satarupa22/MacromolecularLigandDB huggingface dataset:
Crystal structure of Cyclin-G associated kinase (GAK) complexed with selective 12i inhibitor (PDB entry 4Y8D)
Macromolecule: Cyclin-G-associated kinase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 340 residues
Sequence: SMPGSLGGASGRDQSDFVGQTVELGELRLRVRRVLAEGGFAFVYEAQDVGSGREYALKRLLSNEEEKNRAIIQEVCFMKKLSGHPNIVQFCSAASIGKEESDTGQAEFLLLTELCKGQLVEFLKKMESRGPLSCDTVLKIFYQTCRAVQHMHRQKPPIIHRDLKVENLLLSNQGTIKLCDFGSATTISHYPDYSWSAQRRALVEEEITRNTTPMYRTPEIIDLYSNFPIGEKQDIWALGCILYLLCFRQHPFEDGAKLRIVNGKYSIPPHDTQYTVFHSLIRAMLQVNPEERLSIAEVVHQLQEIAAARNVNPKSPITELLEQNGGYGSATLSRGPPPPV
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.1
R work: 0.19234
R free: 0.23154
Average B factor: 70.498
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.2
Crystallization temperature (K): 293.15
Crystal growth procedure: 9% Broad-molecular weight PEG Smears (BMW PEG smears), 0.1M MES pH 6.2, 0.15M calcium chloride
Matthews coefficient: 2.01
Solvent content (%): 38.75
Ligand: 2-methoxy-4-[3-(morpholin-4-yl)[1,2]thiazolo[4,3-b]pyridin-6-yl]aniline (49J)
Ligand formula: C17 H18 N4 O2 S
Ligand molecular weight: 342.415
Ligand SMILES: COc1cc(ccc1N)c2cc3c(c(sn3)N4CCOCC4)nc2
Ligand InChI: InChI=1S/C17H18N4O2S/c1-22-15-9-11(2-3-13(15)18)12-8-14-16(19-10-12)17(24-20-14)21-4-6-23-7-5-21/h2-3,8-10H,4-7,18H2,1H3
Release date: 2015-04-08
Crystal Structure of human phosphodiesterase 10 in complex with 8-chloro-5,7-dimethyl-2-[2-(2-methyl-5-pyrrolidin-1-yl-1,2,4-triazol-3-yl)ethyl]-[1,2,4]triazolo[1,5-c]pyrimidine (PDB entry 5SHT)
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): 2.27
R work: 0.1766
R free: 0.2278
Average B factor: 51.778
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: 2.63
Solvent content (%): 53.29
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
PanDDA analysis group deposition -- Crystal Structure of human NUDT22 in complex with N13725a (PDB entry 5R5B)
Macromolecule: Uridine diphosphate glucose pyrophosphatase NUDT22
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.1.45
Sequence length: 304 residues
Sequence: SMDPEVTLLLQCPGGGLPQEQIQAELSPAHDRRPLPGGDEAITAIWETRLKAQPWLFDAPKFRLHSATLAPIGSRGPQLLLRLGLTSYRDFLGTNWSSSAAWLRQQGATDWGDTQAYLADPLGVGAALATADDFLVFLRRSRQVAEAPGLVDVPGGHPEPQALCPGGSPQHQDLAGQLVVHELFSSVLQEICDEVNLPLLTLSQPLLLGIARNETSAGRASAEFYVQCSLTSEQVRKHYLSGGPEAHESTGIFFVETQNVRRLPETEMWAELCPSAKGAIILYNRVQGSPTGAALGSPALLPPL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.53
R work: 0.1884
R free: 0.2199
Average B factor: 24.407
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.1M HEPES pH 7.5, 0.3M sodium/potassium phosphate, 15% PEG Smear High, 20% ethylene glycol
Matthews coefficient: 2.02
Solvent content (%): 39
Ligand: 4-[(phenylmethyl)amino]benzoic acid (S1G)
Ligand formula: C14 H13 N O2
Ligand molecular weight: 227.259
Ligand SMILES: c1ccc(cc1)CNc2ccc(cc2)C(=O)O
Ligand InChI: InChI=1S/C14H13NO2/c16-14(17)12-6-8-13(9-7-12)15-10-11-4-2-1-3-5-11/h1-9,15H,10H2,(H,16,17)
Release date: 2020-07-01
Crystal structure of the PTP1B YopH WPD loop Chimera 4 bound to tungstate (PDB entry 6XEG)
