satarupa22/MacromolecularLigandDB huggingface dataset:
Bruton's tyrosine kinase in complex with compound 6 (PDB entry 6W06)
Macromolecule: Tyrosine-protein kinase BTK
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 293 residues
Sequence: GPLGSRLKYPVSQQNKNAPSTAGLGYGSWEIDPKDLTFLKELGTGQFGVVKYGKWRGQYDVAIKMIKEGSMSEDEFIEEAKVMMNLSHEKLVQLYGVCTKQRPIFIITEYMANGCLLNYLREMRHRFQTQQLLEMCKDVCEAMEYLESKQFLHRDLAARNCLVNDQGVVKVSDFGLSRYVLDDEYTSSVGSKFPVRWSPPEVLMYSKFSSKSDIWAFGVLMWEIYSLGKMPYERFTNSETAEHIAQGLRLYRPHLASEKVYTIMYSCWHEKADERPTFKILLSNILDVMDEES
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.55
R work: 0.1954
R free: 0.2249
Average B factor: 26.44
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 277
Crystal growth procedure: bis-tris, ammonium salt, PEG
Matthews coefficient: 2.11
Solvent content (%): 41.82
Ligand: 2,3-DIHYDROXY-1,4-DITHIOBUTANE (DTT)
Ligand formula: C4 H10 O2 S2
Ligand molecular weight: 154.251
Ligand SMILES: C(C(C(CS)O)O)S
Ligand InChI: InChI=1S/C4H10O2S2/c5-3(1-7)4(6)2-8/h3-8H,1-2H2/t3-,4-/m0/s1
Release date: 2020-12-16
Human pancreatic alpha-amylase in complex with mini-montbretin A (PDB entry 5E0F)
Macromolecule: Pancreatic alpha-amylase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.2.1.1
Sequence length: 496 residues
Sequence: QYSPNTQQGRTSIVHLFEWRWVDIALECERYLAPKGFGGVQVSPPNENVAIYNPFRPWWERYQPVSYKLCTRSGNEDEFRNMVTRCNNVGVRIYVDAVINHMCGNAVSAGTSSTCGSYFNPGSRDFPAVPYSGWDFNDGKCKTGSGDIENYNDATQVRDCRLTGLLDLALEKDYVRSKIAEYMNHLIDIGVAGFRLDASKHMWPGDIKAILDKLHNLNSNWFPAGSKPFIYQEVIDLGGEPIKSSDYFGNGRVTEFKYGAKLGTVIRKWNGEKMSYLKNWGEGWGFVPSDRALVFVDNHDNQRGHGAGGASILTFWDARLYKMAVGFMLAHPYGFTRVMSSYRWPRQFQNGNDVNDWVGPPNNNGVIKEVTINPDTTCGNDWVCEHRWRQIRNMVIFRNVVDGQPFTNWYDNGSNQVAFGRGNRGFIVFNNDDWSFSLTLQTGLPAGTYCDVISGDKINGNCTGIKIYVSDDGKAHFSISNSAEDPFIAIHAESKL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.4
R work: 0.155
R free: 0.1811
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: 100 mM sodium cacodylate, 58% MPD
Matthews coefficient: 2.29
Solvent content (%): 46.27
Ligand: 5,7-dihydroxy-4-oxo-2-(3,4,5-trihydroxyphenyl)-4H-chromen-3-yl 6-deoxy-2-O-{6-O-[(2E)-3-(3,4-dihydroxyphenyl)prop-2-enoyl]-beta-D-glucopyranosyl}-alpha-L-mannopyranoside (5J7)
Ligand formula: C36 H36 O20
Ligand molecular weight: 788.659
Ligand SMILES: CC1C(C(C(C(O1)OC2=C(Oc3cc(cc(c3C2=O)O)O)c4cc(c(c(c4)O)O)O)OC5C(C(C(C(O5)COC(=O)C=Cc6ccc(c(c6)O)O)O)O)O)O)O
Ligand InChI: InChI=1S/C36H36O20/c1-12-25(44)30(49)34(56-35-31(50)29(48)27(46)22(54-35)11-51-23(43)5-3-13-2-4-16(38)17(39)6-13)36(52-12)55-33-28(47)24-18(40)9-15(37)10-21(24)53-32(33)14-7-19(41)26(45)20(42)8-14/h2-10,12,22,25,27,29-31,34-42,44-46,48-50H,11H2,1H3/b5-3+/t12-,22+,25-,27+,29-,30+,31+,34+,35-,36-/m0/s1
