satarupa22/MacromolecularLigandDB huggingface dataset:
The crystal structure of CK2alpha in complex with CAM4712 (PDB entry 5OTY)
Macromolecule: Casein kinase II subunit alpha
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 342 residues
Sequence: SGPVPSRARVYTDVNTHRPSEYWDYESHVVEWGNQDDYQLVRKLGRGKYSEVFEAINITNNEKVVVKILKPVAAAKIKREIKILENLRGGPNIITLADIVKDPVSRTPALVFEHVNNTDFKQLYQTLTDYDIRFYMYEILKALDYCHSMGIMHRDVKPHNVMIDHEHRKLRLIDWGLAEFYHPGQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRKEPFFHGHDNYDQLVRIAKVLGTEDLYDYIDKYNIELDPRFNDILGRHSRKRWERFVHSENQHLVSPEALDFLDKLLRYDHQSRLTAREAMEHPYFYTVVKREAMEHPYFYTVVK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.48
R work: 0.1694
R free: 0.1922
Average B factor: 27.3
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 298
Crystal growth procedure: 112.5mM Mes pH 6.5, 35% glycerol ethoxylate, 180 mM ammonium acetate
Matthews coefficient: 1.94
Solvent content (%): 36.56
Ligand: ACETATE ION (ACT)
Ligand formula: C2 H3 O2
Ligand molecular weight: 59.044
Ligand SMILES: CC(=O)[O-]
Ligand InChI: InChI=1S/C2H4O2/c1-2(3)4/h1H3,(H,3,4)/p-1
Release date: 2018-02-28
Crystal structure of human AKR1B10 complexed with NADP+ and the inhibitor MK319 (PDB entry 5LIW)
Macromolecule: Aldo-keto reductase family 1 member B10
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.1.1
Sequence length: 316 residues
Sequence: MATFVELSTKAKMPIVGLGTWKSPLGKVKEAVKVAIDAGYRHIDCAYVYQNEHEVGEAIQEKIQEKAVKREDLFIVSKLWPTFFERPLVRKAFEKTLKDLKLSYLDVYLIHWPQGFKSGDDLFPRDDKGNAIGGKATFLDAWEAMEELVDEGLVKALGVSNFSHFQIEKLLNKPGLKYKPVTNQVECHPYLTQEKLIQYCHSKGITVTAYSPLGSPDRPWAKPEDPSLLEDPKIKEIAAKHKKTAAQVLIRFHIQRNVIVIPKSVTPARIVENIQVFDFKLSDEEMATILSFNRNWRACNLLQSSHLEDYPFNAEY
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.75
R work: 0.1778
R free: 0.2086
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 9
Crystallization temperature (K): 293
Crystal growth procedure: 30% PEG 6000, 100 mM sodium cacodylate
Matthews coefficient: 2.51
Solvent content (%): 51.02
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: 2016-07-27
Human P300 complexed with an azaindazole inhibitor (PDB entry 7SZQ)
Macromolecule: Histone acetyltransferase p300
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1.48
Sequence length: 389 residues
Sequence: GSARTRKENKFSAKRLPSTRLGTFLENRVNDFLRRQNHPESGEVTVRVVHASDKTVEVKPGMKARFVDSGEMAESFPYRTKALFAFEEIDGVDLCFFGMHVQEYGSDCPPPNQRRVYISYLDSVHFFRPKCLRTAVYHEILIGYLEYVKKLGYTTGHIWACPPSEGDDYIFHCHPPDQKIPKPKRLQEWFKKMLDKAVSERIVHDYKDIFKQATEDRLTSAKELPYFEGDFWPNVLEESIKELEQEEEERKREENTSNESTDVTKGDSKNAKKKNNKKTSKNKSSLSRGNKKKPGMPNVSNDLSQKLYATMEKHKEVFFVIRLIAGPAANSLPPIVDPDPLIPCDLMDGRDAFLTLARDKHLEFSSLRRAQWSTMCMLVELHTQSQDRF