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: MEMEKEFEQIDKSGSWAAIYQDIRHEASDFPCRVAKLPKNKNRNRYRDVSPFDHSRIKLHQEDNDYINASLIKMEEAQRSYILTQGPLPNTCGHFWEMVWEQKSRGVVMLNRVMEKGSLKCAQYWPQKEEKEMIFEDTNLKLTLISEDIKSYYTVRQLELENLTTQETREILHFHYTNWPDQTAPESPASFLNFLFKVRESGSLSPEHGPVVVHCSAGIGRSGTFCLADTCLLLMDKRKDPSSVDIKKVLLEMRKFRMGLIQTADQLRFSYLAVIEGAKFIMGDSSVQDQWKELSHEDLEPPPEHIPPPPRPPKRILEPHN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.549
R work: 0.1613
R free: 0.2072
Average B factor: 47.2032
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.8
Crystallization temperature (K): 295
Crystal growth procedure: tris hydrochloride pH 7.8, magnesium acetate tetrahydrate, PEG 8000 and benzamidine
Matthews coefficient: 3.18
Solvent content (%): 61.28
Ligand: BENZAMIDINE (BEN)
Ligand formula: C7 H8 N2
Ligand molecular weight: 120.152
Ligand SMILES: [H]N=C(c1ccccc1)N
Ligand InChI: InChI=1S/C7H8N2/c8-7(9)6-4-2-1-3-5-6/h1-5H,(H3,8,9)
Release date: 2021-12-15
Crystal structure of human Sirt3 at an improved resolution (PDB entry 5D7N)
Macromolecule: NAD-dependent protein deacetylase sirtuin-3, mitochondrial
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.5.1
Sequence length: 281 residues
Sequence: GHMSDKGKLSLQDVAELIRARACQRVVVMVGAGISTPSGIPDFRSPGSGLYSNLQQYDLPYPEAIFELPFFFHNPKPFFTLAKELYPGNYKPNVTHYFLRLLHDKGLLLRLYTQNIDGLERVSGIPASKLVEAHGTFASATCTVCQRPFPGEDIRADVMADRVPRCPVCTGVVKPDIVFFGEPLPQRFLLHVVDFPMADLLLILGTSLEVEPFASLTEAVRSSVPRLLINRDLVGPLAWHPRSRDVAQLGDVVHGVESLVELLGWTEEMRDLVQRETGKLD
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.83
R work: 0.17494
R free: 0.20316
Average B factor: 24.762
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 0.2 M magnesium chloride, 25 % (w/v) PEG 3350
Matthews coefficient: 2.61
Solvent content (%): 52.92
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: 2015-12-02
Crystal structure of the p97 D2 domain in a helical split-washer conformation (PDB entry 6G2W)
Macromolecule: Transitional endoplasmic reticulum ATPase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.4.6
Sequence length: 306 residues
Sequence: GPGSALRETVVEVPQVTWEDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANECQANFISIKGPELLTMWFGESEANVREIFDKARQAAPCVLFFDELDSIAKARGGNIGDGGGAADRVINQILTEMDGMSTKKNVFIIGATNRPDIIDPAILRPGRLDQLIYIPLPDEKSRVAILKANLRKSPVAKDVDLEFLAKMTNGFSGADLTEICQRACKLAIRESIESEIRRERERQTNPSAMEVEEDDPVPEIRRDHFEEAMRFARRSVSDNDIRKYEMFAQTLQQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.678
R work: 0.2367
R free: 0.3243
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.08M L-Na-Glutamate; 0.08M Alanine (racemic); 0.08M Glycine; 0.08M Lysine HCl (racemic); 0.08M Serine (racemic), 0.08M Tris, 0.08M BICINE, 10% v/v MPD; 10% PEG 1000; 10% w/v PEG 3350 at pH 8.5
Matthews coefficient: 2.36
Solvent content (%): 47.8
Ligand: (4S)-2-METHYL-2,4-PENTANEDIOL (MPD)
Ligand formula: C6 H14 O2
Ligand molecular weight: 118.174
Ligand SMILES: CC(CC(C)(C)O)O
Ligand InChI: InChI=1S/C6H14O2/c1-5(7)4-6(2,3)8/h5,7-8H,4H2,1-3H3/t5-/m0/s1
Release date: 2019-04-10
Crystal structure of the human METTL3-METTL14 complex with compound UOZ031 (PDB entry 7NI7)
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): 2.5
R work: 0.2081
R free: 0.2837
Average B factor: 47.25
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 295
Crystal growth procedure: 20% PEG 3350, 400mM Mg acetate
Matthews coefficient: 2.17
