satarupa22/MacromolecularLigandDB huggingface dataset:
Structure of the nuclease subunit of human mitochondrial RNase P (MRPP3) at 1.8A (PDB entry 4XGL)
Macromolecule: Mitochondrial ribonuclease P protein 3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.26.5
Sequence length: 379 residues
Sequence: SMTLEPRGYSLLIRGLIHSDRWREALLLLEDIKKVITPSKKNYNDCIQGALLHQDVNTAWNLYQELLGHDIVPMLETLKAFFDFGKDIKDDNYSNKLLDILSYLRNNQLYPGESFAHSIKTWFESVPGKQWKGQFTTVRKSGQCSGCGKTIESIQLSPEEYECLKGKIMRDVIDGGDQYRKTTPQELKRFENFIKSRPPFDVVIDGLNVAKMFPKVRESQLLLNVVSQLAKRNLRLLVLGRKHMLRRSSQWSRDEMEEVQKQASCFFADDISEDDPFLLYATLHSGNHCRFITRDLMRDHKACLPDAKTQRLFFKWQQGHQLAIVNRFPGSKLTFQRILSYDTVVQTTGDSWHIPYDEDLVERCSCEVPTKWLCLHQKT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.1885
R free: 0.2276
Average B factor: 61.5153
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6
Crystallization temperature (K): 298
Crystal growth procedure: potassium citrate, PEG3350, magnesium chloride
Matthews coefficient: 2.84
Solvent content (%): 56.74
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: 2015-05-13
Aspartyl/Asparaginyl beta-hydroxylase (AspH) oxygenase and TPR domains in complex with L-2-hydroxyglutarate and factor X-derived peptide (39mer-4Ser) (PDB entry 7YB9)
Macromolecule: Coagulation factor X
Type: Protein, polypeptide(L)
Source organism: synthetic construct
EC number: 3.4.21.6
Sequence length: 39 residues
Sequence: DGDQSETSPSQNQGKCKDGLGEYTCTSLEGFEGKNSELF
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.54
R work: 0.1849
R free: 0.2147
Average B factor: 43.47
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.2 M lithium chloride, 20 % w/v Polyethylene glycol 6,000, 0.1 M Bis-Tris propane
Matthews coefficient: 2.61
Solvent content (%): 52.86
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: 2023-07-05
PanDDA analysis group deposition -- Crystal Structure of ATAD2 in complex with JKH93A (PDB entry 5QXY)
Macromolecule: ATPase family AAA domain-containing protein 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.1.3
Sequence length: 130 residues
Sequence: SMQEEDTFRELRIFLRNVTHRLAIDKRFRVFTKPVDPDEVPDYRTVIKEPMDLSSVISKIDLHKYLTVKDYLRDIDLICSNALEYNPDRDPGDRLIRHRACALRDTAYAIIKEELDEDFEQLCEEIQESR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.54
R work: 0.1626
R free: 0.1724
Average B factor: 23.401
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 277
Crystal growth procedure: 1.6M Ammonium Sulfate, 0.1M bis-tris pH 5.5
Matthews coefficient: 4.2
Solvent content (%): 70.7
Ligand: ethyl (2R,3S)-3-(5-bromopyridin-2-yl)-2-fluoro-3-hydroxypropanoate (RK7)
Ligand formula: C10 H11 Br F N O3
Ligand molecular weight: 292.102
Ligand SMILES: CCOC(=O)C(C(c1ccc(cn1)Br)O)F
Ligand InChI: InChI=1S/C10H11BrFNO3/c1-2-16-10(15)8(12)9(14)7-4-3-6(11)5-13-7/h3-5,8-9,14H,2H2,1H3/t8-,9+/m1/s1
Release date: 2020-04-08
Crystal structure of Trk-A in complex with the Pan-Trk Kinase Inhibitor, compound 13b. (PDB entry 6DKG)
Macromolecule: High affinity nerve growth factor receptor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 320 residues
Sequence: GSTEGKGSGLQGHIIENPQYFSDACVHHIKRRDIVLKWELGEGAFGKVFLAECHNLLPEQDKMLVAVKALKEASESARQDFQREAELLTMLQHQHIVRFFGVCTEGRPLLMVFEYMRHGDLNRFLRSHGPDAKLLAGGEDVAPGPLGLGQLLAVASQVAAGMVYLAGLHFVHRDLATRNCLVGQGLVVKIGDFGMSRDIYSTDYYRVGGRTMLPIRWMPPESILYRKFTTESDVWSFGVVLWEIFTYGKQPWYQLSNTEAIDCITQGRELERPRACPPEVYAIMRGCWQREPQQRHSIKDVHARLQALAQAPPVYLDVLG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.53
R work: 0.1875
R free: 0.2254
Average B factor: 54.8
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 294
Crystal growth procedure: Compound 13b soaked for 30 min into preformed crystals of TrkA.