Release date: 2016-09-07
Crystal structure of Tyrosine-protein kinase receptor (PDB entry 6D22)
Macromolecule: Tyrosine-protein kinase receptor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 307 residues
Sequence: HHHHHHLVPRGSVHHIKRRDIVLKWELGEGAFGKVFLAECHNLLPEQDKMLVAVKALKEASESARQDFQREAELLTMLQHQHIVRFFGVCTEGRPLLMVFEYMRHGDLNRFLRSHGPDAKLLAGGEDVAPGPLGLGQLLAVASQVAAGMVYLAGLHFVHRDLATRNCLVGQGLVVKIGDFGMSRDIYSTDYYRVGGRTMLPIRWMPPESILYRKFTTESDVWSFGVVLWEIFTYGKQPWYQLSNTEAIDCITQGRELERPRACPPEVYAIMRGCWQREPQQRHSIKDVHARLQALAQAPPVYLDVLG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.46
R work: 0.1755
R free: 0.2361
Average B factor: 37.404
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 294
Crystal growth procedure: 0.1M tri-Sodium citrate + 20% PEG3K
Matthews coefficient: 3.1
Solvent content (%): 60.32
Release date: 2018-05-02
Crystal structure of the alpha gamma heterodimer of human IDH3 in complex with Mg(2+), isocitrate and ADP (PDB entry 5GRL)
Macromolecule: Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.1.1.41
Sequence length: 339 residues
Sequence: TGGVQTVTLIPGDGIGPEISAAVMKIFDAAKAPIQWEERNVTAIQGPGGKWMIPSEAKESMDKNKMGLKGPLKTPIAAGHPSMNLLLRKTFDLYANVRPCVSIEGYKTPYTDVNIVTIRENTEGEYSGIEHVIVDGVVQSIKLITEGASKRIAEFAFEYARNNHRSNVTAVHKANIMRMSDGLFLQKCREVAESCKDIKFNEMYLDTVCLNMVQDPSQFDVLVMPNLYGDILSDLCAGLIGGLGVTPSGNIGANGVAIFESVHGTAPDIAGKDMANPTALLLSAVMMLRHMGLFDHAARIEAACFATIKDGKSLTKDLGGNAKCSDFTEEICRRVKDLD
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.79
R work: 0.2262
R free: 0.2736
Average B factor: 39.353
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M HEPES-Na, pH 7.5, 12% (w/v) PEG 3350
Matthews coefficient: 3.44
Solvent content (%): 64.24
Ligand: ADENOSINE-5'-DIPHOSPHATE (ADP)
Ligand formula: C10 H15 N5 O10 P2
Ligand molecular weight: 427.201
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
Ligand InChI: InChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
Release date: 2017-02-15
HsNMT1 in complex with both MyrCoA and GNCFSKRRAA substrates (PDB entry 6QRM)
Macromolecule: Apoptosis-inducing factor 3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1
Sequence length: 10 residues
Sequence: GNCFSKRRAA
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.3
R work: 0.172
R free: 0.2033
Average B factor: 30.6342
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 293
Crystal growth procedure: 24% PEG8K, 100mM Sodium Citrate pH 5.5, 100mM MgCl2, 100mM NaCl.