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.8
R work: 0.1694
R free: 0.2348
Average B factor: 38.5963
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 9.5
Crystallization temperature (K): 277
Crystal growth procedure: 30% PEG400, 0.1 M CHES pH 9.5
Matthews coefficient: 2.25
Solvent content (%): 45.21
Ligand: 1-[1-(4-chlorophenyl)cyclopentane-1-carbonyl]-N-1H-pyrazolo[4,3-b]pyridin-5-yl-D-prolinamide (ETL)
Ligand formula: C23 H24 Cl N5 O2
Ligand molecular weight: 437.922
Ligand SMILES: c1cc(ccc1C2(CCCC2)C(=O)N3CCCC3C(=O)Nc4ccc5c(n4)cn[nH]5)Cl
Ligand InChI: InChI=1S/C23H24ClN5O2/c24-16-7-5-15(6-8-16)23(11-1-2-12-23)22(31)29-13-3-4-19(29)21(30)27-20-10-9-17-18(26-20)14-25-28-17/h5-10,14,19H,1-4,11-13H2,(H,25,28)(H,26,27,30)/t19-/m1/s1
Release date: 2022-11-09
X-ray structure of AAV-2 OBD bound to AAVS1 site 3:1 (PDB entry 4ZQ9)
Macromolecule: Protein Rep68
Type: Protein, polypeptide(L)
Source organism: Adeno-associated virus 2 Srivastava/1982
EC number: 3.6.4.12
Sequence length: 211 residues
Sequence: GSHMPGFYEIVIKVPSDLDEHLPGISDSFVNWVAEKEWELPPDSDMDLNLIEQAPLTVAEKLQRDFLTEWRRVSKAPEALFFVQFEKGESYFHMHVLVETTGVKSMVLGRFLSQIREKLIQRIYRGIEPTLPNWFAVTKTRNGAGGGNKVVDESYIPNFLLPKTQPELQWAWTNMEQYLSACLNLTERKRLVAQHLTHVSQTQEQNKENQN
Oligomeric state: Homo 3-mer
Stoichiometry: A3
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.6
R work: 0.2046
R free: 0.2295
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 273
Crystal growth procedure: PEG 6K, Sodium Citrate, Lithium Chloride
Matthews coefficient: 4.17
Solvent content (%): 70.51
Ligand: MANGANESE (II) ION (MN)
Ligand formula: Mn
Ligand molecular weight: 54.938
Ligand SMILES: [Mn+2]
Ligand InChI: InChI=1S/Mn/q+2
Release date: 2015-09-23
Thrombin in complex with MI2105 (PDB entry 6ROT)
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): 1.339
R work: 0.1371
R free: 0.1574
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7
Crystallization temperature (K): 277
Crystal growth procedure: 20mM sodium dihydrogen phosphate ph 7.5
350mM NaCl
27% PEG 8000
Matthews coefficient: 2.48
Solvent content (%): 50
Ligand: (2~{S})-~{N}-[[5-chloranyl-2-(hydroxymethyl)phenyl]methyl]-1-[2-[(phenylmethyl)sulfonylamino]ethanoyl]pyrrolidine-2-carboxamide (KDQ)
Ligand formula: C22 H26 Cl N3 O5 S
Ligand molecular weight: 479.977
Ligand SMILES: c1ccc(cc1)CS(=O)(=O)NCC(=O)N2CCCC2C(=O)NCc3cc(ccc3CO)Cl
Ligand InChI: InChI=1S/C22H26ClN3O5S/c23-19-9-8-17(14-27)18(11-19)12-24-22(29)20-7-4-10-26(20)21(28)13-25-32(30,31)15-16-5-2-1-3-6-16/h1-3,5-6,8-9,11,20,25,27H,4,7,10,12-15H2,(H,24,29)/t20-/m0/s1
Release date: 2019-11-27
Crystal structure of the Fyn SH3 domain in space group P1 at pH 7.5 (PDB entry 7A2K)
