satarupa22/MacromolecularLigandDB huggingface dataset:
Structure of DYRK1A in complex with compound 51 (PDB entry 7AJY)
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): 2.2
R work: 0.1832
R free: 0.2251
Average B factor: 33.603
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 30% PegMME 5k, 0.1M ammonium sulphate, 0.1M ADA buffer pH 6.5
Matthews coefficient: 2.4
Solvent content (%): 48.85
Ligand: 4-[2-methyl-3-[(2~{R})-2-phenoxypropyl]imidazo[4,5-b]pyridin-5-yl]pyridine-2,6-diamine (RKZ)
Ligand formula: C21 H22 N6 O
Ligand molecular weight: 374.439
Ligand SMILES: Cc1nc2ccc(nc2n1CC(C)Oc3ccccc3)c4cc(nc(c4)N)N
Ligand InChI: InChI=1S/C21H22N6O/c1-13(28-16-6-4-3-5-7-16)12-27-14(2)24-18-9-8-17(25-21(18)27)15-10-19(22)26-20(23)11-15/h3-11,13H,12H2,1-2H3,(H4,22,23,26)/t13-/m1/s1
Release date: 2021-05-26
Crystal Structure of Factor VIIa in complex with 1-[[3-[2-hydroxy-3-(1H-pyrrolo[3,2-c]pyridin-2-yl)phenyl]phenyl]methyl]-3-phenylurea (PDB entry 5PAB)
Macromolecule: Coagulation factor VII heavy chain
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.21
Sequence length: 254 residues
Sequence: IVGGKVCPKGECPWQVLLLVNGAQLCGGTLINTIWVVSAAHCFDKIKNWRNLIAVLGEHDLSEHDGDEQSRRVAQVIIPSTYVPGTTNHDIALLRLHQPVVLTDHVVPLCLPERTFSERTLAFVRFSLVSGWGQLLDRGATALELMVLNVPRLMTQDCLQQSRKVGDSPNITEYMFCAGYSDGSKDSCKGDSGGPHATHYRGTWYLTGIVSWGQGCATVGHFGVYTRVSQYIEWLQKLMRSEPRPGVLLRAPFP
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.99
R work: 0.186
R free: 0.2196
Average B factor: 26.796
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 277
Crystal growth procedure: 16 mg/ml protein in 20mM Tris/HCl pH 8.4, 5 mM benzamidine, 0.1 M NaCl, 50 mM CaCl2 mixed 1+1 with 32-35% AMMONIUM SULPHATE, 2% PEG 4000, 0.1 M Bicine-NaOH pH 8.5, 15% glycerol
Matthews coefficient: 3.75
Solvent content (%): 67.21
Ligand: 1-[[3-[2-oxidanyl-3-(1~{H}-pyrrolo[3,2-c]pyridin-2-yl)phenyl]phenyl]methyl]-3-phenyl-urea (7XD)
Ligand formula: C27 H22 N4 O2
Ligand molecular weight: 434.489
Ligand SMILES: c1ccc(cc1)NC(=O)NCc2cccc(c2)c3cccc(c3O)c4cc5cnccc5[nH]4
Ligand InChI: InChI=1S/C27H22N4O2/c32-26-22(10-5-11-23(26)25-15-20-17-28-13-12-24(20)31-25)19-7-4-6-18(14-19)16-29-27(33)30-21-8-2-1-3-9-21/h1-15,17,31-32H,16H2,(H2,29,30,33)
Release date: 2017-06-21
The co-crystal structure of DYRK2 with a small molecule inhibitor 8 (PDB entry 7DHV)
Macromolecule: Dual specificity tyrosine-phosphorylation-regulated kinase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.12.1
Sequence length: 327 residues
Sequence: QVPHDHVAYRYEVLKVIGKGSFGQVVKAYDHKVHQHVALKMVRNEKRFHRQAAEEIRILEHLRKQDKDNTMNVIHMLENFTFRNHICMTFELLSMNLYELIKKNKFQGFSLPLVRKFAHSILQCLDALHKNRIIHCDLKPENILLKQQGRSGIKVIDFGSSCYEHQRVYTYIQSRFYRAPEVILGARYGMPIDMWSLGCILAELLTGYPLLPGEDEGDQLACMIELLGMPSQKLLDASKRAKNFVSSKGYPRYCTVTTLSDGSVVLNGGRSRRGKLRGPPESREWGNALKGCDDPLFLDFLKQCLEWDPAVRMTPGQALRHPWLRRR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.679