Matthews coefficient: 2.24
Solvent content (%): 45
Ligand: COENZYME A (COA)
Ligand formula: C21 H36 N7 O16 P3 S
Ligand molecular weight: 767.534
Ligand SMILES: CC(C)(COP(=O)(O)OP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)C(C(=O)NCCC(=O)NCCS)O
Ligand InChI: InChI=1S/C21H36N7O16P3S/c1-21(2,16(31)19(32)24-4-3-12(29)23-5-6-48)8-41-47(38,39)44-46(36,37)40-7-11-15(43-45(33,34)35)14(30)20(42-11)28-10-27-13-17(22)25-9-26-18(13)28/h9-11,14-16,20,30-31,48H,3-8H2,1-2H3,(H,23,29)(H,24,32)(H,36,37)(H,38,39)(H2,22,25,26)(H2,33,34,35)/t11-,14-,15-,16+,20-/m1/s1
Release date: 2020-03-18
Binary complex of human DNA Polymerase Mu with 2-nt gapped DNA substrate (PDB entry 4YCX)
Macromolecule: DNA-directed DNA/RNA polymerase mu
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 354 residues
Sequence: GSAAASPAWMPAYACQRPTPLTHHNTGLSEALEILAEAAGFEGSEGRLLTFCRAASVLKALPSPVTTLSQLQGLPHFGEHSSRVVQELLEHGVCEEVERVRRSERYQTMKLFTQIFGVGVKTADRWYREGLRTLDDLREQPQKLTQQQKAGLQHHQDLSTPVLRSDVDALQQVVEEAVGQALPGATVTLTGGFRRGKLQGHDVDFLITHPKEGQEAGLLPRVMCRLQDQGLILYHQHQHSCCESPTRLAQQSHMDAFERSFCIFRLPQPGSWKAVRVDLVVAPVSQFPFALLGWTGSKLFQRELRRFSRKEKGLWLNSHGLFDPEQKTFFQAASEEDIFRHLGLEYLPPEQRNA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.1
R work: 0.201
R free: 0.234
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 294
Crystal growth procedure: 0.1M Tris, 20% PEG 8K, 0.2M MgCl2
Matthews coefficient: 2.65
Solvent content (%): 53.56
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: 2015-08-05
The crystal structure of human Rtel1 HHD2 domain (PDB entry 8YA8)
Macromolecule: Regulator of telomere elongation helicase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.4.12
Sequence length: 90 residues
Sequence: GVPRAGKQGQHAVSAYLADARRALGSAGCSQLLAALTAYKQDDDLDKVLAVLAALTTAKPEDFPLLHRFSMFVRPHHKQRFSQTCTDLTG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.85
R work: 0.2391
R free: 0.2684
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 296.15
Crystal growth procedure: 0.2 M Potassium sulfate, 20% (v/v) PEG 3350
Matthews coefficient: 2.39
Solvent content (%): 53.39
Release date: 2024-02-28
Human Casein kinase 1 delta in complex with phosphorylated human PERIOD2 FASP peptide (PDB entry 8D7O)
Macromolecule: Casein kinase I isoform delta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 301 residues
Sequence: GAMDPEFMELRVGNRYRLGRKIGSGSFGDIYLGTDIAAGEEVAIKLECVKTKHPQLHIESKIYKMMQGGVGIPTIRWCGAEGDYNVMVMELLGPSLEDLFNFCSRKFSLKTVLLLADQMISRIEYIHSKNFIHRDVKPDNFLMGLGKKGNLVYIIDFGLAKKYRDARTHQHIPYRENKNLTGTARYASINTHLGIEQSRRDDLESLGYVLMYFNLGSLPWQGLKAATKRQKYERISEKKMSTPIEVLCKGYPSEFATYLNFCRSLRFDDKPDYSYLRQLFRNLFHRQGFSYDYVFDWNMLK
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.65
R work: 0.1725
R free: 0.2094
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 295
Crystal growth procedure: 0.13M Succinic Acid (5.5)
27%PEG3350
Matthews coefficient: 2.48
Solvent content (%): 50.46
Release date: 2023-05-17
HDM2 in complex with compound 62 (PDB entry 7NA3)
Macromolecule: Isoform 11 of E3 ubiquitin-protein ligase Mdm2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2.27
