satarupa22/MacromolecularLigandDB huggingface dataset:
Crystal structure of BACE complex with BMC021 (PDB entry 5QCW)
Macromolecule: Beta-secretase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.23.46
Sequence length: 402 residues
Sequence: GPDEEPEEPGRRGSFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHPFLHRYYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTVRANIAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTHVPNLFSLQLCGAGFPLNQSEVLASVGGSMIIGGIDHSLYTGSLWYTPIRREWYYEVIIVRVEINGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVKSIKAASSTEKFPDGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRITILPQQYLRPVEDVATSQDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSACHVHDEFRTAAVEGPFVTLDMEDCGYNI
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.1
R work: 0.174
R free: 0.204
Average B factor: 51.44
Crystallization method: sitting drop
Crystallization pH: 5.5
Crystallization temperature (K): 292
Crystal growth procedure: PROTEIN STOCK WAS BACE MUT46B (14-447)7.3MG/ML IN 10MM TRIS-HCL PH 7.4, 25MM NACL. CRYSTALLIZATION SOLUTION WAS 1.0M
AMMONIUM SULFATE IN WATER (JBS 6 A2). CRYSTALS WERE GROWN BY VAPOR DIFFUSION IN SITTING DROPS IN 96-WELL CORNING
MICROTITER PLATES. CRYO-PROTECTANT WAS 80% WELL SOLUTION, 20% 1,2-PROPANEDIOL.
Matthews coefficient: 3.05
Solvent content (%): 59.69
Ligand: (2R,4S)-N-butyl-4-[(2S,5S,7R)-2,7-dimethyl-3,15-dioxo-1,4-diazacyclopentadecan-5-yl]-4-hydroxy-2-methylbutanamide (AR9)
Ligand formula: C24 H45 N3 O4
Ligand molecular weight: 439.632
Ligand SMILES: CCCCNC(=O)C(C)CC(C1CC(CCCCCCCC(=O)NC(C(=O)N1)C)C)O
Ligand InChI: InChI=1S/C24H45N3O4/c1-5-6-14-25-23(30)18(3)16-21(28)20-15-17(2)12-10-8-7-9-11-13-22(29)26-19(4)24(31)27-20/h17-21,28H,5-16H2,1-4H3,(H,25,30)(H,26,29)(H,27,31)/t17-,18-,19+,20+,21+/m1/s1
Release date: 2020-06-03
Crystal structure of human exonuclease 1 Exo1 (D225A) in complex with 5' recessed-end DNA (rVII) (PDB entry 5V09)
Macromolecule: Exonuclease 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1
Sequence length: 358 residues
Sequence: MGIQGLLQFIKEASEPIHVRKYKGQVVAVDTYCWLHKGAIACAEKLAKGEPTDRYVGFCMKFVNMLLSHGIKPILVFDGCTLPSKKEVERSRRERRQANLLKGKQLLREGKVSEARECFTRSINITHAMAHKVIKAARSQGVDCLVAPYEADAQLAYLNKAGIVQAIITEDSDLLAFGCKKVILKMDQFGNGLEIDQARLGMCRQLGDVFTEEKFRYMCILSGCAYLSSLRGIGLAKACKVLRLANNPDIVKVIKKIGHYLKMNITVPEDYINGFIRANNTFLYQLVFDPIKRKLIPLNAYEDDVDPETLSYAGQYVDDSIALQIALGNKDINTFEQIDDYNPDTAMPAHSRENLYFQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.75
R work: 0.2181
R free: 0.2541
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 290
Crystal growth procedure: 100 mM sodium acetate, pH 7.0, 10 mM potassium chloride, 2-4% PEG4000
Matthews coefficient: 2.6
Solvent content (%): 52.67
Ligand: MANGANESE (II) ION (MN)
Ligand formula: Mn
Ligand molecular weight: 54.938
Ligand SMILES: [Mn+2]
Ligand InChI: InChI=1S/Mn/q+2
Release date: 2017-05-24