Macromolecule: Tyrosine-protein kinase Fyn
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 60 residues
Sequence: GVTLFVALYDYEARTEDDLSFHKGEKFQILNSSEGDWWEARSLTTGETGYIPSNYVAPVD
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.5
R work: 0.2019
R free: 0.2358
Average B factor: 44.1676
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 298
Crystal growth procedure: 4.5M sodium formate, 0.1M Hepes
Matthews coefficient: 2.66
Solvent content (%): 53.8
Ligand: SODIUM ION ()
Ligand formula: Na
Ligand molecular weight: 22.99
Ligand SMILES: [Na+]
Ligand InChI: InChI=1S/Na/q+1
Release date: 2021-08-25
Crystal structure of human ACBD3 GOLD domain in complex with 3A protein of enterovirus-D68 (fusion protein) (PDB entry 6HM8)
Macromolecule: Golgi resident protein GCP60
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 168 residues
Sequence: GAMESLPVIAAPSMWTRPQIKDFKEKIQQDADSVITVGRGEVVTVRVPTHEEGSYLFWEFATDNYDIGFGVYFEWTDSPNTAVSVHVSESSDDDEEEEENIGCEEKAKKNANKPLLDEIVPVYRRDCHEEVYAGSHQYPGRGVYLLKFDNSYSLWRSKSVYYRVYYTR
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.277
R work: 0.2177
R free: 0.2332
Average B factor: 59.8
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 10% w/v PEG 8000, 6% v/v 1,5-pentanediol, 14% v/v PEG 200, 10 mM spermine, 10 mM spermidine, 10 mM DL-ornithine, 10 mM 1,4-diaminobutane, 200 mM NaCl, 100 mM GlyGly/AMPD pH 8.5
Matthews coefficient: 3.22
Solvent content (%): 61.76
Release date: 2019-07-24
Crystal Structure of human phosphodiesterase 10 in complex with 3-methyl-6-[2-(2-methyl-5-pyrrolidin-1-yl-1,2,4-triazol-3-yl)ethyl]-2-(trifluoromethyl)imidazo[1,2-b]pyridazine (PDB entry 5SIB)
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): 2.54
R work: 0.1715
R free: 0.2486
Average B factor: 52.474
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 (%): 53.46
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: 2022-10-12
Crystal structure of human heparanase in complex with HepMer M04S02a (PDB entry 5E98)
Macromolecule: Heparanase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.2.1.166
Sequence length: 389 residues
Sequence: DPGKKFKNSTYSRSSVDVLYTFANCSGLDLIFGLNALLRTADLQWNSSNAQLLLDYCSSKGYNISWELGNEPNSFLKKADIFINGSQLGEDFIQLHKLLRKSTFKNAKLYGPDVGQPRRKTAKMLKSFLKAGGEVIDSVTWHHYYLNGRTATREDFLNPDVLDIFISSVQKVFQVVESTRPGKKVWLGETSSAYGGGAPLLSDTFAAGFMWLDKLGLSARMGIEVVMRQVFFGAGNYHLVDENFDPLPDYWLSLLFKKLVGTKVLMASVQGSKRRKLRVYLHCTNTDNPRYKEGDLTLYAINLHNVTKYLRLPYPFSNKQVDKYLLRPLGPHGLLSKSVQLNGLTLKMVDDQTLPPLMEKPLRPGSSLGLPAFSYSFFVIRNAKVAACI
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.63
R work: 0.1697
R free: 0.2063
Average B factor: 35.312
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M MES [5.5]