Sequence length: 110 residues
Sequence: GSQIPASEQETLVRPKPLLLKLLKSVGAQKDTYTMKEVLFYLGQYIMTKRLYDEKQQHIVYCSNDLLGDLFGVPSFSVKEHRKIYTMIYRNLVVVNQQESSDSGTSVSEN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.21
R work: 0.1957
R free: 0.2191
Average B factor: 55.29
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 293
Crystal growth procedure: undisclosed
Matthews coefficient: 1.92
Solvent content (%): 36
Ligand: 3-[4-(5-chloropyridin-3-yl)-2-[(2S)-1-methoxypropan-2-yl]-3-{(1R)-1-[(1r,4R)-4-methylcyclohexyl]ethyl}-3H-imidazo[4,5-c]pyridin-6-yl]-1,2,4-oxadiazol-5(4H)-one (1I3)
Ligand formula: C26 H31 Cl N6 O3
Ligand molecular weight: 511.016
Ligand SMILES: CC1CCC(CC1)C(C)n2c3c(cc(nc3c4cc(cnc4)Cl)C5=NOC(=O)N5)nc2C(C)COC
Ligand InChI: InChI=1S/C26H31ClN6O3/c1-14-5-7-17(8-6-14)16(3)33-23-20(30-25(33)15(2)13-35-4)10-21(24-31-26(34)36-32-24)29-22(23)18-9-19(27)12-28-11-18/h9-12,14-17H,5-8,13H2,1-4H3,(H,31,32,34)/t14-,15-,16-,17-/m1/s1
Release date: 2021-11-10
Bruton's tyrosine kinase (BTK) with compound G-744 (PDB entry 5VGO)
Macromolecule: Tyrosine-protein kinase BTK
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 271 residues
Sequence: MGSWEIDPKDLTFLKELGTGQFGVVKYGKWRGQYDVAIKMIKEGSMSEDEFIEEAKVMMNLSHEKLVQLYGVCTKQRPIFIITEYMANGCLLNYLREMRHRFQTQQLLEMCKDVCEAMEYLESKQFLHRDLAARNCLVNDQGVVKVSDFGLSRYVLDDEYTSSVGSKFPVRWSPPEVLMYSKFSSKSDIWAFGVLMWEIYSLGKMPYERFTNSETAEHIAQGLRLYRPHLASEKVYTIMYSCWHEKADERPTFKILLSNILDVMDENLYFQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.621
R work: 0.161
R free: 0.1843
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 286
Crystal growth procedure: reservoir 0.1 M LiSO4, 0.1 M citric acid pH 5.5, 6% PEG 10K, 0.4% beta-octylglucoside

protein 8 mg/mL 10 mM Tris 8.5, 0.1 M NaCl, 0.5 mM TCEP, G-744 made 0.5 mM using 10 mM DMSO stock

drop 1:2 protein/reservoir.
Matthews coefficient: 2.27
Solvent content (%): 45.76
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: 2017-07-05
Crystal Structure of Ephrin A2 (EphA2) Receptor Protein Kinase with Compound 12 (PDB entry 8BOF)
Macromolecule: Ephrin type-A receptor 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 306 residues
Sequence: GDPNQAVLKFTTEIHPSCVTRQKVIGAGEFGEVYKGMLKTSSGKKEVPVAIKTLKAGYTEKQRVDFLGEAGIMGQFSHHNIIRLEGVISKYKPMMIITEYMENGALDKFLREKDGEFSVLQLVGMLRGIAAGMKYLANMNYVHRDLAARNILVNSNLVCKVSDFGLSRVLEDDPEATYTTSGGKIPIRWTAPEAISYRKFTSASDVWSFGIVMWEVMTYGERPYWELSNHEVMKAINDGFRLPTPMDCPSAIYQLMMQCWQQERARRPKFADIVSILDKLIRAPDSLKTLADFDPRVSIRLPSTSG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.82
R work: 0.1857
R free: 0.2163
Average B factor: 28.83
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 291
Crystal growth procedure: 37,5 % Precipitant Mix 4 (25% (v/v) Hexylene glycol, 25% (w/v) Poly(ethylene glycol) 1000, 25% (w/v) Poly(ethylene glycol) 3350), 0.1M Buffer system 3 pH 8.5 (1M BICINE, 1M
Trizma base), 0.275 M Amino acids Mix (0.2 M DL-Alanine,0.2M DL-Glutamic acid monohydrate, 0.2M
DL-Lysine monohydrochloride, 0.2M