Crystal structure of Omicron BA.2 RBD complexed with hACE2 (PDB entry 7XB0)
Macromolecule: Angiotensin-converting enzyme 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.17.23
Sequence length: 596 residues
Sequence: STIEEQAKTFLDKFNHEAEDLFYQSSLASWNYNTNITEENVQNMNNAGDKWSAFLKEQSTLAQMYPLQEIQNLTVKLQLQALQQNGSSVLSEDKSKRLNTILNTMSTIYSTGKVCNPDNPQECLLLEPGLNEIMANSLDYNERLWAWESWRSEVGKQLRPLYEEYVVLKNEMARANHYEDYGDYWRGDYEVNGVDGYDYSRGQLIEDVEHTFEEIKPLYEHLHAYVRAKLMNAYPSYISPIGCLPAHLLGDMWGRFWTNLYSLTVPFGQKPNIDVTDAMVDQAWDAQRIFKEAEKFFVSVGLPNMTQGFWENSMLTDPGNVQKAVCHPTAWDLGKGDFRILMCTKVTMDDFLTAHHEMGHIQYDMAYAAQPFLLRNGANEGFHEAVGEIMSLSAATPKHLKSIGLLSPDFQEDNETEINFLLKQALTIVGTLPFTYMLEKWRWMVFKGEIPKDQWMKKWWEMKREIVGVVEPVPHDETYCDPASLFHVSNDYSFIRYYTRTLYQFQFQEALCQAAKHEGPLHKCDISNSTEAGQKLFNMLRLGKSEPWTLALENVVGAKNMNVRPLLNYFEPLFTWLKDQNKNSFVGWSTDWSPYA
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.9
R work: 0.2156
R free: 0.2552
Average B factor: 58.03
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 291
Crystal growth procedure: 0.1 M ammonium acetate, 0.1 M Bis-Tris
Matthews coefficient: 3.29
Solvent content (%): 62.62
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: 2022-07-06
The ubiquitin-associated domain of human thirty-eight negative kinase-1 flexibly fused to the 1TEL crystallization chaperone via a 2-glycine linker and crystallized at very low protein concentration (PDB entry 7U4Z)
Macromolecule: Transcription factor ETV6,Non-receptor tyrosine-protein kinase TNK1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 155 residues
Sequence: GSIRLPAHLRLQPIYWSRDDVAQWLKWAENEFSLSPIDSNTFEMNGKALLLLTKEDFRYRSPHSGDELYELLQHILGGELQRKIMEVELSVHGVTHQEAQTALGATGGDVVSAIRNLKVDQLFHLSSRSRADAWRILEHYQWDLSAASRYVLARP
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.03
R work: 0.2019
R free: 0.2318
Average B factor: 33.07
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6
Crystallization temperature (K): 298
Crystal growth procedure: 1.2 uL of 0.5 mg/mL protein combined with 1.2 uL of 100 mM Bis-Tris, pH 6.00, 630-750 mM Mg-Formate.
Matthews coefficient: 2.04
Solvent content (%): 39.66
Ligand: POTASSIUM ION (K)
Ligand formula: K
Ligand molecular weight: 39.098
Ligand SMILES: [K+]
Ligand InChI: InChI=1S/K/q+1
Release date: 2023-03-08
Crystal structure of CREBBP bromodomain complexd with PA10 (PDB entry 6FRF)
Macromolecule: CREB-binding protein
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1.48
Sequence length: 119 residues
Sequence: SMRKKIFKPEELRQALMPTLEALYRQDPESLPFRQPVDPQLLGIPDYFDIVKNPMDLSTIKRKLDTGQYQEPWQYVDDVWLMFNNAWLYNRKTSRVYKFCSKLAEVFEQEIDPVMQSLG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.1
R work: 0.1759
R free: 0.2283
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 0.1 M Sodium Citrate, pH 5.6, 1.3 M Ammonium Sulfate
Matthews coefficient: 2.81
Solvent content (%): 56.25
Ligand: ~{N}-[3-(3,5-dimethyl-1,2-oxazol-4-yl)-5-(5-ethanoyl-2-ethoxy-phenyl)phenyl]furan-2-carboxamide (E3T)