R work: 0.1898
R free: 0.2495
Average B factor: 51.3565
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 0.36 M-0.5 M sodium citrate tribasic dehydrate, 0.01 M sodium borate, pH 7.5-9.5
Matthews coefficient: 3.63
Solvent content (%): 66.11
Ligand: 2,7-dimethoxy-9-(piperidin-4-ylmethylsulfanyl)acridine-4-carboxylic acid (H7X)
Ligand formula: C22 H24 N2 O4 S
Ligand molecular weight: 412.502
Ligand SMILES: COc1ccc2c(c1)c(c3cc(cc(c3n2)C(=O)O)OC)SCC4CCNCC4
Ligand InChI: InChI=1S/C22H24N2O4S/c1-27-14-3-4-19-16(9-14)21(29-12-13-5-7-23-8-6-13)17-10-15(28-2)11-18(22(25)26)20(17)24-19/h3-4,9-11,13,23H,5-8,12H2,1-2H3,(H,25,26)
Release date: 2021-11-17
Polymerase Eta post-insertion binary complex with cytarabine (AraC) (PDB entry 6D0M)
Macromolecule: DNA polymerase eta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 435 residues
Sequence: GPHMATGQDRVVALVDMDCFFVQVEQRQNPHLRNKPCAVVQYKSWKGGGIIAVSYEARAFGVTRSMWADDAKKLCPDLLLAQVRESRGKANLTKYREASVEVMEIMSRFAVIERASIDEAYVDLTSAVQERLQKLQGQPISADLLPSTYIEGLPQGPTTAEETVQKEGMRKQGLFQWLDSLQIDNLTSPDLQLTVGAVIVEEMRAAIERETGFQCSAGISHNKVLAKLACGLNKPNRQTLVSHGSVPQLFSQMPIRKIRSLGGKLGASVIEILGIEYMGELTQFTESQLQSHFGEKNGSWLYAMCRGIEHDPVKPRQLPKTIGCSKNFPGKTALATREQVQWWLLQLAQELEERLTKDRNDNDRVATQLVVSIRVQGDKRLSSLRRCCALTRYDAHKMSHDAFTVIKNMNTSGIQTEWSPPLTMLFLCATKFSAS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.832
R work: 0.1603
R free: 0.1962
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6
Crystallization temperature (K): 293
Crystal growth procedure: MES buffer, 
PEG1500
Matthews coefficient: 2.08
Solvent content (%): 40.75
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: 2018-09-05
Crystal structure of XIAP BIR1 domain (PDB entry 4OXC)
Macromolecule: E3 ubiquitin-protein ligase XIAP
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 6.3.2
Sequence length: 111 residues
Sequence: MGSSHHHHHHSSGLVPQGSHMKTCVPADINKEEEFVEEFNRLKTFANFPSGSPVSASTLARAGFLYTGEGDTVRCFSCHAAVDRWQYGDSAVGRHRKVSPNCRFINGFYLE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.9
R work: 0.176
R free: 0.251
Average B factor: 56.4
Crystallization method: LIQUID DIFFUSION
Crystallization pH: 8.5
Crystallization temperature (K): 293
Crystal growth procedure: PEG 4000, Sodium Acetate
Matthews coefficient: 1.86
Solvent content (%): 34.04
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: 2015-02-11
Human Sirt6 in complex with ADP-ribose and fragment 4-nitrocatechol (PDB entry 8AKB)
Macromolecule: NAD-dependent protein deacetylase sirtuin-6
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1.286
Sequence length: 302 residues