Well volume: 50.0 uL
Well Ingredients:
Polymer: 9.0 %w/v (9.0 uL of stock 50.0 %w/v) PEG 3350
Buffer: 15.8 %v/v (7.9 uL of stock 100.0 %v/v) tacsimate (pH 8.00)
Additive: 0.025 M (12.5 uL of stock 0.1 M) TCEP hydrochloride

Plate setup temperature: 13 C
Plate incubation temperature: 21 C

Drop volume from well: 0.0050 uL
Drop protein volume: 0.34 uL
Matthews coefficient: 2.25
Solvent content (%): 45.28
Ligand: 5-phenylthieno[2,3-d]pyrimidin-4(3H)-one (22L)
Ligand formula: C12 H8 N2 O S
Ligand molecular weight: 228.27
Ligand SMILES: c1ccc(cc1)c2csc3c2C(=O)NC=N3
Ligand InChI: InChI=1S/C12H8N2OS/c15-11-10-9(8-4-2-1-3-5-8)6-16-12(10)14-7-13-11/h1-7H,(H,13,14,15)
Release date: 2018-07-11
Structure of human beta 1,3-N-acetylglucosaminyltransferase 2 with UDP (PDB entry 7JHO)
Macromolecule: N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.4.1.149
Sequence length: 370 residues
Sequence: MHHHHHHHHENLYFQGSKEKFWKISTPPEAYWNREQEKLNRQYNPILSMLTNQTGEAGRLSNISHLNYCEPDLRVTSVVTGFNNLPDRFKDFLLYLRCRNYSLLIDQPDKCAKKPFLLLAIKSLTPHFARRQAIRESWGQESNAGNQTVVRVFLLGQTPPEDNHPDLSDMLKFESEKHQDILMWNYRDTFFNLSLKEVLFLRWVSTSCPDTEFVFKGDDDVFVNTHHILNYLNSLSKTKAKDLFIGDVIHNAGPHRDKKLKYYIPEVVYSGLYPPYAGGGGFLYSGHLALRLYHITDQVHLYPIDDVYTGMCLQKLGLVPEKHKGFRTFDIEEKNKNNICSYVDLMLVHSRKPQEMIDIWSQLQSAHLKC
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.85
R work: 0.1649
R free: 0.2111
Average B factor: 25.4806
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 24% PEG1500, 20% glycerol
Matthews coefficient: 2.36
Solvent content (%): 47.97
Ligand: URIDINE-5'-DIPHOSPHATE (UDP)
Ligand formula: C9 H14 N2 O12 P2
Ligand molecular weight: 404.161
Ligand SMILES: C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)O)O)O
Ligand InChI: InChI=1S/C9H14N2O12P2/c12-5-1-2-11(9(15)10-5)8-7(14)6(13)4(22-8)3-21-25(19,20)23-24(16,17)18/h1-2,4,6-8,13-14H,3H2,(H,19,20)(H,10,12,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1
Release date: 2020-11-18
Human carbonic anhydrase II in complex with 6-SULFAMOYL-SACCHARIN (PDB entry 4XE1)
Macromolecule: Carbonic anhydrase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 262 residues
Sequence: MGMSHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHAFNVEFDDSQDKAVLKGGPLDGTYRLIQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDFGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTKGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLLECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.168
R free: 0.214
Average B factor: 14.2
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: AMMONIUM SULPHATE 2.6M, TRIS-HCL 0.1M, SODIUM CHLORIDE 0.3M, 4-HYDROXYMERCURYBENZOATE