DL-Serine, 0.2M Glycine)
Matthews coefficient: 1.92
Solvent content (%): 35.98
Ligand: 4-methyl-~{N}-(3-methylphenyl)-3-[(1-methyl-6-pyridin-3-yl-pyrazolo[3,4-d]pyrimidin-4-yl)amino]benzamide (R3L)
Ligand formula: C26 H23 N7 O
Ligand molecular weight: 449.507
Ligand SMILES: Cc1cccc(c1)NC(=O)c2ccc(c(c2)Nc3c4cnn(c4nc(n3)c5cccnc5)C)C
Ligand InChI: InChI=1S/C26H23N7O/c1-16-6-4-8-20(12-16)29-26(34)18-10-9-17(2)22(13-18)30-24-21-15-28-33(3)25(21)32-23(31-24)19-7-5-11-27-14-19/h4-15H,1-3H3,(H,29,34)(H,30,31,32)
Release date: 2023-03-08
Structure of SlyD delta-IF from Thermus thermophilus in complex with FK506 (PDB entry 4ODR)
Macromolecule: Peptidyl-prolyl cis-trans isomerase SlyD, Peptidyl-prolyl cis-trans isomerase FKBP1A chimera
Type: Protein, polypeptide(L)
Source organism: Thermus thermophilus
EC number: 5.2.1.8
Sequence length: 110 residues
Sequence: MKVGQDKVVTIRYTLQVEGEVLDQGELSYLHGHRNLIPGLEEALEGREEGEAFQAHVPAEKAYGATGHPGIIPPHATLDFQVEVVKVREATPEELLHGHAHPSGHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.929
R work: 0.1527
R free: 0.1699
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5
Crystallization temperature (K): 277
Crystal growth procedure: 20% PEG6000, 0.1 M sodium acetate, pH 5.0, 0.2 M zinc chloride, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Matthews coefficient: 4.83
Solvent content (%): 74.52
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: 2015-01-14
Structure of an inhibited GRK2-G-beta and G-gamma complex (PDB entry 7PWD)
Macromolecule: Beta-adrenergic receptor kinase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.15
Sequence length: 697 residues
Sequence: MADLEAVLADVSYLMAMEKSKATPAARASKKILLPEPSIRSVMQKYLEDRGEVTFEKIFSQKLGYLLFRDFCLNHLEEARPLVEFYEEIKKYEKLETEEERVARSREIFDSYIMKELLACSHPFSKSATEHVQGHLGKKQVPPDLFQPYIEEICQNLRGDVFQKFIESDKFTRFCQWKNVELNIHLTMNDFSVHRIIGRGGFGEVYGCRKADTGKMYAMKCLDKKRIKMKQGETLALNERIMLSLVSTGDCPFIVCMSYAFHTPDKLSFILDLMNGGDLHYHLSQHGVFSEADMRFYAAEIILGLEHMHNRFVVYRDLKPANILLDEHGHVRISDLGLACDFSKKKPHASVGTHGYMAPEVLQKGVAYDSSADWFSLGCMLFKLLRGHSPFRQHKTKDKHEIDRMTLTMAVELPDSFSPELRSLLEGLLQRDVNRRLGCLGRGAQEVKESPFFRSLDWQMVFLQKYPPPLIPPRGEVNAADAFDIGSFDEEDTKGIKLLDSDQELYRNFPLTISERWQQEVAETVFDTINAETDRLEARKKAKNKQLGHEEDYALGKDCIMHGYMSKMGNPFLTQWQRRYFYLFPNRLEWRGEGEAPQSLLTMEEIQSVEETQIKERKCLLLKIRGGKQFILQCDSDPELVQWKKELRDAYREAQQLVQRVPKMKNKPRAPVVELSKVPLVQRGSANGLGSHHHHHH
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.6
R work: 0.1917
R free: 0.2295
Average B factor: 73.697
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 277
Crystal growth procedure: ethylene glycol, PEG 3350, MES, NaCl
Matthews coefficient: 3.29
Solvent content (%): 62.59
Ligand: 4-chloranyl-N-[2-(4-chlorophenyl)ethyl]thieno[2,3-c]pyridine-2-carboxamide (8DS)
Ligand formula: C16 H12 Cl2 N2 O S
Ligand molecular weight: 351.25
Ligand SMILES: c1cc(ccc1CCNC(=O)c2cc3c(s2)cncc3Cl)Cl
Ligand InChI: InChI=1S/C16H12Cl2N2OS/c17-11-3-1-10(2-4-11)5-6-20-16(21)14-7-12-13(18)8-19-9-15(12)22-14/h1-4,7-9H,5-6H2,(H,20,21)
Release date: 2021-10-20
Human DYRK1A in complex with PKC412 (PDB entry 4NCT)