Sequence: GIDPFTADKGKCGLPEIFDPPEELERKVWELARLVWQSSSVVFHTGAGISTASGIPDFRGPHGVWTMEERGLAPKFDTTFESARPTQTHMALVQLERVGLLRFLVSQNVDGLHVRSGFPRDKLAELHGNMFVEECAKCKTQYVRDTVVGTMGLKATGRLCTVAKARGLRACRGELRDTILDWEDSLPDRDLALADEASRNADLSITLGTSLQIRPSGNLPLATKRRGGRLVIVNLQPTKHDRHADLRIHGYVDEVMTRLMKHLGLEIPAWDGPRVLERALPPLPRPPTPKLEPKEESPTRIN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.13
R work: 0.2112
R free: 0.2608
Average B factor: 51.57
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.7
Crystallization temperature (K): 293
Crystal growth procedure: 1.6 M (NH4)2SO4, 10% PEG 400, and Bis-Tris buffer pH 5.7
Matthews coefficient: 2.61
Solvent content (%): 52.94
Ligand: [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL
[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE (AR6)
Ligand formula: C15 H23 N5 O14 P2
Ligand molecular weight: 559.316
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)O)O)O)O)O)N
Ligand InChI: InChI=1S/C15H23N5O14P2/c16-12-7-13(18-3-17-12)20(4-19-7)14-10(23)8(21)5(32-14)1-30-35(26,27)34-36(28,29)31-2-6-9(22)11(24)15(25)33-6/h3-6,8-11,14-15,21-25H,1-2H2,(H,26,27)(H,28,29)(H2,16,17,18)/t5-,6-,8-,9-,10-,11-,14-,15+/m1/s1
Release date: 2023-08-16
PCSK9 in complex with a Fab and compound 14 (PDB entry 6U36)
Macromolecule: Proprotein convertase subtilisin/kexin type 9
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21
Sequence length: 707 residues
Sequence: QEDEDGDYEELVLALRSEEDGLAEAPEHGTTATFHRCAKDPWRLPGTYVVVLKEETHLSQSERTARRLQAQAARRGYLTKILHVFHGLLPGFLVKMSGDLLELALKLPHVDYIEEDSSVFAQSIPWNLERITPPRYRADEYQPPDGGSLVEVYLLDTSIQSDHREIEGRVMVTDFENVPEEDGTRFHRQASKCDSHGTHLAGVVSGRDAGVAKGASMRSLRVLNCQGKGTVSGTLIGLEFIRKSQLVQPVGPLVVLLPLAGGYSRVLNAACQRLARAGVVLVTAAGNFRDDACLYSPASAPEVITVGATNAQDQPVTLGTLGTNFGRCVDLFAPGEDIIGASSDCSTCFVSQSGTSQAAAHVAGIAAMMLSAEPELTLAELRQRLIHFSAKDVINEAWFPEDQRVLTPNLVAALPPSTHGAGWQLFCRTVWSAHSGPTRMATAIARCAPDEELLSCSSFSRSGKRRGERMEAQGGKLVCRAHNAFGGEGVYAIARCCLLPQANCSVHTAPPAEASMGTRVHCHQQGHVLTGCSSHWEVEDLGTHKPPVLRPRGQPNQCVGHREASIHASCCHAPGLECKVKEHGIPAPQEQVTVACEEGWTLTGCSALPGTSHVLGAYAVDNTCVVRSRDVSTTGSTSEEAVTAVAICCRSRHLAQASQELQKGNSADIQHSGGRSSLEGPRFEGKPIPNPLLGLDSTRTGHHHHHH
Oligomeric state: Hetero 4-mer
Stoichiometry: A1, B1, C1, D1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.7
R work: 0.24
R free: 0.251
Average B factor: 73.79
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 277
Crystal growth procedure: 0.1M Bicine pH9.0, 2% dioxane, 10% PEG 20000
Matthews coefficient: 4.97
Solvent content (%): 75.24
Ligand: 2-fluoro-4-{[(1R)-6-(2-{4-[1-(4-methoxyphenyl)-5-methyl-6-oxo-1,6-dihydropyridazin-3-yl]-1H-1,2,3-triazol-1-yl}ethoxy)-1-methyl-1-{2-oxo-2-[(1,3-thiazol-2-yl)amino]ethyl}-1,2,3,4-tetrahydroisoquinolin-7-yl]oxy}benzoic acid (PVM)
Ligand formula: C38 H35 F N8 O7 S
Ligand molecular weight: 766.797
Ligand SMILES: CC1=CC(=NN(C1=O)c2ccc(cc2)OC)c3cn(nn3)CCOc4cc5c(cc4Oc6ccc(c(c6)F)C(=O)O)C(NCC5)(C)CC(=O)Nc7nccs7
