satarupa22/MacromolecularLigandDB huggingface dataset:
A fragment-based inhibitor of SHP2 (PDB entry 8RZW)
Macromolecule: Tyrosine-protein phosphatase non-receptor type 11
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 537 residues
Sequence: HMTSRRWFHPNITGVEAENLLLTRGVDGSFLARPSKSNPGDFTLSVRRNGAVTHIKIQNTGDYYDLYGGEKFATLAELVQYYMEHHGQLKEKNGDVIELKYPLNCADPTSERWFHGHLSGKEAEKLLTEKGKHGSFLVRESQSHPGDFVLSVRTGDDKGESNDGKSKVTHVMIRCQELKYDVGGGERFDSLTDLVEHYKKNPMVETLGTVLQLKQPLNTTRINAAEIESRVRELSKLAETTDKVKQGFWEEFETLQQQECKLLYSRKEGQRQENKNKNRYKNILPFDHTRVVLHDGDPNEPVSDYINANIIMPEFETKCNNSKPKKSYIATQGCLQNTVNDFWRMVFQENSRVIVMTTKEVERGKSKCVKYWPDEYALKEYGVMRVRNVKESAAHDYTLRELKLSKVGQGNTERTVWQYHFRTWPDHGVPSDPGGVLDFLEEVHHKQESIMDAGPVVVHCSAGIGRTGTFIVIDILIDIIREKGVDCDIDVPKTIQMVRSQRSGMVQTEAQYRFIYMAVQHYIETLQRRLEHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.02
R work: 0.21556
R free: 0.27183
Average B factor: 50.892
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8
Crystallization temperature (K): 293
Crystal growth procedure: 0.5M K formate
15% PEG 3350
0.1M pH=8 Bis-Tris propane/HCl
Matthews coefficient: 2.2
Solvent content (%): 44.03
Ligand: 3,5-bis(chloranyl)pyrazin-2-amine (A1H4N)
Ligand formula: C4 H3 Cl2 N3
Ligand molecular weight: 163.993
Ligand SMILES: c1c(nc(c(n1)N)Cl)Cl
Ligand InChI: InChI=1S/C4H3Cl2N3/c5-2-1-8-4(7)3(6)9-2/h1H,(H2,7,8)
Release date: 2024-03-20
The crystal structure of CK2alpha in complex with compound 3 (PDB entry 5ORJ)
Macromolecule: Casein kinase II subunit alpha
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 352 residues
Sequence: GSMDIEFDDDADDDGSGSGSGSGSSGPVPSRARVYTDVNTHRPSEYWDYESHVVEWGNQDDYQLVRKLGRGKYSEVFEAINITNNEKVVVKILKPVKKKKIKREIKILENLRGGPNIITLADIVKDPVSRTPALVFEHVNNTDFKQLYQTLTDYDIRFYMYEILKALDYCHSMGIMHRDVKPHNVMIDHEHRKLRLIDWGLAEFYHPGQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRKEPFFHGHDNYDQLVRIAKVLGTEDLYDYIDKYNIELDPRFNDILGRHSRKRWERFVHSENQHLVSPEALDFLDKLLRYDHQSRLTAREAMEHPYFYTVVK
Oligomeric state: Homo 2-mer
Stoichiometry: A2
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.99
R work: 0.2
R free: 0.221
Average B factor: 62.6
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: 2.24
Solvent content (%): 44.97
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: 2018-02-28
Structure of human TUT7 catalytic module (CM) in complex with UMPNPP and U2 RNA (PDB entry 5W0N)
Macromolecule: Terminal uridylyltransferase 7
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.52
Sequence length: 403 residues
Sequence: VVCSLCKREGHLKKDCPEDFKRIQLEPLPPLTPKFLNILDQVCIQCYKDFSPTIIEDQAREHIRQNLESFIRQDFPGTKLSLFGSSKNGFGFKQSDLDVCMTINGLETAEGLDCVRTIEELARVLRKHSGLRNILPITTAKVPIVKFFHLRSGLEVDISLYNTLALHNTRLLSAYSAIDPRVKYLCYTMKVFTKMCDIGDASRGSLSSYAYTLMVLYFLQQRNPPVIPVLQEIYKGEKKPEIFVDGWNIYFFDQIDELPTYWSECGKNTESVGQLWLGLLRFYTEEFDFKEHVISIRRKSLLTTFKKQWTSKYIVIEDPFDLNHNLGAGLSRKMTNFIMKAFINGRRVFGIPVKGFPKDYPSKMEYFFDPDVLTEGELAPNDRCCRICGKIGHFMKDCPMRRK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.497