Ligand formula: C26 H24 N2 O5
Ligand molecular weight: 444.479
Ligand SMILES: CCOc1ccc(cc1c2cc(cc(c2)NC(=O)c3ccco3)c4c(noc4C)C)C(=O)C
Ligand InChI: InChI=1S/C26H24N2O5/c1-5-31-23-9-8-18(16(3)29)14-22(23)19-11-20(25-15(2)28-33-17(25)4)13-21(12-19)27-26(30)24-7-6-10-32-24/h6-14H,5H2,1-4H3,(H,27,30)
Release date: 2018-08-29
Structure of SETD3 bound to SAH and methylated actin (PDB entry 6ICT)
Macromolecule: Histone-lysine N-methyltransferase setd3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1.43
Sequence length: 504 residues
Sequence: GMGKKSRVKTQKSGTGATATVSPKEILNLTSELLQKCSSPAPGPGKEWEEYVQIRTLVEKIRKKQKGLSVTFDGKREDYFPDLMKWASENGASVEGFEMVNFKEEGFGLRATRDIKAEELFLWVPRKLLMTVESAKNSVLGPLYSQDRILQAMGNIALAFHLLCERASPNSFWQPYIQTLPSEYDTPLYFEEDEVRYLQSTQAIHDVFSQYKNTARQYAYFYKVIQTHPHANKLPLKDSFTYEDYRWAVSSVMTRQNQIPTEDGSRVTLALIPLWDMCNHTNGLITTGYNLEDDRCECVALQDFRAGEQIYIFYGTRSNAEFVIHSGFFFDNNSHDRVKIKLGVSKSDRLYAMKAEVLARAGIPTSSVFALHFTEPPISAQLLAFLRVFCMTEEELKEHLLGDSAIDRIFTLGNSEFPVSWDNEVKLWTFLEDRASLLLKTYKTTIEEDKSVLKNHDLSVRAKMAIKLRLGEKEILEKAVKSAAVNREYYRQQMEEKAPLPKYE
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.952
R work: 0.1784
R free: 0.2138
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 0.2M Magnesium acetate tetrahydrate
0.1M Sodium cacodylate trihydrate pH 6.5
20% Polyethylene glycol 8000
Matthews coefficient: 2.74
Solvent content (%): 55.15
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: 2019-02-27
Fragment-Based Drug Design of a Novel, Covalent Bruton's Tyrosine Kinase Inhibitor (PDB entry 7N5Y)
Macromolecule: Tyrosine-protein kinase BTK
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 283 residues
Sequence: GPLPGKNAPSTAGLGYGSWEIDPKDLTFLKELGTGQFGVVKYGKWRGQYDVAIKMIKEGSMSEDEFIEEAKVMMNLSHEKLVQLYGVCTKQRPIFIITEYMANGCLLNYLREMRHRFQTQQLLEMCKDVCEAMEYLESKQFLHRDLAARNCLVNDQGVVKVSDFGLSRYVLDDEYTSSVGSKFPVRWSPPEVLMYSKFSSKSDIWAFGVLMWEIYSLGKMPYERFTNSETAEHIAQGLRLYRPHLASEKVYTIMYSCWHEKADERPTFKILLSNILDVMDEES
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.85
R work: 0.1627
R free: 0.2015
Average B factor: 17.138
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 277
Crystal growth procedure: 10% polyethylene glycol 4000, 20% glycerol, 0.1M imidazole/MES, pH 6.5 and 0.12M alcohol mixture
Matthews coefficient: 2.22
Solvent content (%): 44.5
Ligand: IMIDAZOLE (IMD)
Ligand formula: C3 H5 N2
Ligand molecular weight: 69.085
Ligand SMILES: c1c[nH+]c[nH]1
Ligand InChI: InChI=1S/C3H4N2/c1-2-5-3-4-1/h1-3H,(H,4,5)/p+1
Release date: 2021-09-08
APE1 exonuclease substrate complex D148E (PDB entry 6W3N)
Macromolecule: TCGACGGATCC
Type: DNA, polydeoxyribonucleotide
Source organism: synthetic construct
Sequence length: 11 residues
Sequence: TCGACGGATCC
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.69
R work: 0.2491
R free: 0.3084
Average B factor: 57.64
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 7% PEG20000, 100 mM sodium citrate, 15% glycerol, 5 mM calcium chloride