Matthews coefficient: 2.07
Solvent content (%): 40.7
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: 2015-03-18
Crystal structure of compound 6 in complex with the bromodomain of human SMARCA2 and pVHL:ElonginC:ElonginB (PDB entry 7Z77)
Macromolecule: Elongin-B
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 104 residues
Sequence: MDVFLMIRRHKTTIFTDAKESSTVFELKRIVEGILKRPPDEQRLYKDDQLLDDGKTLGECGFTSQTARPQAPATVGLAFRADDTFEALCIEPFSSPPELPDVMK
Oligomeric state: Hetero 4-mer
Stoichiometry: A1, B1, C1, D1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.97
R work: 0.213
R free: 0.251
Average B factor: 55.34
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: 20 % PEG 3350, 0.1 M BIS_TRIS propane pH 7.5, 200 mM sodium formate
Matthews coefficient: 2.52
Solvent content (%): 51.13
Ligand: (2~{S},4~{R})-~{N}-[(1~{S})-4-[4-(4-bromanyl-7-cyclopentyl-5-oxidanylidene-benzimidazolo[1,2-a]quinazolin-9-yl)piperidin-1-yl]-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]butyl]-1-[(2~{S})-2-[(1-fluoranylcyclopropyl)carbonylamino]-3,3-dimethyl-butanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide (IFF)
Ligand formula: C53 H62 Br F N8 O5 S
Ligand molecular weight: 1022.077
Ligand SMILES: Cc1c(scn1)c2ccc(cc2)C(CCCN3CCC(CC3)c4ccc5c(c4)N(C6=NC(=O)c7c(cccc7Br)N56)C8CCCC8)NC(=O)C9CC(CN9C(=O)C(C(C)(C)C)NC(=O)C1(CC1)F)O
Ligand InChI: InChI=1S/C53H62BrFN8O5S/c1-31-45(69-30-56-31)34-16-14-33(15-17-34)39(57-47(65)43-28-37(64)29-61(43)49(67)46(52(2,3)4)58-50(68)53(55)22-23-53)12-8-24-60-25-20-32(21-26-60)35-18-19-40-42(27-35)62(36-9-5-6-10-36)51-59-48(66)44-38(54)11-7-13-41(44)63(40)51/h7,11,13-19,27,30,32,36-37,39,43,46,64H,5-6,8-10,12,20-26,28-29H2,1-4H3,(H,57,65)(H,58,68)/t37-,39+,43+,46-/m1/s1
Release date: 2022-09-14
Crystal structure of human DNMT3B (Q772R)-DNMT3L complex (PDB entry 6KDT)
Macromolecule: DNA (cytosine-5)-methyltransferase 3B
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1.37
Sequence length: 286 residues
Sequence: GHMRRRPIRVLSLFDGIATGYLVLKELGIKVGKYVASEVCEESIAVGTVKHEGNIKYVNDVRNITKKNIEEWGPFDLVIGGSPCNDLSNVNPARKGLYEGTGRLFFEFYHLLNYSRPKEGDDRPFFWMFENVVAMKVGDKRDISRFLECNPVMIDAIKVSAAHRARYFWGNLPGMNRPVIASKNDKLELQDCLEYNRIAKLKKVRTITTKSNSIKQGKNQLFPVVMNGKEDVLWCTELERIFGFPVHYTDVSNMGRGARQKLLGRSWSVPVIRHLFAPLKDYFACE
Oligomeric state: Hetero 4-mer
Stoichiometry: A2, B2
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.87
R work: 0.1938
R free: 0.2422
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 278
Crystal growth procedure: 2.2 M sodium formate
Matthews coefficient: 3.74
Solvent content (%): 67.11
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: 2020-02-19