R work: 0.1867
R free: 0.2151
Average B factor: 69.0815
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 0.8-1.0 M lithium sulfate, 0.075-0.2 M potassium iodide, 0.05-0.2 M trisodium citrate, pH 5-6
Matthews coefficient: 3.46
Solvent content (%): 64.47
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: 2017-06-28
Crystal Structure of Serine protease Hepsin in complex with Inhibitor (PDB entry 5CE1)
Macromolecule: Serine protease hepsin
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.106
Sequence length: 372 residues
Sequence: SDQEPLYPVQVSSADARLMVFDKTEGTWRLLCSSRSNARVAGLSCEEMGFLRALTHSELDVRTAGANGTSGFFCVDEGRLPHTQRLLEVISVCDCPRGRFLAAICQDCGRRKLPVDRIVGGRDTSLGRWPWQVSLRYDGAHLCGGSLLSGDWVLTAAHCFPERNRVLSRWRVFAGAVAQASPHGLQLGVQAVVYHGGYLPFRDPNSEENSNDIALVHLSSPLPLTEYIQPVCLPAAGQALVDGKICTVTGWGNTQYYGQQAGVLQEARVPIISNDVCNGADFYGNQIKPKMFCAGYPEGGIDACQGDSGGPFVCEDSISRTPRWRLCGIVSWGTGCALAQKPGVYTKVSDFREWIFQAIKTHSEASGMVTQL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.5
R work: 0.18714
R free: 0.2815
Average B factor: 25.094
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6
Crystallization temperature (K): 293
Crystal growth procedure: Activated hepsin was incubated with 10 mM Benzamidine at 4 oC for 2 hours and concentrated to7 mg/ml using 10 KDa cut off centricon [Millipore]. 1microlit of protein was mixed with 1 microlit of reservoir buffer containing 100 mM sodium Cacodylate (6.0), 22% PEG 3350, and 200 mM ammonium fluoride. Plate clusters with a dimension of 50 micron m x 100 micron m were observed after 2 days of crystallization set up.
Matthews coefficient: 2.06
Solvent content (%): 40.19
Ligand: 2-[6-(1-hydroxycyclohexyl)pyridin-2-yl]-1H-indole-5-carboximidamide (50K)
Ligand formula: C20 H22 N4 O
Ligand molecular weight: 334.415
Ligand SMILES: c1cc(nc(c1)C2(CCCCC2)O)c3cc4cc(ccc4[nH]3)C(=N)N
Ligand InChI: InChI=1S/C20H22N4O/c21-19(22)13-7-8-15-14(11-13)12-17(23-15)16-5-4-6-18(24-16)20(25)9-2-1-3-10-20/h4-8,11-12,23,25H,1-3,9-10H2,(H3,21,22)
Release date: 2016-07-06
Human cyclophilin A at 278K, Data set 1 (PDB entry 5KUZ)
Macromolecule: Peptidyl-prolyl cis-trans isomerase A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 5.2.1.8
Sequence length: 164 residues
Sequence: VNPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGFGYKGSCFHRIIPGFMCQGGDFTRHNGTGGKSIYGEKFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKTEWLDGKHVVFGKVKEGMNIVEAMERFGSRNGKTSKKITIADCGQLE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.7
R work: 0.1532
R free: 0.1844
Average B factor: 21.0504
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 291
Crystal growth procedure: CRYSTALS WERE GROWN BY MIXING EQUAL VOLUMES OF WELL SOLUTION (100 MM HEPES PH 7.5, 23% PEG 3350, 5 MM TCEP) AND PROTEIN (60 MG/ML IN 20 MM HEPES PH 7.5, 100 MM NACL, 0.5 MM TCEP) IN THE HANGING-DROP FORMAT.