0.1 M MgCl2
17% PEG3350
Matthews coefficient: 2.32
Solvent content (%): 47
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: 2015-11-18
Structure of DYRK1A in complex with compound 53 (PDB entry 7AK2)
Macromolecule: Dual specificity tyrosine-phosphorylation-regulated kinase 1A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.12.1
Sequence length: 359 residues
Sequence: MGSSHHHHHHSSGLVPRGSHMIVKNGEKWMDRYEIDSLIGKGSFGQVVKAYDRVEQEWVAIKIIKNKKAFLNQAQIEVRLLELMNKHDTEMKYYIVHLKRHFMFRNHLCLVFEMLSYNLYDLLRNTNFRGVSLNLTRKFAQQMCTALLFLATPELSIIHCDLKPENILLCNPKRSAIKIVDFGSSCQLGQRIYQYIQSRFYRSPEVLLGMPYDLAIDMWSLGCILVEMHTGEPLFSGANEVDQMNKIVEVLGIPPAHILDQAPKARKFFEKLPDGTWNLKKTKDGKREYKPPGTRKLHNILGVETGGPGGRRAGESGHTVADYLKFKDLILRMLDYDPKTRIQPYYALQHSFFKKTADE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.1
R work: 0.1966
R free: 0.2308
Average B factor: 39.554
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 293
Crystal growth procedure: 15% PEG 4K, 0.2M ammonium sulphate, 0.1M sodium DL-malate buffer pH 5.5
Matthews coefficient: 2.4
Solvent content (%): 48.7
Ligand: PHOSPHATE ION (PO4)
Ligand formula: O4 P
Ligand molecular weight: 94.971
Ligand SMILES: [O-]P(=O)([O-])[O-]
Ligand InChI: InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4)/p-3
Release date: 2021-05-26
PIM1 in complex with Cpd16 (5-amino-N-(5-((4R,5R)-4-amino-5-fluoroazepan-1-yl)-1-methyl-1H-pyrazol-4-yl)-2-(2,6-difluorophenyl)thiazole-4-carboxamide) (PDB entry 6NO9)
Macromolecule: Serine/threonine-protein kinase pim-1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 273 residues
Sequence: PLESQYQVGPLLGSGGFGSVYSGIRVSDNLPVAIKHVEKDRISDWGELPNGTRVPMEVVLLKKVSSGFSGVIRLLDWFERPDSFVLILERPEPVQDLFDFITERGALQEELARSFFWQVLEAVRHCHNCGVLHRDIKDENILIDLNRGELKLIDFGSGALLKDTVYTDFDGTRVYSPPEWIRYHRYHGRSAAVWSLGILLYDMVCGDIPFEHDEEIIRGQVFFRQRVSSECQHLIRWCLALRPSDRPTFEEIQNHPWMQDVLLPQETAEIHLH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.712
R work: 0.1678
R free: 0.2047
Average B factor: 44.8973
Crystallization method: EVAPORATION
Crystallization pH: 8.5
Crystallization temperature (K): 292
Crystal growth procedure: 0.1 M Tris 8.5, 0.1-0.3M LiSO4, and 29-33% PEG 4000
Matthews coefficient: 3.45
Solvent content (%): 64.36
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: 2019-02-27
Crystal structure of human testis Angiotensin-1 converting enzyme in complex with Sampatrilat-Asp. (PDB entry 6F9U)
Macromolecule: Angiotensin-converting enzyme
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.2.1
Sequence length: 591 residues