Matthews coefficient: 2.66
Solvent content (%): 53.75
Ligand: CALCIUM ION (CA)
Ligand formula: Ca
Ligand molecular weight: 40.078
Ligand SMILES: [Ca+2]
Ligand InChI: InChI=1S/Ca/q+2
Release date: 2020-06-10
Co-complex CYP46A1 with 8114 (3f) (PDB entry 7LS3)
Macromolecule: Cholesterol 24-hydroxylase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.14.25
Sequence length: 474 residues
Sequence: MHHHHHHSRYEHIPGPPRPSFLLGHLPCFWKKDEVGGRVLQDVFLDWAKKYGPVVRVNVFHKTSVIVTSPESVKKFLMSTKYNKDSKMYRALQTVFGERLFGQGLVSECNYERWHKQRRVIDLAFSRSSLVSLMETFNEKAEQLVEILEAKADGQTPVSMQDMLTYTAMDILAKAAFGMETSMLLGAQKPLSQAVKLMLEGITASRNTLAKFLPGKRKQLREVRESIRFLRQVGRDWVQRRREALKRGEEVPADILTQILKAEEGAQDDEGLLDNFVTFFIAGHETSANHLAFTVMELSRQPEIVARLQAEVDEVIGSKRYLDFEDLGRLQYLSQVLKESLRLYPPAWGTFRLLEEETLIDGVRVPGNTPLLFSTYVMGRMDTYFEDPLTFNPDRFGPGAPKPRFTYFPFSLGHRSCIGQQFAQMEVKVVMAKLLQRLEFRLVPGQRFGLQEQATLKPLDPVLCTLRPRGWQPA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.15
R work: 0.1944
R free: 0.2439
Average B factor: 37.98
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 17.% PEG 3350, 0.35M Calcium Cl
Matthews coefficient: 2.1
Solvent content (%): 41.38
Ligand: PROTOPORPHYRIN IX CONTAINING FE (HEM)
Ligand formula: C34 H32 Fe N4 O4
Ligand molecular weight: 616.487
Ligand SMILES: Cc1c2n3c(c1CCC(=O)O)C=C4C(=C(C5=[N]4[Fe]36[N]7=C(C=C8N6C(=C5)C(=C8C)C=C)C(=C(C7=C2)C)C=C)C)CCC(=O)O
Ligand InChI: InChI=1S/C34H34N4O4.Fe/c1-7-21-17(3)25-13-26-19(5)23(9-11-33(39)40)31(37-26)16-32-24(10-12-34(41)42)20(6)28(38-32)15-30-22(8-2)18(4)27(36-30)14-29(21)35-25;/h7-8,13-16H,1-2,9-12H2,3-6H3,(H4,35,36,37,38,39,40,41,42);/q;+2/p-2/b25-13-,26-13-,27-14-,28-15-,29-14-,30-15-,31-16-,32-16-;
Release date: 2021-08-25
JAK2 JH1 in complex with PN2-118 (PDB entry 6VNG)
Macromolecule: Tyrosine-protein kinase JAK2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 308 residues
Sequence: HHHHHHHHENLYFQGDPTQFEERHLKFLQQLGKGNFGSVEMCRYDPLQDNTGEVVAVKKLQHSTEEHLRDFEREIEILKSLQHDNIVKYKGVCYSAGRRNLKLIMEYLPYGSLRDYLQKHKERIDHIKLLQYTSQICKGMEYLGTKRYIHRDLATRNILVENENRVKIGDFGLTKVLPQDKEYYKVKEPGESPIFWYAPESLTESKFSVASDVWSFGVVLYELFTYIEKSKSPPAEFMRMIGNDKQGQMIVFHLIELLKNNGRLPRPDGCPDEIYMIMTECWNNNVNQRPSFRDLALRVDQIRDNMAG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.5
R work: 0.2121
R free: 0.2506
Average B factor: 59.2892
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 291
Crystal growth procedure: 0.1 M Bis-Tris pH 5.5, 0.2 M NaCl, 25% PEG 3350
Matthews coefficient: 3.06
Solvent content (%): 59.76
Ligand: N-{2-fluoro-5-[(2-{[3-fluoro-4-(1-methylpiperidin-4-yl)phenyl]amino}-5-methylpyrimidin-4-yl)amino]phenyl}-2-methylpropane-2-sulfonamide (R6M)
Ligand formula: C27 H34 F2 N6 O2 S
Ligand molecular weight: 544.66
Ligand SMILES: Cc1cnc(nc1Nc2ccc(c(c2)NS(=O)(=O)C(C)(C)C)F)Nc3ccc(c(c3)F)C4CCN(CC4)C