Ligand InChI: InChI=1S/C38H35FN8O7S/c1-22-16-30(44-47(35(22)49)24-4-6-25(52-3)7-5-24)31-21-46(45-43-31)13-14-53-32-17-23-10-11-41-38(2,20-34(48)42-37-40-12-15-55-37)28(23)19-33(32)54-26-8-9-27(36(50)51)29(39)18-26/h4-9,12,15-19,21,41H,10-11,13-14,20H2,1-3H3,(H,50,51)(H,40,42,48)/t38-/m1/s1
Release date: 2019-11-06
Crystal structure of p300 CH1 domain in complex with CITIF (a CITED2-HIF-1alpha hybrid) (PDB entry 7QGS)
Macromolecule: Histone acetyltransferase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1.48
Sequence length: 96 residues
Sequence: GPIGSADPEKRKLIQQQLVLLLHAHKCQRREQANGEVRQCNLPHCRTMKNVLNHMTHCQSGKSCQVAHCASSRQIISHWKNCTRHDCPVCLPLKNA
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.0
R work: 0.2208
R free: 0.245
Average B factor: 79.04
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M HEPES pH 6.5, PEG 6K 35%
Matthews coefficient: 1.66
Solvent content (%): 25.78
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: 2022-05-11
PanDDA analysis group deposition -- Crystal structure of PTP1B in complex with FMOOA000523a (PDB entry 7FQO)
Macromolecule: Tyrosine-protein phosphatase non-receptor type 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 321 residues
Sequence: MEMEKEFEQIDKSGSWAAIYQDIRHEASDFPSRVAKLPKNKNRNRYRDVSPFDHSRIKLHQEDNDYINASLIKMEEAQRSYILTQGPLPNTVGHFWEMVWEQKSRGVVMLNRVMEKGSLKCAQYWPQKEEKEMIFEDTNLKLTLISEDIKSYYTVRQLELENLTTQETREILHFHYTTWPDFGVPESPASFLNFLFKVRESGSLSPEHGPVVVHCSAGIGRSGTFCLADTCLLLMDKRKDPSSVDIKKVLLEMRKFRMGLIQTADQLRFSYLAVIEGAKFIMGDSSVQDQWKELSHEDLEPPPEHIPPPPRPPKRILEPHN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.93
R work: 0.162
R free: 0.2004
Average B factor: 43.849
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M HEPES, 0.3 M magnesium acetate, 13.5% PEG 8000, 2% ethanol, and 1 mM BME
Matthews coefficient: 3.3
Solvent content (%): 62.74
Ligand: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL (TRS)
Ligand formula: C4 H12 N O3
Ligand molecular weight: 122.143
Ligand SMILES: C(C(CO)(CO)[NH3+])O
Ligand InChI: InChI=1S/C4H11NO3/c5-4(1-6,2-7)3-8/h6-8H,1-3,5H2/p+1
Release date: 2022-11-23
Crystal structure of human Fibrillarin in complex with compound 1a (PDB entry 7SEC)
Macromolecule: rRNA 2'-O-methyltransferase fibrillarin
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1
Sequence length: 242 residues
Sequence: SNAGKNVMVEPHRHEGVFICRGKEDALVTKNLVPGESVYGEKRVSISEGDDKIEYRAWNPFRSKLAAAILGGVDQIHIKPGAKVLYLGAASGTTVSHVSDIVGPDGLVYAVEFSHRSGRDLINLAKKRTNIIPVIEDARHPHKYRMLIAMVDVIFADVAQPDQTRIVALNAHTFLRNGGHFVISIKANCIDSTASAEAVFASEVKKMQQENMKPQEQLTLEPYERDHAVVVGVYRPPPKVKN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.9
R work: 0.2225
R free: 0.2663
Average B factor: 39.98
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 2.75-3.3 M Sodium Formate
Matthews coefficient: 3.01
Solvent content (%): 59.14
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: 2022-02-09