Sequence: LVTDEAEASKFVEEYDRTSQVVWNEYAGANWNYNTNITTETSKILLQKNMQIAQHTLKYGTQARKFDVNQLQNTTIKRIIKKVQDLERAALPAQELEEYNKILLDMETTYSVATVCHPQGSCLQLEPDLTNVMATSRKYEDLLWAWEGWRDKAGRAILQFYPKYVELINQAARLNGYVDAGDSWRSMYETPSLEQDLERLFQELQPLYLNLHAYVRRALHRHYGAQHINLEGPIPAHLLGNMWAQTWSNIYDLVVPFPSAPSMDTTEAMLKQGWTPRRMFKEADDFFTSLGLLPVPPEFWQKSMLEKPTDGREVVCHASAWDFYNGKDFRIKQCTTVNLEDLVVAHHEMGHIQYFMQYKDLPVALREGANPGFHEAIGDVLALSVSTPKHLHSLNLLSSEGGSDEHDINFLMKMALDKIAFIPFSYLVDQWRWRVFDGSITKENYNQEWWSLRLKYQGLCPPVPRTQGDFDPGAKFHIPSSVPYIRYFVSFIIQFQFHEALCQAAGHTGPLHKCDIYQSKEAGQRLATAMKLGFSRPWPEAMQLITGQPQMSASAMLSYFKPLLDWLRTENELHGEKLGWPQYNWTPNSAR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.9
R work: 0.1672
R free: 0.2088
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 4
Crystallization temperature (K): 289
Crystal growth procedure: 0.1 M MIB Buffer pH 4.0, 5% Glycerol, 15% PEG 3350
Matthews coefficient: 2.36
Solvent content (%): 47.85
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: 2018-03-07
HIF PROLYL HYDROXYLASE 2 (PHD2/EGLN1) IN COMPLEX WITH N-OXALYLGLYCINE (NOG) AND HIF-2 ALPHA CODD (523-542) (PDB entry 7Q5V)
Macromolecule: Egl nine homolog 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11.29
Sequence length: 233 residues
Sequence: GSHMASPNGQTKPLPALKLALEYIVPCMNKHGICVVDDFLGKETGQQIGDEVRALHDTGKFTDGQLVSQKSDSSKDIRGDKITWIEGKEPGCETIGLLMSSMDDLIRHCNGKLGSYKINGRTKAMVACYPGNGTGYVRHVDNPNGDGRCVTCIYYLNKDWDAKVSGGILRIFPEGKAQFADIEPKFDRLLFFWSDRRNPHEVQPAYATRYAITVWYFDADERARAKVKYLTGE
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.17
R work: 0.157
R free: 0.1792
Average B factor: 23.6567
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 298
Crystal growth procedure: Sample: 1.0 mM PHD2, 1.2 mM MnCl2, 2.0 mM NOG, 2 mM 3C, 2-4 mM HIF-2alpha-CODD; Reservoir: 0.31 M Magnesium formate (range: 0.25-0.39 M), 16.6% w/v polyethylene glycol 3350 (range: 18-22%); Sitting drop (200 nl): protein-to-well ratio, 1:1; Cryo-protectant: 15% v/v dilution of reservoir with glycerol
Matthews coefficient: 1.9
Solvent content (%): 35.17
Ligand: MANGANESE (II) ION (MN)
Ligand formula: Mn
Ligand molecular weight: 54.938
Ligand SMILES: [Mn+2]
Ligand InChI: InChI=1S/Mn/q+2
Release date: 2022-11-16
CRYSTAL STRUCTURE OF HUMAN METHIONINE AMINOPEPTIDASE-2 IN COMPLEX WITH AN INHIBITOR 5,6-Difluoro-3-(2-isopropoxy-4-piperazin-1-yl-phenyl)-1H-indole-2-carboxylic acid amide (PDB entry 6QEI)
Macromolecule: Methionine aminopeptidase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.11.18
Sequence length: 378 residues
Sequence: MGPKVQTDPPSVPICDLYPNGVFPKGQECEYPPTQDGRTAAWRTTSEEKKALDQASEEIWNDFREAAEAHRQVRKYVMSWIKPGMTMIEICEKLEDCSRKLIKENGLNAGLAFPTGCSLNNCAAHYTPNAGDTTVLQYDDICKIDFGTHISGRIIDCAFTVTFNPKYDTLLKAVKDATNTGIKCAGIDVRLCDVGEAIQEVMESYEVEIDGKTYQVKPIRNLNGHSIGQYRIHAGKTVPIVKGGEATRMEEGEVYAIETFGSTGKGVVHDDMECSHYMKNFDVGHVPIRLPRTKHLLNVINENFGTLAFCRRWLDRLGESKYLMALKNLCDLGIVDPYPPLCDIKGSYTAQFEHTILLRPTCKEVVSRGDDYHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.189
