-1108) at 12 mg/ml in 25 mM Tris pH 9.7, 300 mM NaCl, 0.5 mM TCEP crystallised from 20% PEG 3350, 0.2 M ammonium sulfate, 0.1 M Bis-Tris pH 6.25. Ligands were introduced by soaking, cryo-protection with 20 % glycerol.
Matthews coefficient: 4.11
Solvent content (%): 70.06
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: 2022-01-19
Crystal structure of the ES2 intermediate form of human hydroxymethylbilane synthase (PDB entry 7CCZ)
Macromolecule: Porphobilinogen deaminase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.5.1.61
Sequence length: 361 residues
Sequence: MSGNGNAAATAEENSPKMRVIRVGTRKSQLARIQTDSVVATLKASYPGLQFEIIAMSTTGDKILDTALSKIGEKSLFTKELEHALEKNEVDLVVHSLKDLPTVLPPGFTIGAICKRENPHDAVVFHPKFVGKTLETLPEKSVVGTSSLRRAAQLQRKFPHLEFRSIRGNLNTRLRKLDEQQEFSAIILATAGLQRMGWHNRVGQILHPEECMYAVGQGALGVEVRAKDQDILDLVGVLHDPETLLRCIAERAFLRHLEGGCSVPVAVHTAMKDGQLYLTGGVWSLDGSDSIQETMQATIHVPAQHEDGPEDDPQLVGITARNIPRGPQLAAQNLGISLANLLLSKGAKNILDVARQLNDAH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.79
R work: 0.1982
R free: 0.2428
Average B factor: 34.85
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.3
Crystallization temperature (K): 293
Crystal growth procedure: PEG 3350, diammonium hydrogen citrate, dithiothreitol
Matthews coefficient: 2.23
Solvent content (%): 44.96
Ligand: 3-[4-(2-hydroxy-2-oxoethyl)-5-[[4-(2-hydroxy-2-oxoethyl)-5-[[4-(2-hydroxy-2-oxoethyl)-5-[[4-(2-hydroxy-2-oxoethyl)-3-(3-hydroxy-3-oxopropyl)-5-methyl-1~{H}-pyrrol-2-yl]methyl]-3-(3-hydroxy-3-oxopropyl)-1~{H}-pyrrol-2-yl]methyl]-3-(3-hydroxy-3-oxopropyl)-1~{H}-pyrrol-2-yl]methyl]-1~{H}-pyrrol-3-yl]propanoic acid (7J8)
Ligand formula: C40 H46 N4 O16
Ligand molecular weight: 838.81
Ligand SMILES: Cc1c(c(c([nH]1)Cc2c(c(c([nH]2)Cc3c(c(c([nH]3)Cc4c(c(c[nH]4)CCC(=O)O)CC(=O)O)CCC(=O)O)CC(=O)O)CCC(=O)O)CC(=O)O)CCC(=O)O)CC(=O)O
Ligand InChI: InChI=1S/C40H46N4O16/c1-18-23(10-37(53)54)20(3-7-34(47)48)28(42-18)15-31-26(13-40(59)60)22(5-9-36(51)52)30(44-31)16-32-25(12-39(57)58)21(4-8-35(49)50)29(43-32)14-27-24(11-38(55)56)19(17-41-27)2-6-33(45)46/h17,41-44H,2-16H2,1H3,(H,45,46)(H,47,48)(H,49,50)(H,51,52)(H,53,54)(H,55,56)(H,57,58)(H,59,60)
Release date: 2021-03-17