Crystal structure of RPA70N-BLMp2 fusion (PDB entry 7XUW)
Macromolecule: fusion protein of Replication protein A 70 kDa DNA-binding subunit and Bloom syndrome protein
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.4.12
Sequence length: 146 residues
Sequence: MVGQLSEGAIAAIMQKGDTNIKPILQVINIRPITTGNSPPRYRLLMSDGLNTLSSFMLATQLNPLVEEEQLSSNCVCQIHRFIVNTLKDGRRVVILMELEVLKSAEAVGVKIGNPVPYNEGTSSGSYDIDNFDIDDFDDDDDWEDI
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.1928
R free: 0.2174
Average B factor: 26.7718
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 4.6
Crystallization temperature (K): 278
Crystal growth procedure: 8% PEG 4000
Matthews coefficient: 2.1
Solvent content (%): 41.39
Release date: 2023-06-14
Crystal structure of the human METTL3-METTL14 complex with compound UOZ038 (PDB entry 7OEF)
Macromolecule: N6-adenosine-methyltransferase catalytic subunit
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1.348
Sequence length: 246 residues
Sequence: MGHHHHHHSSGRENLYFQGALTQSVGGDSSADRLFPPQWICCDIRYLDVSILGKFAVVMADPPWDIHMELPYGTLTDDEMRRLNIPVLQDDGFLFLWVTGRAMELGRECLNLWGYERVDEIIWVKTNQLQRIIRTGRTGHWLNHGKEHCLVGVKGNPQGFNQGLDCDVIVAEVRSTSHKPDEIYGMIERLSPGTRKIELFGRPHNVQPNWITLGNQLDGIHLLDPDVVARFKQRYPDGIISKPKNL
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.03
R work: 0.1942
R free: 0.2349
Average B factor: 45.84
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 295
Crystal growth procedure: 20% PEG 3350, 400mM Mg acetate
Matthews coefficient: 2.14
Solvent content (%): 42.65
Ligand: 4-(2-azaspiro[3.4]octan-2-ylmethyl)-~{N}-[[(3~{R})-3-oxidanyl-1-[6-[(phenylmethyl)amino]pyrimidin-4-yl]piperidin-3-yl]methyl]benzamide (VAT)
Ligand formula: C32 H40 N6 O2
Ligand molecular weight: 540.699
Ligand SMILES: c1ccc(cc1)CNc2cc(ncn2)N3CCCC(C3)(CNC(=O)c4ccc(cc4)CN5CC6(C5)CCCC6)O
Ligand InChI: InChI=1S/C32H40N6O2/c39-30(27-11-9-26(10-12-27)19-37-21-31(22-37)13-4-5-14-31)34-20-32(40)15-6-16-38(23-32)29-17-28(35-24-36-29)33-18-25-7-2-1-3-8-25/h1-3,7-12,17,24,40H,4-6,13-16,18-23H2,(H,34,39)(H,33,35,36)/t32-/m1/s1
Release date: 2021-10-20
Crystal structure of DYRK1A complexed with KuFal319 (compound 11) (PDB entry 6T6A)
Macromolecule: Dual specificity tyrosine-phosphorylation-regulated kinase 1A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.12.1
Sequence length: 361 residues
Sequence: SMSSHKKERKVYNDGYDDDNYDYIVKNGEKWMDRYEIDSLIGKGSFGQVVKAYDRVEQEWVAIKIIKNKKAFLNQAQIEVRLLELMNKHDTEMKYYIVHLKRHFMFRNHLCLVFEMLSYNLYDLLRNTNFRGVSLNLTRKFAQQMCTALLFLATPELSIIHCDLKPENILLCNPKRSAIKIVDFGSSCQLGQRIYQYIQSRFYRSPEVLLGMPYDLAIDMWSLGCILVEMHTGEPLFSGANEVDQMNKIVEVLGIPPAHILDQAPKARKFFEKLPDGTWNLKKTKDGKREYKPPGTRKLHNILGVETGGPGGRRAGESGHTVADYLKFKDLILRMLDYDPKTRIQPYYALQHSFFKKTADE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.8
R work: 0.2054
R free: 0.242
Average B factor: 48.579