R free: 0.209
Average B factor: 45.29
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 20% METHANOL, 0.1 M CITRATE, PH 6.0,
Matthews coefficient: 2.66
Solvent content (%): 53.74
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: 2019-05-01
Caspase-3 Mutant- T245A (PDB entry 6BFK)
Macromolecule: Caspase-3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.22.56
Sequence length: 175 residues
Sequence: MENTENSVDSKSIKNLEPKIIHGSESMDSGISLDNSYKMDYPEMGLCIIINNKNFHKSTGMTSRSGTDVDAANLRETFRNLKYEVRNKNDLTREEIVELMRDVSKEDHSKRSSFVCVLLSHGEEGIIFGTNGPVDLKKITNFFRGDRCRSLTGKPKLFIIQACRGTELDCGIETD
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.753
R work: 0.1527
R free: 0.1798
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: 2.21
Solvent content (%): 44.34
Ligand: SODIUM ION ()
Ligand formula: Na
Ligand molecular weight: 22.99
Ligand SMILES: [Na+]
Ligand InChI: InChI=1S/Na/q+1
Release date: 2018-02-21
Crystal structural of human glutathione-specific gamma-glutamylcyclotransferase 2 (ChaC2)mutant with Glutamate 83 replaced by Glutamine (PDB entry 6KY1)
Macromolecule: Glutathione-specific gamma-glutamylcyclotransferase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.3.2.7
Sequence length: 182 residues
Sequence: KVPRGSHMWVFGYGSLIWKVDFPYQDKLVGYITNYSRRFWQGSTDHRGVPGKPGRVVTLVEDPAGCVWGVAYRLPVGKEEEVKAYLDFGQKGGYRTTTVIFYPKDPTTKPFSVLLYIGTCDNPDYLGPAPLEDIAEQIFNAAGPSGRNTEYLFELANSIRNLVPEEADEHLFALEKLVKERL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.04
R work: 0.2254
R free: 0.2555
Average B factor: 59.567
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 295
Crystal growth procedure: 3 M sodium acetate trihydrate (pH 7.0)
Matthews coefficient: 2.57
Solvent content (%): 52.2
Release date: 2020-07-29
Human cathepsin B in complex with the carbamate inhibitor 7 (PDB entry 8B4T)
Macromolecule: Cathepsin B
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.22.1
Sequence length: 255 residues
Sequence: KLPASFDAREQWPQCPTIKEIRDQGSCGSCWAFGAVEAISDRICIHTNAHVSVEVSAEDLLTCCGSMCGDGCNGGYPAEAWNFWTRKGLVSGGLYESHVGCRPYSIPPCEHHVNGARPPCTGEGDTPKCSKICEPGYSPTYKQDKHYGYNSYSVSNSEKDIMAEIYKNGPVEGAFSVYSDFLLYKSGVYQHVTGEMMGGHAIRILGWGVENGTPYWLVANSWNTDWGDNGFFKILRGQDHCGIESEVVAGIPRTD
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.45
R work: 0.1773
R free: 0.2081
Average B factor: 19.795
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 291
Crystal growth procedure: 0.1 M Sodium Acetate pH 5.5, 20% PEG 2000 MME
Matthews coefficient: 2.1
Solvent content (%): 41.31
Ligand: (2S)-2-[[(2S)-2-[(4-chloranylphenoxy)carbonylamino]-3-cyclohexyl-propanoyl]amino]-3-phenyl-propanoic acid (P9F)