Macromolecule: Dual specificity tyrosine-phosphorylation-regulated kinase 1A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.12.1
Sequence length: 368 residues
Sequence: GASDSSHKKERKVYNDGYDDDNYDYIVKNGEKWMDRYEIDSLIGKGSFGQVVKAYDRVEQEWVAIKIIKNKKAFLNQAQIEVRLLELMNKHDTEMKYYIVHLKRHFMFRNHLCLVFEMLSYNLYDLLRNTNFRGVSLNLTRKFAQQMCTALLFLATPELSIIHCDLKPENILLCNPKRSAIKIVDFGSSCQLGQRIYQYIQSRFYRSPEVLLGMPYDLAIDMWSLGCILVEMHTGEPLFSGANEVDQMNKIVEVLGIPPAHILDQAPKARKFFEKLPDGTWNLKKTKDGKREYKPPGTRKLHNILGVETGGPGGRRAGESGHTVADYLKFKDLILRMLDYDPKTRIQPYYALQHSFFKKTADEGTNTS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.597
R work: 0.20805
R free: 0.24946
Average B factor: 49.922
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.8
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M KSCN; 0.05M LiCl; 10% PEG 3350, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Matthews coefficient: 2.6
Solvent content (%): 52.65
Ligand: PKC412 (2K2)
Ligand formula: C35 H30 N4 O4
Ligand molecular weight: 570.637
Ligand SMILES: CC12C(C(CC(O1)n3c4ccccc4c5c3c6n2c7ccccc7c6c8c5C(=O)NC8)N(C)C(=O)c9ccccc9)OC
Ligand InChI: InChI=1S/C35H30N4O4/c1-35-32(42-3)25(37(2)34(41)19-11-5-4-6-12-19)17-26(43-35)38-23-15-9-7-13-20(23)28-29-22(18-36-33(29)40)27-21-14-8-10-16-24(21)39(35)31(27)30(28)38/h4-16,25-26,32H,17-18H2,1-3H3,(H,36,40)/t25-,26-,32-,35+/m1/s1
Release date: 2015-04-01
CRYSTAL STRUCTURE OF THE Activin receptor type-2A LIGAND BINDING DOMAIN IN COMPLEX WITH BIMAGRUMAB FV (PDB entry 5NH3)
Macromolecule: Activin receptor type-2A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.30
Sequence length: 122 residues
Sequence: AILGRSETQECLFFNANWEKDRTNQTGVEPCYGDKDKRRHCFATWKNISGSIEIVKQGCWLDDINCYDRTDCVEKKDSPEVYFCCCEGNMCNEKFSYFPEMEVTQPTSNPVTPKPPEFRHDS
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.35
R work: 0.1658
R free: 0.2083
Average B factor: 39.78
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M sodium citrate tribasic dihydrate pH3.5
25% PEG 3350
Matthews coefficient: 2.98
Solvent content (%): 58.7
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: 2017-11-15
Human DNA polymerase eta-DNA-dGMPNPP ternary mismatch complex in 0.025 mM Mg2+ for 600s (PDB entry 7U7S)
Macromolecule: DNA (5'-D(*CP*AP*TP*TP*AP*TP*GP*AP*CP*GP*CP*T)-3')
Type: DNA, polydeoxyribonucleotide
Source organism: synthetic construct
Sequence length: 12 residues
Sequence: CATTATGACGCT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.6
R work: 0.188
R free: 0.2074
Average B factor: 32.3187
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6
Crystallization temperature (K): 298
Crystal growth procedure: 10% PEG 2000MME, 0.1 M MES
Matthews coefficient: 2.1
Solvent content (%): 41.52
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: 2022-05-04
Ligand binding to HDAC2 (PDB entry 7ZZT)
Macromolecule: Histone deacetylase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.5.1.98
Sequence length: 498 residues