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277.15
Crystal growth procedure: 31% PEG 400, 0.2 M lithium sulfate and 0.1 M tris, pH 7.5
Matthews coefficient: 3.19
Solvent content (%): 61.4
Ligand: TETRAETHYLENE GLYCOL (PG4)
Ligand formula: C8 H18 O5
Ligand molecular weight: 194.226
Ligand SMILES: C(COCCOCCOCCO)O
Ligand InChI: InChI=1S/C8H18O5/c9-1-3-11-5-7-13-8-6-12-4-2-10/h9-10H,1-8H2
Release date: 2019-12-04
Human OMPD-domain of UMPS (K314AcK) in complex with UMP at 1.1 Angstroms resolution (PDB entry 6YWU)
Macromolecule: Uridine 5'-monophosphate synthase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.4.2.10
Sequence length: 260 residues
Sequence: GAMELSFGARAELPRIHPVASKLLRLMQKKETNLCLSADVSLARELLQLADALGPSICMLKTHVDILNDFTLDVMKELITLAKCHEFLIFEDRKFADIGNTVKKQYEGGIFKIASWADLVNAHVVPGSGVVKGLQEVGLPLHRGCLLIAEMSSTGSLATGDYTRAAVRMAEEHSEFVVGFISGSRVSMKPEFLHLTPGVQLEAGGDNLGQQYNSPQEVIGKRGSDIIIVGRGIISAADRLEAAEMYRKAAWEAYLSRLGV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.1
R work: 0.138
R free: 0.1584
Average B factor: 13.673
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: Crystallization: 100 mM Tris/HCl pH 7.8, 1.8 - 2.0 M Ammonium sulfate, 10 mM Glutathion, 5% (v/v) Glycerol, 12.5 mM UMP
Cryo-protection: 100 mM Tris/HCl pH 7.8, 2.0 M Ammonium sulfate, 10 mM Glutathion, 5% (v/v) Glycerol, 12.5 mM UMP, 2 M L-proline
Matthews coefficient: 2.46
Solvent content (%): 49.96
Ligand: URIDINE-5'-MONOPHOSPHATE (U5P)
Ligand formula: C9 H13 N2 O9 P
Ligand molecular weight: 324.181
Ligand SMILES: C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)O)O)O
Ligand InChI: InChI=1S/C9H13N2O9P/c12-5-1-2-11(9(15)10-5)8-7(14)6(13)4(20-8)3-19-21(16,17)18/h1-2,4,6-8,13-14H,3H2,(H,10,12,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1
Release date: 2022-02-23
Aurora A Kinase in Complex with AA30 and JNJ-7706621 in Space Group P6122 (PDB entry 5DR6)
Macromolecule: Aurora kinase A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 273 residues
Sequence: MGRQWALEDFEIGRPLGKGKFGNVYLAREKQSKFILALKVLFKAQLEKAGVEHQLRREVEIQSHLRHPNILRLYGYFHDATRVYLILEYAPLGTVYRELQKLSKFDEQRTATYITELANALSYCHSKRVIHRDIKPENLLLGSAGELKIADFGWSVHAPSSRRATLCGTLDYLPPEMIEGRMHDEKVDLWSLGVLCYEFLVGKPPFEANTYQETYKRISRVEFTFPDFVTEGARDLISRLLKHNPSQRPMLREVLEHPWITANSSKPHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.534
R work: 0.21795
R free: 0.27794
Average B factor: 87.418
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.4
Crystallization temperature (K): 292
Crystal growth procedure: 100 mM HEPES pH 7.4, 200 mM magnesium sulfate, 2-20% PEG3350
Matthews coefficient: 2.82
Solvent content (%): 56.31
Ligand: 2-(3-bromophenyl)quinoline-4-carboxylic acid (5E1)
Ligand formula: C16 H10 Br N O2
Ligand molecular weight: 328.16
Ligand SMILES: c1ccc2c(c1)c(cc(n2)c3cccc(c3)Br)C(=O)O