Ligand formula: C25 H29 Cl N2 O5
Ligand molecular weight: 472.961
Ligand SMILES: c1ccc(cc1)CC(C(=O)O)NC(=O)C(CC2CCCCC2)NC(=O)Oc3ccc(cc3)Cl
Ligand InChI: InChI=1S/C25H29ClN2O5/c26-19-11-13-20(14-12-19)33-25(32)28-21(15-17-7-3-1-4-8-17)23(29)27-22(24(30)31)16-18-9-5-2-6-10-18/h2,5-6,9-14,17,21-22H,1,3-4,7-8,15-16H2,(H,27,29)(H,28,32)(H,30,31)/t21-,22-/m0/s1
Release date: 2023-10-04
A X-ray cocrystal structure of XMU-MP-5 bound to the ALK kinase domain (PDB entry 7BTT)
Macromolecule: ALK tyrosine kinase receptor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 320 residues
Sequence: QGNPNYCFAGKTSSISDLKEVPRKNITLIRGLGHGAFGEVYEGQVSGMPNDPSPLQVAVKTLPEVCSEQDELDFLMEALIISKFNHQNIVRCIGVSLQSLPRFILLELMAGGDLKSFLRETRPRPSQPSSLAMLDLLHVARDIACGCQYLEENHFIHRDIAARNCLLTCPGPGRVAKIGDFGMARDIYRAGYYRKGGCAMLPVKWMPPEAFMEGIFTSKTDTWSFGVLLWEIFSLGYMPYPSKSNQEVLEFVTSGGRMDPPKNCPGPVYRIMTQCWQHQPEDRPNFAIILERIEYCTQDPDVINTALPIEYGPLVEEEEK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.86
R work: 0.1867
R free: 0.2091
Average B factor: 36.87
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 277.15
Crystal growth procedure: 0.2 M Sodium chloride, 25% w/v Polyethylene glycol 3,350, 0.1 M Tris pH 8.5
Matthews coefficient: 2.17
Solvent content (%): 43.33
Ligand: 2-(dimethylamino)-1-[5-methoxy-6-[[4-[(2-propan-2-ylsulfonylphenyl)amino]-5H-pyrrolo[3,2-d]pyrimidin-2-yl]amino]-2,3-dihydroindol-1-yl]ethanone (F8R)
Ligand formula: C28 H33 N7 O4 S
Ligand molecular weight: 563.671
Ligand SMILES: CC(C)S(=O)(=O)c1ccccc1Nc2c3c(cc[nH]3)nc(n2)Nc4cc5c(cc4OC)CCN5C(=O)CN(C)C
Ligand InChI: InChI=1S/C28H33N7O4S/c1-17(2)40(37,38)24-9-7-6-8-19(24)30-27-26-20(10-12-29-26)31-28(33-27)32-21-15-22-18(14-23(21)39-5)11-13-35(22)25(36)16-34(3)4/h6-10,12,14-15,17,29H,11,13,16H2,1-5H3,(H2,30,31,32,33)
Release date: 2021-04-07
Rapid Discovery of Pyrido[3,4-d]pyrimidine Inhibitors of Monopolar Spindle kinase 1 (MPS1) Using a Structure-Based Hydridization Approach (PDB entry 5EHL)
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): 2.66
R work: 0.1888
R free: 0.2192
Average B factor: 70.46
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 291.15
Crystal growth procedure: 0.1M Bis Tris propane pH 7.5
0.2M MgCl2
0.2M Sodium formate
25% PEG3350
Matthews coefficient: 2.93
Solvent content (%): 58.02
Ligand: 1-[3-tert-butyl-1-(4-methylphenyl)-1H-pyrazol-5-yl]urea (0SQ)
Ligand formula: C15 H20 N4 O
Ligand molecular weight: 272.346
Ligand SMILES: Cc1ccc(cc1)n2c(cc(n2)C(C)(C)C)NC(=O)N
Ligand InChI: InChI=1S/C15H20N4O/c1-10-5-7-11(8-6-10)19-13(17-14(16)20)9-12(18-19)15(2,3)4/h5-9H,1-4H3,(H3,16,17,20)
Release date: 2016-11-09