DYRK1A in complex with hydroxy benzothiazole fragment (PDB entry 5A3X)
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): 2.26
R work: 0.23484
R free: 0.25867
Average B factor: 47.633
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.8
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M KSCN; 0.1M KCL; 14% PEG 3350, PH 6.8, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K
Matthews coefficient: 2.6
Solvent content (%): 53
Ligand: N-(5-oxidanyl-1,3-benzothiazol-2-yl)ethanamide (QIV)
Ligand formula: C9 H8 N2 O2 S
Ligand molecular weight: 208.237
Ligand SMILES: CC(=O)Nc1nc2cc(ccc2s1)O
Ligand InChI: InChI=1S/C9H8N2O2S/c1-5(12)10-9-11-7-4-6(13)2-3-8(7)14-9/h2-4,13H,1H3,(H,10,11,12)
Release date: 2016-06-29
Crystal Structure of Ubc9 (K48A/K49A/E54A) complexed with Fragment 8 (JSS190B146) (PDB entry 5F6U)
Macromolecule: SUMO-conjugating enzyme UBC9
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 6.3.2
Sequence length: 157 residues
Sequence: SGIALSRLAQERKAWRKDHPFGFVAVPTKNPDGTMNLMNWECAIPGAAGTPWAGGLFKLRMLFKDDYPSSPPKCKFEPPLFHPNVYPSGTVCLSILEEDKDWRPAITIKQILLGIQELLNEPNIQDPAQAEAYTIYCQNRVEYEKRVRAQAKKFAPS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.552
R work: 0.1755
R free: 0.203
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 294
Crystal growth procedure: 0.1M Tris pH 8.5, 8% (w/v) polyethylene glycol
Matthews coefficient: 2.75
Solvent content (%): 55.29
Ligand: ethyl 3-[4-(2-hydroxyphenyl)-3-oxidanyl-phenyl]propanoate (5VK)
Ligand formula: C17 H18 O4
Ligand molecular weight: 286.322
Ligand SMILES: CCOC(=O)CCc1ccc(c(c1)O)c2ccccc2O
Ligand InChI: InChI=1S/C17H18O4/c1-2-21-17(20)10-8-12-7-9-14(16(19)11-12)13-5-3-4-6-15(13)18/h3-7,9,11,18-19H,2,8,10H2,1H3
Release date: 2016-04-27
USP7 IN COMPLEX WITH LIGAND COMPOUND 7 (PDB entry 6VN5)
Macromolecule: Ubiquitin carboxyl-terminal hydrolase 7
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.19.12
Sequence length: 350 residues
Sequence: GSKKHTGYVGLKNQGATCYMNSLLQTLFFTNQLRKAVYMMPTEGDDSSKSVPLALQRVFYELQHSDKPVGTKKLTKSFGWETLDSFMQHDVQELCRVLLDNVENKMKGTCVEGTIPKLFRGKMVSYIQCKEVDYRSDRREDYYDIQLSIKGKKNIFESFVDYVAVEQLDGDNKYDAGEHGLQEAEKGVKFLTLPPVLHLQLMRFMYDPQTDQNIKINDRFEFPEQLPLDEFLQKTDPKDPANYILHAVLVHSGDNHGGHYVVYLNPKGDGKWCKFDDDVVSRCTKEEAIEHNYGGHDDDLSVRHCTNAYMLVYIRESKLSEVLQAVTDHDIPQQLVERLQEEKRIEAQKR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.9
R work: 0.2135
R free: 0.2678
Average B factor: 82.634
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 277
Matthews coefficient: 2.5
Solvent content (%): 50.75
Ligand: [(2R)-7-(2-aminopyridin-4-yl)-5-chloro-2,3-dihydro-1-benzofuran-2-yl](piperazin-1-yl)methanone (R41)