Ligand InChI: InChI=1S/C27H34F2N6O2S/c1-17-16-30-26(32-19-6-8-21(23(29)14-19)18-10-12-35(5)13-11-18)33-25(17)31-20-7-9-22(28)24(15-20)34-38(36,37)27(2,3)4/h6-9,14-16,18,34H,10-13H2,1-5H3,(H2,30,31,32,33)
Release date: 2021-02-17
PanDDA analysis group deposition -- Crystal structure of PTP1B in complex with compound_FMOPL000619a (PDB entry 5QGE)
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): 1.703
R work: 0.1925
R free: 0.2226
Average B factor: 39.1384
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: well solution: 0.3 M magnesium acetate, 0.1 M HEPES pH 7.5, 0.1% beta-mercaptoethanol, 13-14% PEG 8000, 2% ethanol
Matthews coefficient: 3.36
Solvent content (%): 63.34
Ligand: 4-({[(thiophen-2-yl)methyl]amino}methyl)phenol (JKG)
Ligand formula: C12 H13 N O S
Ligand molecular weight: 219.303
Ligand SMILES: c1cc(sc1)CNCc2ccc(cc2)O
Ligand InChI: InChI=1S/C12H13NOS/c14-11-5-3-10(4-6-11)8-13-9-12-2-1-7-15-12/h1-7,13-14H,8-9H2
Release date: 2018-10-10
Carbonic anhydrase II in complex with 4-(3-formylphenyl)-benzenesulfonamide (PDB entry 5SZ2)
Macromolecule: Carbonic anhydrase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 257 residues
Sequence: HWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHAFNVEFDDSQDKAVLKGGPLDGTYRLIQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDFGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTKGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLLECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.63
R work: 0.1503
R free: 0.1797
Average B factor: 17.032
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 296
Crystal growth procedure: 1.6M Sodium Citrate, 50mM Tris pH 7.8
Matthews coefficient: 2.11
Solvent content (%): 41.72
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: 2016-12-21
NaClO4--Interactions between Hofmeister Anions and the Binding Pocket of a Protein (PDB entry 4YGL)
Macromolecule: Carbonic anhydrase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 258 residues
Sequence: HHWGYGGHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHAFNVEFDDSQDKAVLKGGPLDGTYRLIQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDFGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTKGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLLECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.51
R work: 0.18783
R free: 0.21335
Average B factor: 11.346
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.8
Crystallization temperature (K): 277
Crystal growth procedure: 100 mM Tris-Cl, 1.15 M sodium citrate, pH 7.8
Matthews coefficient: 2.11
Solvent content (%): 41.68
Ligand: PERCHLORATE ION (LCP)
Ligand formula: Cl O4
Ligand molecular weight: 99.451
Ligand SMILES: [O-]Cl(=O)(=O)=O
Ligand InChI: InChI=1S/ClHO4/c2-1(3,4)5/h(H,2,3,4,5)/p-1
Release date: 2015-03-25
Structure of DYRK1A in complex with AMPNP (PDB entry 7A4O)
Macromolecule: Dual specificity tyrosine-phosphorylation-regulated kinase 1A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.12.1