Solvent content (%): 43.38
Ligand: (R)-4-((4,4-dimethylpiperidin-1-yl)methyl)-2-hydroxy-N-((3-hydroxy-1-(6-((3-(methylcarbamoyl)benzyl)amino)pyrimidin-4-yl)piperidin-3-yl)methyl)benzamide (UEH)
Ligand formula: C34 H45 N7 O4
Ligand molecular weight: 615.766
Ligand SMILES: CC1(CCN(CC1)Cc2ccc(c(c2)O)C(=O)NCC3(CCCN(C3)c4cc(ncn4)NCc5cccc(c5)C(=O)NC)O)C
Ligand InChI: InChI=1S/C34H45N7O4/c1-33(2)11-14-40(15-12-33)20-25-8-9-27(28(42)17-25)32(44)37-21-34(45)10-5-13-41(22-34)30-18-29(38-23-39-30)36-19-24-6-4-7-26(16-24)31(43)35-3/h4,6-9,16-18,23,42,45H,5,10-15,19-22H2,1-3H3,(H,35,43)(H,37,44)(H,36,38,39)/t34-/m1/s1
Release date: 2021-10-20
Crystal structure of FGFR4 domain 3 in complex with a de novo-designed mini-binder (PDB entry 7N1J)
Macromolecule: Fibroblast growth factor receptor 4
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 132 residues
Sequence: MGSSHHHHHHSSGLVPRGSHMSPHRPILQAGLPANTTAVVGSDVELLCKVYSDAQPHIQWLKHIVINGSSFGADGFPYVQVLKTADINSSEVEVLYLRNVSAEDAGEYTCLAGNSIGLSYQSAWLTVLPEED
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.99
R work: 0.2086
R free: 0.2329
Average B factor: 59.93
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 277.15
Crystal growth procedure: 0.2 M sodium chloride, 0.1 M MES (pH 6.0), 20% PEG 3,350
Matthews coefficient: 2.64
Solvent content (%): 53.45
Release date: 2022-04-06
Meta-Carborane propyl-sulfonamide in complex with CA IX mimic (PDB entry 6YO2)
Macromolecule: Carbonic anhydrase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 260 residues
Sequence: MSHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHSFQVTFDDSQDKAVLKGGPLDGTYRLLQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDVGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTEGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLAECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.2
R work: 0.1452
R free: 0.1644
Average B factor: 17.013
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.8
Crystallization temperature (K): 291
Crystal growth procedure: 1.6 M sodium citrate, 50 mM Tris-H2SO4
Matthews coefficient: 2.1
Solvent content (%): 41.4
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: 2020-08-19
Aurora A kinase in complex with TPX2-inhibitor 9 (PDB entry 8C1E)
Macromolecule: Aurora kinase A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 272 residues
Sequence: GSMGSKRQWALEDFEIGRPLGKGKFGNVYLAREKQSKFILALKVLFKAQLEKAGVEHQLRREVEIQSHLRHPNILRLYGYFHDATRVYLILEYAPLGTVYRELQKLSKFDEQRTATYITELANALSYCHSKRVIHRDIKPENLLLGSAGELKIADFGWSVHAPSSRRTTLCGTLDYLPPEMIEGRMHDEKVDLWSLGVLCYEFLVGKPPFEANTYQETYKRISRVEFTFPDFVTEGARDLISRLLKHNPSQRPMLREVLEHPWITANSSKPS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.798
R work: 0.1726
R free: 0.2388
Average B factor: 48.803
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 6.5
Crystallization temperature (K): 298
Crystal growth procedure: 5% DMSO, 0.2M MgSO4, 0.05 M HEPES 7.4: soaking: 0.2M MgSO4, 0.05M HEPES 7.4, 30% glycerol, 10% DMSO, 5 mM compound
Matthews coefficient: 3.62
Solvent content (%): 66.06
Ligand: 4-(4-chloranyl-3-cyano-phenyl)-7-methyl-1~{H}-indole-6-carboxylic acid (T0X)
Ligand formula: C17 H11 Cl N2 O2
Ligand molecular weight: 310.734
Ligand SMILES: Cc1c(cc(c2c1[nH]cc2)c3ccc(c(c3)C#N)Cl)C(=O)O