Matthews coefficient: 2.82
Solvent content (%): 56.31
Release date: 2016-08-10
Crystal Structure of human phosphodiesterase 10 in complex with ethyl 1-methyl-5-(propylcarbamoyl)pyrazole-4-carboxylate (PDB entry 5SGF)
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): 2.3
R work: 0.1994
R free: 0.2567
Average B factor: 53.906
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: 2.61
Solvent content (%): 52.94
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
Structure of protein tyrosine phosphatase 1B complexed with inhibitor (PTP1B:CPT157633) (PDB entry 4Y14)
Macromolecule: Tyrosine-protein phosphatase non-receptor type 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 308 residues
Sequence: GHMASMEMEKEFEQIDKSGSWAAIYQDIRHEASDFPCRVAKLPKNKNRNRYRDVSPFDHSRIKLHQEDNDYINASLIKMEEAQRSYILTQGPLPNTCGHFWEMVWEQKSRGVVMLNRVMEKGSLKCAQYWPQKEEKEMIFEDTNLKLTLISEDIKSYYTVRQLELENLTTQETREILHFHYTTWPDFGVPESPASFLNFLFKVRESGSLSPEHGPVVVHCSAGIGRSGTFCLADTCLLLMDKRKDPSSVDIKKVLLEMRKFRMGLIQTADQLRFSYLAVIEGAKFIMGDSSVQDQWKELSHEDLEPHN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.898
R work: 0.1661
R free: 0.2059
Average B factor: 25.0077
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.4
Crystallization temperature (K): 277
Crystal growth procedure: Tris, pH 7.4, 20% PEG8000, 0.2 M MgCl2
Matthews coefficient: 2.31
Solvent content (%): 46.76
Ligand: CHLORIDE ION (CL)
Ligand formula: Cl
Ligand molecular weight: 35.453
Ligand SMILES: [Cl-]
Ligand InChI: InChI=1S/ClH/h1H/p-1
Release date: 2015-08-05
Structure of HDAC6 zinc-finger ubiquitin binding domain in complex with 3-(3-(2-(methylamino)-2-oxoethyl)-4-oxo-3,4-dihydroquinazolin-2-yl)propanoic acid (PDB entry 8G43)
Macromolecule: Histone deacetylase 6
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.5.1.98
Sequence length: 107 residues
Sequence: GSPLPWCPHLVAVCPIPAAGLDVTQPCGDCGTIQENWVCLSCYQVYCGRYINGHMLQHHGNSGHPLVLSYIDLSAWCYYCQAYVHHQALLDVKNIAHQNKFGEDMPH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.55
R work: 0.16074
R free: 0.177
Average B factor: 12.136
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 2 M sodium formate, 0.2 M sodium acetate pH4.6, 5 % ethylene glycol
Matthews coefficient: 2.27
Solvent content (%): 45.72
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: 2023-05-03
The crystal structure of Lp-PLA2 in complex with a novel inhibitor (PDB entry 5YE7)
Macromolecule: Platelet-activating factor acetylhydrolase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.1.47
Sequence length: 388 residues
Sequence: GPLGSAAASFGQTKIPRGNGPYSVGCTDLMFDHTNKGTFLRLYYPSQDNDRLDTLWIPNKEYFWGLSKFLGTHWLMGNILRLLFGSMTTPANWNSPLRPGEKYPLVVFSHGLGAFRTLYSAIGIDLASHGFIVAAVEHRDRSASATYYFKDQSAAEIGDKSWLYLRTLKQEEETHIRNEQVRQRAKECSQALSLILDIDHGKPVKNALDLKFDMEQLKDSIDREKIAVIGHSFGGATVIQTLSEDQRFRCGIALDAWMFPLGDEVYSRIPQPLFFINSEYFQYPANIIKMKKCYSPDKERKMITIRGSVHQNFADFTFATGKIIGHMLKLKGDIDSNVAIDLSNKASLAFLQKHLGLHKDFDQWDCLIEGDDENLIPGTNINTTNQHI
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.312
R work: 0.1807
R free: 0.2443
Average B factor: 33.4991
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.6
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M MOPS pH 6.6, 0.4M Li2SO4, 27% (w/v) (NH4)2SO4, 1M Na-Ac, 1.4% 1,4-butanediol
Matthews coefficient: 2.41
Solvent content (%): 49.04
Ligand: N-[4-[(4-naphthalen-2-yloxyphenyl)sulfamoyl]phenyl]ethanamide (8U0)
Ligand formula: C24 H20 N2 O4 S
Ligand molecular weight: 432.492
Ligand SMILES: CC(=O)Nc1ccc(cc1)S(=O)(=O)Nc2ccc(cc2)Oc3ccc4ccccc4c3