Sequence length: 382 residues
Sequence: MHHHHHHSSGVDLGTENLYFQSMSSHKKERKVYNDGYDDDNYDYIVKNGEKWMDRYEIDSLIGKGSFGQVVKAYDRVEQEWVAIKIIKNKKAFLNQAQIEVRLLELMNKHDTEMKYYIVHLKRHFMFRNHLCLVFEMLSYNLYDLLRNTNFRGVSLNLTRKFAQQMCTALLFLATPELSIIHCDLKPENILLCNPKRSAIKIVDFGSSCQLGQRIYQYIQSRFYRSPEVLLGMPYDLAIDMWSLGCILVEMHTGEPLFSGANEVDQMNKIVEVLGIPPAHILDQAPKARKFFEKLPDGTWNLKKTKDGKREYKPPGTRKLHNILGVETGGPGGRRAGESGHTVADYLKFKDLILRMLDYDPKTRIQPYYALQHSFFKKTADE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.9
R work: 0.179
R free: 0.203
Average B factor: 30.01
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M MES buffer at pH 6.5, 12% Peg3350, 0.2M MgCl2
Matthews coefficient: 2.25
Solvent content (%): 45.24
Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER (ANP)
Ligand formula: C10 H17 N6 O12 P3
Ligand molecular weight: 506.196
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(NP(=O)(O)O)O)O)O)N
Ligand InChI: InChI=1S/C10H17N6O12P3/c11-8-5-9(13-2-12-8)16(3-14-5)10-7(18)6(17)4(27-10)1-26-31(24,25)28-30(22,23)15-29(19,20)21/h2-4,6-7,10,17-18H,1H2,(H,24,25)(H2,11,12,13)(H4,15,19,20,21,22,23)/t4-,6-,7-,10-/m1/s1
Release date: 2021-06-30
Scaffold Hopping via Ring Opening Enables Identification of Acyclic Compounds as New Complement Factor D Inhibitors (PDB entry 8D95)
Macromolecule: Complement factor D
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.46
Sequence length: 230 residues
Sequence: ILGGREAEAHARPYMASVQLNGAHLCGGVLVAEQWVLSAAHCLEDAADGKVQVLLGAHSLSQPEPSKRLYDVLRAVPHPDSQPDTIDHDLLLLQLSEKATLGPAVRPLPWQRVDRDVAPGTLCDVAGWGIVNHAGRRPDSLQHVLLPVLDRATCNRRTHHDGAITERLMCAESNRRDSCKGDSGGPLVCGGVLEGVVTSGSRVCGNRKKPGIYTRVASYAAWIDSVLASA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.166
R work: 0.2018
R free: 0.2629
Average B factor: 30.734
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.8
Crystallization temperature (K): 300
Crystal growth procedure: PEG 6k
Matthews coefficient: 1.97
Solvent content (%): 37
Ligand: N-(6-bromopyridin-2-yl)-1-[(3-cyanophenyl)acetyl]-L-prolinamide (QIE)
Ligand formula: C19 H17 Br N4 O2
Ligand molecular weight: 413.268
Ligand SMILES: c1cc(cc(c1)C#N)CC(=O)N2CCCC2C(=O)Nc3cccc(n3)Br
Ligand InChI: InChI=1S/C19H17BrN4O2/c20-16-7-2-8-17(22-16)23-19(26)15-6-3-9-24(15)18(25)11-13-4-1-5-14(10-13)12-21/h1-2,4-5,7-8,10,15H,3,6,9,11H2,(H,22,23,26)/t15-/m0/s1
Release date: 2022-11-02
SelDeg51 in complex with FKBP51FK1 domain and pVHL:EloB:EloC (PDB entry 8PC2)
Macromolecule: von Hippel-Lindau disease tumor suppressor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 162 residues
Sequence: GSMEAGRPRPVLRSVNSREPSQVIFCNRSPRVVLPVWLNFDGEPQPYPTLPPGTGRRIHSYRGHLWLFRDAGTHDGLLVNQTELFVPSLNVDGQPIFANITLPVYTLKERCLQVVRSLVKPENYRRLDIVRSLYEDLEDHPNVQKDLERLTQERIAHQRMGD
Oligomeric state: Hetero 4-mer
Stoichiometry: A1, B1, C1, D1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.8
R work: 0.2104
R free: 0.2607
Average B factor: 74.69