Ligand InChI: InChI=1S/C17H11ClN2O2/c1-9-13(17(21)22)7-14(12-4-5-20-16(9)12)10-2-3-15(18)11(6-10)8-19/h2-7,20H,1H3,(H,21,22)
Release date: 2024-01-10
Crystal structure of JAK2 in complex with peficitinib (PDB entry 6AAJ)
Macromolecule: Tyrosine-protein kinase JAK2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 299 residues
Sequence: GAFEDRDPTQFEERHLKFLQQLGKGNFGSVEMCRYDPLQDNTGEVVAVKKLQHSTEEHLRDFEREIEILKSLQHDNIVKYKGVCYSAGRRNLKLIMEYLPYGSLRDYLQAHAERIDHIKLLQYTSQICKGMEYLGTKRYIHRDLATRNILVENENRVKIGDFGLTKVLPQDKEYYKVKEPGESPIFWYAPESLTESKFSVASDVWSFGVVLYELFTYIEKSKSPPAEFMRMIGNDKQGQMIVFHLIELLKNNGRLPRPDGCPDEIYMIMTECWNNNVNQRPSFRDLALRVDQIRDNMAG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.37
R work: 0.20819
R free: 0.26163
Average B factor: 59.196
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 50mM sodium citrate(pH6.5), 100mM ammonium phosphate, 20% PEG4000
Matthews coefficient: 2.74
Solvent content (%): 55.16
Ligand: 4-[[(1S,3R)-5-oxidanyl-2-adamantyl]amino]-1H-pyrrolo[2,3-b]pyridine-5-carboxamide (9T6)
Ligand formula: C18 H22 N4 O2
Ligand molecular weight: 326.393
Ligand SMILES: c1c[nH]c2c1c(c(cn2)C(=O)N)NC3C4CC5CC3CC(C5)(C4)O
Ligand InChI: InChI=1S/C18H22N4O2/c19-16(23)13-8-21-17-12(1-2-20-17)15(13)22-14-10-3-9-4-11(14)7-18(24,5-9)6-10/h1-2,8-11,14,24H,3-7H2,(H2,19,23)(H2,20,21,22)/t9-,10-,11+,14-,18-
Release date: 2018-08-15
Crystal structure of human SYK in complex with compound 24 (PDB entry 8RRQ)
Macromolecule: Tyrosine-protein kinase SYK
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 282 residues
Sequence: GPEEIRPKEVYLDRKLLTLEDKELGSGNFGTVKKGYYQMKKVVKTVAVKILKNEANDPALKDELLAEANVMQQLDNPYIVRMIGICEAESWMLVMEMAELGPLNKYLQQNRHVKDKNIIELVHQVSMGMKYLEESNFVHRDLAARNVLLVTQHYAKISDFGLSKALRADENYYKAQTHGKWPVKWYAPECINYYKFSSKSDVWSFGVLMWEAFSYGQKPYRGMKGSEVTAMLEKGERMGCPAGCPREMYDLMNLCWTYDVENRPGFAAVELRLRNYYYDVVN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.6
R work: 0.1766
R free: 0.2107
Average B factor: 25.887
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 6.5
Crystallization temperature (K): 277
Crystal growth procedure: 20% PEG 3350, 0.1 M bis tris propane pH 6.5, 0.2 M Na formate
Matthews coefficient: 2.08
Solvent content (%): 41
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: 2024-04-24
Cyclophilin A complexed with tri-vector ligand 10. (PDB entry 6GJL)
Macromolecule: Peptidyl-prolyl cis-trans isomerase A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 5.2.1.8
Sequence length: 165 residues
Sequence: MVNPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGFGYKGSCFHRIIPGFMCQGGDFTRHNGTGGKSIYGEKFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKTEWLDGKHVVFGKVKEGMNIVEAMERFGSRNGKTSKKITIADCGQLE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.16
R work: 0.17727
R free: 0.19194
Average B factor: 21.864
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 279.15
Crystal growth procedure: PEG 8000, Tris-HCl
Matthews coefficient: 2.86
Solvent content (%): 57
Ligand: ethyl 2-[[(4-aminophenyl)methyl-(1~{H}-1,2,3,4-tetrazol-5-ylmethyl)carbamoyl]amino]ethanoate (F1Q)
Ligand formula: C14 H19 N7 O3
Ligand molecular weight: 333.346
Ligand SMILES: CCOC(=O)CNC(=O)N(Cc1ccc(cc1)N)Cc2[nH]nnn2