Ligand InChI: InChI=1S/C24H20N2O4S/c1-17(27)25-20-9-14-24(15-10-20)31(28,29)26-21-7-12-22(13-8-21)30-23-11-6-18-4-2-3-5-19(18)16-23/h2-16,26H,1H3,(H,25,27)
Release date: 2018-07-25
Crystal Structure of Ubc13 with a New Active Site Loop Conformation (PDB entry 9BIV)
Macromolecule: Ubiquitin-conjugating enzyme E2 variant 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 145 residues
Sequence: MAVSTGVKVPRNFRLLEELEEGQKGVGDGTVSWGLEDDEDMTLTRWTGMIIGPPRTNYENRIYSLKVECGPKYPEAPPSVRFVTKINMNGINNSSGMVDARSIPVLAKWQNSYSIKVVLQELRRLMMSKENMKLPQPPEGQTYNN
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.68
R work: 0.1438
R free: 0.1766
Crystallization method: BATCH MODE
Crystallization pH: 7.5
Crystallization temperature (K): 298
Crystal growth procedure: Ubc13-Mms2 heterodimer was concentrated to 12 mg/mL and stored in 50 mM Tris pH 7.5, 150 mM NaCl, 1mM TCEP. Complex was left to slowly equilibrate from 277K to 298 overnight
Matthews coefficient: 2.46
Solvent content (%): 50.01
Release date: 2024-05-08
Structure of OTULIN bound to the Met1-linked diubiquitin activity probe (PDB entry 5OE7)
Macromolecule: Ubiquitin thioesterase otulin
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.19.12
Sequence length: 273 residues
Sequence: GPLSVAPEMDIMDYCKKEWRGNTQKATCMKMGYEEVSQKFTSIRRVRGDNYCALRATLFQAMSQAVGLPPWLQDPELMLLPEKLISKYNWIKQWKLGLKFDGKNEDLVDKIKESLTLLRKKWAGLAEMRTAEARQIACDELFTNEAEEYSLYEAVKFLMLNRAIELYNDKEKGKEVPFFSVLLFARDTSNDPGQLLRNHLNQVGHTGGLEQVEMFLLAYAVRHTIQVYRLSKYNTEEFITVYPTDPPKDWPVVTLIAEDDRHYNIPVRVCEET
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.95
R work: 0.223
R free: 0.309
Average B factor: 44.06
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 298
Crystal growth procedure: 1.9-2.1 M Ammonium sulphate, 100 mM bis-tris
Matthews coefficient: 2.84
Solvent content (%): 56.67
Release date: 2017-09-27
HsNMT1 in complex with both MyrCoA and ACE-G-(L-ORN)SFSKPR (PDB entry 7OWP)
Macromolecule: Glycylpeptide N-tetradecanoyltransferase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1.97
Sequence length: 402 residues
Sequence: GGSEFSVGQGPAKTMEEASKRSYQFWDTQPVPKLGEVVNTHGPVEPDKDNIRQEPYTLPQGFTWDALDLGDRGVLKELYTLLNENYVEDDDNMFRFDYSPEFLLWALRPPGWLPQWHCGVRVVSSRKLVGFISAIPANIHIYDTEKKMVEINFLCVHKKLRSKRVAPVLIREITRRVHLEGIFQAVYTAGVVLPKPVGTCRYWHRSLNPRKLIEVKFSHLSRNMTMQRTMKLYRLPETPKTAGLRPMETKDIPVVHQLLTRYLKQFHLTPVMSQEEVEHWFYPQENIIDTFVVENANGEVTDFLSFYTLPSTIMNHPTHKSLKAAYSFYNVHTQTPLLDLMSDALVLAKMKGFDVFNALDLMENKTFLEKLKFGIGDGNLQYYLYNWKCPSMGAEKVGLVLQ
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.81
R work: 0.1552
R free: 0.191
Average B factor: 31.89
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.6
Crystallization temperature (K): 293
Crystal growth procedure: 18% PEG8K, 100mM Sodium Citrate pH 5.6, 100mM MgCl2, 100mM NaCl
Matthews coefficient: 2.23
Solvent content (%): 45
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: 2022-12-21
Crystal structure of human carbonic anhydrase I in complex with 4-(3-(2-((4-bromo-2-hydroxybenzyl)amino)ethyl)ureido) benzenesulfonamide (PDB entry 6XZO)
Macromolecule: Carbonic anhydrase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 261 residues
Sequence: MASPDWGYDDKNGPEQWSKLYPIANGNNQSPVDIKTSETKHDTSLKPISVSYNPATAKEIINVGHSFHVNFEDNDNRSVLKGGPFSDSYRLFQFHFHWGSTNEHGSEHTVDGVKYSAELHVAHWNSAKYSSLAEAASKADGLAVIGVLMKVGEANPKLQKVLDALQAIKTKGKRAPFTNFDPSTLLPSSLDFWTYPGSLTHPPLYESVTWIICKESISVSSEQLAQFRSLLSNVEGDNAVPMQHNNRPTQPLKGRTVRASF
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.44
R work: 0.1823
R free: 0.2164
Average B factor: 21.22
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 200 mM Na-acetate, 30% PEG 4000, 100 mM Tris-HCl pH 9.