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 15% PEG3350, 0.2 M tri-sodium citrate, 0.1 M HEPES-NaOH pH 7.5 and 10% glycol
Matthews coefficient: 3.1
Solvent content (%): 60.34
Ligand: [(1~{R})-3-(3,4-dimethoxyphenyl)-1-[4-[[1-[3-[2-[[[(2~{S},4~{R})-1-[(2~{S})-2-[(1-fluoranylcyclopropyl)carbonylamino]-3,3-dimethyl-butanoyl]-4-oxidanyl-pyrrolidin-2-yl]carbonylamino]methyl]-5-(4-methyl-1,3-thiazol-5-yl)phenoxy]propyl]-1,2,3-triazol-4-yl]methoxy]phenyl]propyl] (2~{S})-1-[(2~{S})-2-cyclohexyl-2-(3,4,5-trimethoxyphenyl)ethanoyl]piperidine-2-carboxylate (XZW)
Ligand formula: C72 H91 F N8 O14 S
Ligand molecular weight: 1343.602
Ligand SMILES: Cc1c(scn1)c2ccc(c(c2)OCCCn3cc(nn3)COc4ccc(cc4)C(CCc5ccc(c(c5)OC)OC)OC(=O)C6CCCCN6C(=O)C(c7cc(c(c(c7)OC)OC)OC)C8CCCCC8)CNC(=O)C9CC(CN9C(=O)C(C(C)(C)C)NC(=O)C1(CC1)F)O
Ligand InChI: InChI=1S/C72H91FN8O14S/c1-44-64(96-43-75-44)48-21-22-49(39-74-66(83)55-38-52(82)41-81(55)68(85)65(71(2,3)4)76-70(87)72(73)29-30-72)58(35-48)93-33-15-31-79-40-51(77-78-79)42-94-53-25-23-46(24-26-53)56(27-19-45-20-28-57(88-5)59(34-45)89-6)95-69(86)54-18-13-14-32-80(54)67(84)62(47-16-11-10-12-17-47)50-36-60(90-7)63(92-9)61(37-50)91-8/h20-26,28,34-37,40,43,47,52,54-56,62,65,82H,10-19,27,29-33,38-39,41-42H2,1-9H3,(H,74,83)(H,76,87)/t52-,54+,55+,56-,62+,65-/m1/s1
Release date: 2023-11-15
In-Gel Activity-Based Protein Profiling of a Clickable Covalent Erk 1/2 Inhibitor (PDB entry 5LCJ)
Macromolecule: Mitogen-activated protein kinase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.24
Sequence length: 368 residues
Sequence: MAHHHHHHMAAAAAAGAGPEMVRGQVFDVGPRYTNLSYIGEGAYGMVCSAYDNVNKVRVAIKKISPFEHQTYCQRTLREIKILLRFRHENIIGINDIIRAPTIEQMKDVYIVQDLMETDLYKLLKTQHLSNDHICYFLYQILRGLKYIHSANVLHRDLKPSNLLLNTTCDLKICDFGLARVADPDHDHTGFLTEYVATRWYRAPEIMLNSKGYTKSIDIWSVGCILAEMLSNRPIFPGKHYLDQLNHILGILGSPSQEDLNCIINLKARNYLLSLPHKNKVPWNRLFPNADSKALDLLDKMLTFNPHKRIEVEQALAHPYLEQYYDPSDEPIAEAPFKFDMELDDLPKEKLKELIFEETARFQPGYRS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.78
R work: 0.162
R free: 0.212
Average B factor: 35.814
Crystallization method: BATCH MODE
Crystallization pH: 7.2
Crystallization temperature (K): 297
Crystal growth procedure: .2M (NH4)2SO4
32% MPEG 2000
.02M Mercaptoethanol
.1M pH=7.2 HEPES/NaOH
Matthews coefficient: 2.31
Solvent content (%): 46.65
Ligand: [(1~{R},4~{Z})-cyclooct-4-en-1-yl] ~{N}-[4-[4-[[5-chloranyl-4-[[2-(propanoylamino)phenyl]amino]pyrimidin-2-yl]amino]pyridin-2-yl]but-3-ynyl]carbamate (6TS)
Ligand formula: C31 H34 Cl N7 O3
Ligand molecular weight: 588.1
Ligand SMILES: CCC(=O)Nc1ccccc1Nc2c(cnc(n2)Nc3ccnc(c3)C#CCCNC(=O)OC4CCCC=CCC4)Cl
Ligand InChI: InChI=1S/C31H34ClN7O3/c1-2-28(40)37-26-15-8-9-16-27(26)38-29-25(32)21-35-30(39-29)36-23-17-19-33-22(20-23)12-10-11-18-34-31(41)42-24-13-6-4-3-5-7-14-24/h3-4,8-9,15-17,19-21,24H,2,5-7,11,13-14,18H2,1H3,(H,34,41)(H,37,40)(H2,33,35,36,38,39)/b4-3-/t24-/m0/s1
Release date: 2016-07-20