Ligand InChI: InChI=1S/C14H19N7O3/c1-2-24-13(22)7-16-14(23)21(9-12-17-19-20-18-12)8-10-3-5-11(15)6-4-10/h3-6H,2,7-9,15H2,1H3,(H,16,23)(H,17,18,19,20)
Release date: 2018-11-07
Crystal structure of human NRMT1 in complex with alpha-N-monomethylated human CENP-A peptide (PDB entry 6KDQ)
Macromolecule: N-terminal Xaa-Pro-Lys N-methyltransferase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1.244
Sequence length: 243 residues
Sequence: MGSSHHHHHHSSGLVPRGSHMTSEVIEDEKQFYSKAKTYWKQIPPTVDGMLGGYGHISSIDINSSRKFLQRFLREGPNKTGTSCALDCGAGIGRITKRLLLPLFREVDMVDITEDFLVQAKTYLGEEGKRVRNYFCCGLQDFTPEPDSYDVIWIQWVIGHLTDQHLAEFLRRCKGSLRPNGIIVIKDNMAQEGVILDDVDSSVCRDLDVVRRIICSAGLSLLAEERQENLPDEIYHVYSFALR
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.499
R work: 0.1575
R free: 0.1803
Average B factor: 20.2055
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 5.7
Crystallization temperature (K): 291
Crystal growth procedure: 0.2M Ammonium acetate, 0.1M Sodium citrate dehydrate pH 5.7, 31% w/v PEG 4000
Matthews coefficient: 2.19
Solvent content (%): 43.85
Ligand: S-ADENOSYL-L-HOMOCYSTEINE (SAH)
Ligand formula: C14 H20 N6 O5 S
Ligand molecular weight: 384.411
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)CSCCC(C(=O)O)N)O)O)N
Ligand InChI: InChI=1S/C14H20N6O5S/c15-6(14(23)24)1-2-26-3-7-9(21)10(22)13(25-7)20-5-19-8-11(16)17-4-18-12(8)20/h4-7,9-10,13,21-22H,1-3,15H2,(H,23,24)(H2,16,17,18)/t6-,7+,9+,10+,13+/m0/s1
Release date: 2020-07-08
Crystal structure of human pro-cathepsin H C26S mutant (PDB entry 6CZS)
Macromolecule: Pro-cathepsin H
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.22.16
Sequence length: 335 residues
Sequence: MWATLPLLCAGAWLLGVPVCGAAELCVNSLEKFHFKSWMSKHRKTYSTEEYHHRLQTFASNWRKINAHNNGNHTFKMALNQFSDMSFAEIKHKYLWSEPQNCSATKSNYLRGTGPYPPSVDWRKKGNFVSPVKNQGACGSSWTFSTTGALESAIAIATGKMLSLAEQQLVDCAQDFNNHGCQGGLPSQAFEYILYNKGIMGEDTYPYQGKDGYCKFQPGKAIGFVKDVANITIYDEEAMVEAVALYNPVSFAFEVTQDFMMYRTGIYSSTSCHKTPDKVNHAVLAVGYGEKNGIPYWIVKNSWGPQWGMNGYFLIERGKNMCGLAACASYPIPLV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.66
R work: 0.1813
R free: 0.2085
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 4.2
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M sodium phosphate dibasic / citric acid, pH 4.2, 2.0 M ammonium sulfate
Matthews coefficient: 3.97
Solvent content (%): 69
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: 2018-08-08
Human DNMT3B PWWP domain in complex with triisopropanolamine (PDB entry 6R3E)
Macromolecule: DNA (cytosine-5)-methyltransferase 3B,DNA (cytosine-5)-methyltransferase 3B
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1.37
Sequence length: 274 residues
Sequence: SEYQDGKEFGIGDLVWGKIKGFSWWPAMVVSWKATSKRQAMSGMRWVQWFGDGKFSEVSADKLVALGLFSQHFNLATFNKLVSYRKAMYHALEKARVRAGKTFPSSPGDSLEDQLKPMLEWAHGGFKPTGIEGLKPNSEYQDGKEFGIGDLVWGKIKGFSWWPAMVVSWKATSKRQAMSGMRWVQWFGDGKFSEVSADKLVALGLFSQHFNLATFNKLVSYRKAMYHALEKARVRAGKTFPSSPGDSLEDQLKPMLEWAHGGFKPTGIEGLKPN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.269
R work: 0.2176
R free: 0.2635
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 298
Crystal growth procedure: 0.1 M MES, 0.2 M Li2SO4, 23-33% PEG3350
Matthews coefficient: 3.77
Solvent content (%): 67.37
Ligand: Triisopropanolamine (96H)
Ligand formula: C9 H21 N O3