Sequence: MAYSQGGGKKKVCYYYDGDIGNYYYGQGHPMKPHRIRMTHNLLLNYGLYRKMEIYRPHKATAEEMTKYHSDEYIKFLRSIRPDNMSEYSKQMQRFNVGEDCPVFDGLFEFCQLSTGGSVAGAVKLNRQQTDMAVNWAGGLHHAKKSEASGFCYVNDIVLAILELLKYHQRVLYIDIDIHHGDGVEEAFYTTDRVMTVSFHKYGEYFPGTGDLRDIGAGKGKYYAVNFPMRDGIDDESYGQIFKPIISKVMEMYQPSAVVLQCGADSLSGDRLGCFNLTVKGHAKCVEVVKTFNLPLLMLGGGGYTIRNVARCWTYETAVALDCEIPNELPYNDYFEYFGPDFKLHISPSNMTNQNTPEYMEKIKQRLFENLRMLPHAPGVQMQAIPEDAVHEDSGDEDGEDPDKRISIRASDKRIACDEEFSDSEDEGEGGRRNVADHKKGAKKARIEEDKKETEDKKTDVKEEDKSKDNSGEKTDTKGTKSEQLSNPGSSGHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.56
R work: 0.148
R free: 0.1733
Average B factor: 26.338
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 40% PEG 300
0.1M pH=8.6 CHES/NaOH
Matthews coefficient: 1.85
Solvent content (%): 33.68
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: 2022-09-21
Crystal structure of human protein kinase CK2alpha (CSNK2A1 gene product) in complex with the ATP-competitive inhibitor 5,6-dibromo-1H-triazolo[4,5-b]pyridine (PDB entry 7A4B)
Macromolecule: Casein kinase II subunit alpha
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 335 residues
Sequence: MSGPVPSRARVYTDVNTHRPREYWDYESHVVEWGNQDDYQLVRKLGRGKYSEVFEAINITNNEKVVVKILKPVKKKKIKREIKILENLRGGPNIITLADIVKDPVSRTPALVFEHVNNTDFKQLYQTLTDYDIRFYMYEILKALDYCHSMGIMHRDVKPHNVMIDHEHRKLRLIDWGLAEFYHPGQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRKEPFFHGHDNYDQLVRIAKVLGTEDLYDYIDKYNIELDPRFNDILGRHSRKRWERFVHSENQHLVSPEALDFLDKLLRYDHQSRLTAREAMEHPYFYTVVKDQARMG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.06
R work: 0.1911
R free: 0.2226
Average B factor: 39.63
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293.15
Crystal growth procedure: 1 MIKROLITER OF THE CK2ALPHA/INHIBITOR MIXTURE (COMPOSITION: 7 MG/ML CK2ALPHA ENZYME, 1 MILLIMOLAR INHIBITOR, 10 % DIMETHYL SULFOXIDE, 450 MM NACL, 22.5 MM TRIS/HCL, PH 8.5) WAS MIXED WITH 1 MIKROLITER RESERVOIR SOLUTION (COMPOSITION: 25 % PEG3350, 0.2 M AMMONIUM SULPHATE, 0.1 M BIS-TRIS BUFFER, PH 5.5) FOLLOWED BY VAPOUR DIFFUSION EQUILIBRATION AGAINST THE RESERVOIR SOLUTION.
Matthews coefficient: 3.18
Solvent content (%): 61.3
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: 2020-12-09
Notum complex with ARUK3003775 (PDB entry 7B3P)
Macromolecule: Palmitoleoyl-protein carboxylesterase NOTUM
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.1.98
Sequence length: 383 residues
Sequence: ETGSAQQLNEDLRLHLLLNTSVTCNDGSPAGYYLKESRGSRRWLLFLEGGWYCFNRENCDSRYDTMRRLMSSRDWPRTRTGTGILSSQPEENPYWWNANMVFIPYCSSDVWSGASSKSEKNEYAFMGALIIQEVVRELLGRGLSGAKVLLLAGSSAGGTGVLLNVDRVAEQLEKLGYPAIQVRGLADSGWFLDNKQYRHTDCVDTITCAPTEAIRRGIRYWNGVVPERCRRQFQEGEEWNCFFGYKVYPTLRSPVFVVQWLFDEAQLTVDNVHLTGQPVQEGLRLYIQNLGRELRHTLKDVPASFAPACLSHEIIIRSHWTDVQVKGTSLPRALHCWDRSLHDSHKASKTPLKGCPVHLVDSCPWPHCNPSCPTGTKHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.28
R work: 0.1876
R free: 0.1986
Average B factor: 22.2427
Crystallization method: EVAPORATION
Crystallization temperature (K): 296
Crystal growth procedure: 1.5 M Ammonium Sulphate
0.1 M Sodium Citrate
Matthews coefficient: 1.93
Solvent content (%): 36.42
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: 2021-12-08