Inhibitor 150 mM NaCl, 10% DMSO,  50 mM Tris pH 7
Matthews coefficient: 2.31
Solvent content (%): 46.71
Ligand: ZINC ION (ZN)
Ligand formula: Zn
Ligand molecular weight: 65.409
Ligand SMILES: [Zn+2]
Ligand InChI: InChI=1S/Zn/q+2
Release date: 2020-09-23
Structure of the IRAK4 kinase domain with compound 5 (PDB entry 6O9D)
Macromolecule: Interleukin-1 receptor-associated kinase 4
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 320 residues
Sequence: MHHHHHHGENLYFQGSVSDTRFHSFSFYELKNVTNNFDERPISVGGNKMGEGGFGVVYKGYVNNTTVAVKKLAAMVDITTEELKQQFDQEIKVMAKCQHENLVELLGFSSDGDDLCLVYVYMPNGSLLDRLSCLDGTPPLSWHMRCKIAQGAANGINFLHENHHIHRDIKSANILLDEAFTAKISDFGLARASEKFAQTVMTSRIVGTTAYMAPEALRGEITPKSDIYSFGVVLLEIITGLPAVDEHREPQLLLDIKEEIEDEEKTIEDYIDKKMNDADSTSVEAMYSVASQCLHEKKNKRPDIKKVQQLLQEMTASGNS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.51
R work: 0.195
R free: 0.239
Average B factor: 47.18
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 277
Crystal growth procedure: 2.6-2.9 M Ammonium Sulfate, Hepes
Matthews coefficient: 2.51
Solvent content (%): 50.9
Ligand: N-{7-[4-(aminomethyl)piperidin-1-yl]quinolin-6-yl}pyrazolo[1,5-a]pyrimidine-3-carboxamide (LTY)
Ligand formula: C22 H23 N7 O
Ligand molecular weight: 401.464
Ligand SMILES: c1cc2cc(c(cc2nc1)N3CCC(CC3)CN)NC(=O)c4cnn5c4nccc5
Ligand InChI: InChI=1S/C22H23N7O/c23-13-15-4-9-28(10-5-15)20-12-18-16(3-1-6-24-18)11-19(20)27-22(30)17-14-26-29-8-2-7-25-21(17)29/h1-3,6-8,11-12,14-15H,4-5,9-10,13,23H2,(H,27,30)
Release date: 2019-05-22
Aurora A kinase bound to an imidazopyridine inhibitor (14b) (PDB entry 5AAG)
Macromolecule: AURORA KINASE A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 285 residues
Sequence: GAMESKKRQWALEDFEIGRPLGKGKFGNVYLAREKQSKFILALKVLFKAQLEKAGVEHQLRREVEIQSHLRHPNILRLYGYFHDATRVYLILEYAPLGTVYRELQKLSKFDEQRTATYITELANALSYCHSKRVIHRDIKPENLLLGSAGELKIADFGWSVHAPSSRRTTLAGTLDYLPPEMIEGRMHDEKVDLWSLGVLCYEFLVGKPPFEANTYQETYKRISRVEFTFPDFVTEGARDLISRLLKHNPSQRPMLREVLEHPWITANSSKPSNAQNKESASKQS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.85
R work: 0.2134
R free: 0.2602
Crystallization pH: 8.9
Crystal growth procedure: 0.1 M TRIS PH 8.9 0.2 M LITHIUM SULFATE 30 % PEG 4000
Matthews coefficient: 2.56
Solvent content (%): 51.93
Ligand: [3-[[4-[6-chloranyl-2-(1,3-dimethylpyrazol-4-yl)-3H-imidazo[4,5-b]pyridin-7-yl]pyrazol-1-yl]methyl]phenyl]-(4-methylpiperazin-1-yl)methanone (6F2)
Ligand formula: C27 H28 Cl N9 O
Ligand molecular weight: 530.024
Ligand SMILES: Cc1c(cn(n1)C)c2[nH]c3c(n2)c(c(cn3)Cl)c4cnn(c4)Cc5cccc(c5)C(=O)N6CCN(CC6)C
Ligand InChI: InChI=1S/C27H28ClN9O/c1-17-21(16-35(3)33-17)25-31-24-23(22(28)13-29-26(24)32-25)20-12-30-37(15-20)14-18-5-4-6-19(11-18)27(38)36-9-7-34(2)8-10-36/h4-6,11-13,15-16H,7-10,14H2,1-3H3,(H,29,31,32)
Release date: 2015-09-02
Human FXIa in complex with small molecule inhibitors. (PDB entry 4D7F)
Macromolecule: COAGULATION FACTOR XI
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.27
Sequence length: 238 residues
Sequence: IVGGTASVRGEWPWQVTLHTTSPTQRHLCGGSIIGNQWILTAAHCFYGVESPKILRVYSGILNQAEIAEDTSFFGVQEIIIHDQYKMAESGYDIALLKLETTVNYADSQRPISLPSKGDRNVIYTDCWVTGWGYRKLRDKIQNTLQKAKIPLVTNEECQKRYRGHKITHKMICAGYREGGKDACKGDSGGPLSCKHNEVWHLVGITSWGEGCAQRERPGVYTNVVEYVDWILEKTQAV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.62