Ligand molecular weight: 191.268
Ligand SMILES: CC(CN(CC(C)O)CC(C)O)O
Ligand InChI: InChI=1S/C9H21NO3/c1-7(11)4-10(5-8(2)12)6-9(3)13/h7-9,11-13H,4-6H2,1-3H3/t7-,8-,9-/m0/s1
Release date: 2020-04-08
CUB2 domain of C1r (PDB entry 6F1D)
Macromolecule: Complement C1r subcomponent
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.41
Sequence length: 117 residues
Sequence: AECSSELYTEASGYISSLEYPRSYPPDLRCNYSIRVERGLTLHLKFLEPFDIEDHPEVPCPYDQLQIYANGKNIGEFCGKQRPPDLDTSSNAVDLLFFTDESGDSRGWKLRYTTEII
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.95
R work: 0.1732
R free: 0.2016
Average B factor: 34.3829
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 298
Crystal growth procedure: 50 mM Tris-HCl at pH 8.5 containing 25% PEG-8K, 2 mM CaCl2 and 3% 1,6-diaminohexane
Matthews coefficient: 2.91
Solvent content (%): 57.7
Ligand: SODIUM ION ()
Ligand formula: Na
Ligand molecular weight: 22.99
Ligand SMILES: [Na+]
Ligand InChI: InChI=1S/Na/q+1
Release date: 2018-01-17
Cyclophilin A complexed with tri-vector ligand 15. (PDB entry 6GJN)
Macromolecule: Peptidyl-prolyl cis-trans isomerase A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 5.2.1.8
Sequence length: 165 residues
Sequence: MVNPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGFGYKGSCFHRIIPGFMCQGGDFTRHNGTGGKSIYGEKFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKTEWLDGKHVVFGKVKEGMNIVEAMERFGSRNGKTSKKITIADCGQLE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.7
R work: 0.16954
R free: 0.2029
Average B factor: 17.689
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 279.15
Crystal growth procedure: PEG 8000, Tris-HCl
Matthews coefficient: 2.76
Solvent content (%): 55.4
Ligand: 1-[(4-aminophenyl)methyl]-3-[2-[(2~{R})-2-(2-bromophenyl)pyrrolidin-1-yl]-2-oxidanylidene-ethyl]-1-[(2-methyl-1,2,3,4-tetrazol-5-yl)methyl]urea (F0Q)
Ligand formula: C23 H27 Br N8 O2
Ligand molecular weight: 527.417
Ligand SMILES: Cn1nc(nn1)CN(Cc2ccc(cc2)N)C(=O)NCC(=O)N3CCCC3c4ccccc4Br
Ligand InChI: InChI=1S/C23H27BrN8O2/c1-30-28-21(27-29-30)15-31(14-16-8-10-17(25)11-9-16)23(34)26-13-22(33)32-12-4-7-20(32)18-5-2-3-6-19(18)24/h2-3,5-6,8-11,20H,4,7,12-15,25H2,1H3,(H,26,34)/t20-/m1/s1
Release date: 2018-11-07
CRYSTAL STRUCTURE OF AP2 ASSOCIATED KINASE 1 COMPLEXED WITH 5-[(4-aminopiperidin-1-yl)methyl]-N-{3-[5-(propan-2-yl)-1,3,4-thiadiazol-2-yl]phenyl}pyrrolo[2,1-f][1,2,4]triazin-4-amine (PDB entry 8GMC)
Macromolecule: AP2-associated protein kinase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 318 residues
Sequence: MHHHHHHLVPRGSSTSGLGSGYIGRVFGIGRQQVTVDEVLAEGGFAIVFLVRTSNGMKCALKRMFVNNEHDLQVCKREIQIMRDLSGHKNIVGYIDSSINNVSSGDVWEVLILMDFCRGGQVVNLMNQRLQTGFTENEVLQIFCDTCEAVARLHQCKTPIIHRDLKVENILLHDRGHYVLCDFGSATNKFQNPQTEGVNAVEDEIKKYTTLSYRAPEMVNLYSGKIITTKADIWALGCLLYKLCYFTLPFGESQVAICDGNFTIPDNSRYSQDMHCLIRYMLEPDPDKRPDIYQVSYFSFKLLKKECPIPNVQNSPIP
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.5
R work: 0.227
R free: 0.256
Average B factor: 44.67
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6
Crystallization temperature (K): 296
Crystal growth procedure: 1.2M AmSO4, 0.1M tri-Na Citrate pH 6.0, 3% isopropanol, 296K
Matthews coefficient: 3.01
Solvent content (%): 59.13
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: 2023-07-12