Ligand InChI: InChI=1S/C16H10BrNO2/c17-11-5-3-4-10(8-11)15-9-13(16(19)20)12-6-1-2-7-14(12)18-15/h1-9H,(H,19,20)
Release date: 2016-07-20
Protein-aromatic foldamer complex crystal structure (PDB entry 6Q9T)
Macromolecule: Carbonic anhydrase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 259 residues
Sequence: SHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHAFNVEFDDSQDKAVLKGGPLDGTYRLIQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDFGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTKGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLLECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.68
R work: 0.2148
R free: 0.26025
Average B factor: 69.834
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.7
Crystallization temperature (K): 293
Crystal growth procedure: Ammonium sulfate 0.2 M, Sodium acetate 0.1 M pH 5.7, PEG 4000 14%, Sodium azide 3 mM
Matthews coefficient: 2.52
Solvent content (%): 51
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: 2019-09-18
PDE2 in complex with compound 1 (PDB entry 6B98)
Macromolecule: cGMP-dependent 3',5'-cyclic phosphodiesterase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.4.17
Sequence length: 373 residues
Sequence: MHHHHHHENLYFQGELSTSLYKKAGFDDDDKSDDEYTKLLHDGIQPVAAIDSNFASFTYTPRSLPEDDTSMAILSMLQDMNFINNYKIDCPTLARFCLMVKKGYRDPPYHNWMHAFSVSHFCYLLYKNLELTNYLEDIEIFALFISCMCHDLDHRGTNNSFQVASKSVLAALYSSEGSVMERHHFAQAIAILNTHGCNIFDHFSRKDYQRMLDLMRDIILATDLAHHLRIFKDLQKMAEVGYDRNNKQHHRLLLCLLMTSCDLSDQTKGWKTTRKIAELIYKEFFSQGDLEKAMGNRPMEMMDREKAYIPELQISFMEHIAMPIYKLLQDLFPKAAELYERVASNREHWTKVSHKFTIRGLPSNNSLDFLDEE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.97
R work: 0.199
R free: 0.24
Average B factor: 38.08
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 12% PEG8000, 0.1M Hepes pH7.5,  1mM TCEP
Matthews coefficient: 1.99
Solvent content (%): 38.19
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: 2017-11-22
Crystal Structure of Thrombin in complex with compound42a (PDB entry 6ZUX)
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): 1.94
R work: 0.1621
R free: 0.206
Average B factor: 28.009
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 283
Crystal growth procedure: 0.02 M phosphate buffer pH 7.5, 
27% PEG 8000, 100 mM NaCl
Matthews coefficient: 2.53
Solvent content (%): 51.35
Ligand: [2-[[(1~{R})-1-(3-chlorophenyl)ethyl]amino]-7-methoxy-1,3-benzoxazol-5-yl]-[(2~{S},5~{S})-5-(2-hydroxyethyl)-2-methyl-morpholin-4-yl]methanone (QQE)
Ligand formula: C24 H28 Cl N3 O5
Ligand molecular weight: 473.949
Ligand SMILES: CC1CN(C(CO1)CCO)C(=O)c2cc3c(c(c2)OC)oc(n3)NC(C)c4cccc(c4)Cl
Ligand InChI: InChI=1S/C24H28ClN3O5/c1-14-12-28(19(7-8-29)13-32-14)23(30)17-10-20-22(21(11-17)31-3)33-24(27-20)26-15(2)16-5-4-6-18(25)9-16/h4-6,9-11,14-15,19,29H,7-8,12-13H2,1-3H3,(H,26,27)/t14-,15+,19-/m0/s1
Release date: 2020-08-26