R work: 0.18357
R free: 0.21054
Average B factor: 36.993
Crystallization pH: 8.5
Crystal growth procedure: 2M AMMONIUM SULFATE, 0.1M TRIS-CL PH 8.5, 0.2M NACL
Matthews coefficient: 2.78
Solvent content (%): 55.74
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: 2016-01-20
Crystal structure analysis of human KRAS mutant (PDB entry 7KMR)
Macromolecule: Isoform 2B of GTPase KRas
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.5.2
Sequence length: 210 residues
Sequence: MHHHHHHGGSGGSGGSGGENLYFQGMTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTEGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKCDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQGVDDAFYTLVREIRKHKEKMSKDGKKKKKKSKTKC
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.51
R work: 0.1615
R free: 0.1967
Average B factor: 28.9888
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 300
Crystal growth procedure: 1.5 M sodium malonate, 0.1 M HEPES, pH 7.5
Matthews coefficient: 2.08
Solvent content (%): 40.86
Ligand: GUANOSINE-5'-DIPHOSPHATE (GDP)
Ligand formula: C10 H15 N5 O11 P2
Ligand molecular weight: 443.201
Ligand SMILES: c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
Ligand InChI: InChI=1S/C10H15N5O11P2/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(25-9)1-24-28(22,23)26-27(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1
Release date: 2021-11-10
Crystal structure of UBE2G2 in complex with the UBE2G2-binding region of AUP1 (PDB entry 7LEW)
Macromolecule: Ubiquitin-conjugating enzyme E2 G2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2.23
Sequence length: 165 residues
Sequence: MAGTALKRLMAEYKQLTLNPPEGIVAGPMNEENFFEWEALIMGPEDTCFEFGVFPAILSFPLDYPLSPPKMRFTCEMFHPNIYPDGRVCISILHAPGDDPMGYESSAERWSPVQSVEKILLSVVSMLAEPNDESGANVDASKMWRDDREQFYKIAKQIVQKSLGL
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.736
R work: 0.1915
R free: 0.2279
Average B factor: 36.2691
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 292
Crystal growth procedure: PEG 4000, ammonium acetate etc.
Matthews coefficient: 2.02
Solvent content (%): 38.97
Release date: 2021-11-10
Crystal structure of human Biliverdin IX-beta reductase B with Pyrantel Pamoate (PPA) (PDB entry 7ERE)
Macromolecule: Flavin reductase (NADPH)
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.5.1.30
Sequence length: 207 residues
Sequence: HMAVKKIAIFGATGQTGLTTLAQAVQAGYEVTVLVRDSSRLPSEGPRPAHVVVGDVLQAADVDKTVAGQDAVIVLLGTRNDLSPTTVMSEGARNIVAAMKAHGVDKVVACTSAFLLWDPTKVPPRLQAVTDDHIRMHKVLRESGLKYVAVMPPHIGDQPLTGAYTVTLDGRGPSRVISKHDLGHFMLRCLTTDEYDGHSTYPSHQYQ
Oligomeric state: Homo 2-mer
Stoichiometry: A2
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.6
R work: 0.1709
R free: 0.198
Average B factor: 23.39
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 291.15
Crystal growth procedure: 1.9-2.0M Ammonium sulfate, 0.1M Bis-tris(pH 6.5)
Matthews coefficient: 2.21
Solvent content (%): 44.38
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: 2022-01-19