Ligand formula: C18 H19 Cl N4 O2
Ligand molecular weight: 358.822
Ligand SMILES: c1cnc(cc1c2cc(cc3c2OC(C3)C(=O)N4CCNCC4)Cl)N
Ligand InChI: InChI=1S/C18H19ClN4O2/c19-13-7-12-8-15(18(24)23-5-3-21-4-6-23)25-17(12)14(10-13)11-1-2-22-16(20)9-11/h1-2,7,9-10,15,21H,3-6,8H2,(H2,20,22)/t15-/m1/s1
Release date: 2020-04-29
PanDDA analysis group deposition -- Crystal structure of PTP1B in complex with compound_FMOMB000140a (PDB entry 5QFC)
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): 1.841
R work: 0.1809
R free: 0.2131
Average B factor: 42.7043
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: 3.32
Solvent content (%): 62.97
Ligand: N-[(thiophen-2-yl)methyl]benzenesulfonamide (JNA)
Ligand formula: C11 H11 N O2 S2
Ligand molecular weight: 253.341
Ligand SMILES: c1ccc(cc1)S(=O)(=O)NCc2cccs2
Ligand InChI: InChI=1S/C11H11NO2S2/c13-16(14,11-6-2-1-3-7-11)12-9-10-5-4-8-15-10/h1-8,12H,9H2
Release date: 2018-10-10
Structure of TYK2 with inhibitor 4: 3-azanyl-5-(2-methylphenyl)-7-(1-methylpyrazol-3-yl)-1~{H}-pyrazolo[4,3-c]pyridin-4-one (PDB entry 5F20)
Macromolecule: Non-receptor tyrosine-protein kinase TYK2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 301 residues
Sequence: MGSPASDPTVFHKRYLKKIRDLGEGHFGKVSLYCYDPTNDGTGEMVAVKALKADCGPQHRSGWKQEIDILRTLYHEHIIKYKGCCEDQGEKSLQLVMEYVPLGSLRDYLPRHSIGLAQLLLFAQQICEGMAYLHSQHYIHRNLAARNVLLDNDRLVKIGDFGLAKAVPEGHEYYRVREDGDSPVFWYAPECLKEYKFYYASDVWSFGVTLYELLTHCDSSQSPPTKFLELIGIAQGQMTVLRLTELLERGERLPRPDKCPCEVYHLMKNCWETEASFRPTFENLIPILKTVHEKYHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.91
R work: 0.2013
R free: 0.2877
Average B factor: 96.157
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6
Crystallization temperature (K): 293
Crystal growth procedure: 15% PEG 5000 MME, and 100 mM Sodium Citrate (pH 6.0)
Matthews coefficient: 2.31
Solvent content (%): 46.74
Ligand: 3-azanyl-5-(2-methylphenyl)-7-(1-methylpyrazol-3-yl)-1~{H}-pyrazolo[4,3-c]pyridin-4-one (5U4)
Ligand formula: C17 H16 N6 O
Ligand molecular weight: 320.349
Ligand SMILES: Cc1ccccc1N2C=C(c3c(c(n[nH]3)N)C2=O)c4ccn(n4)C
Ligand InChI: InChI=1S/C17H16N6O/c1-10-5-3-4-6-13(10)23-9-11(12-7-8-22(2)21-12)15-14(17(23)24)16(18)20-19-15/h3-9H,1-2H3,(H3,18,19,20)
Release date: 2016-01-13
Crystal structure of cGMP dependent protein kinase I alpha (PKG I alpha)CNB-A domain with R177Q mutation (PDB entry 7MBJ)
Macromolecule: cGMP-dependent protein kinase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.12
Sequence length: 134 residues
Sequence: QAFRKFTKSERSKDLIKEAILDNDFMKNLELSQIQEIVDCMYPVEYGKDSCIIKEGDVGSLVYVMEDGKVEVTKEGVKLCTMGPGKVFGELAILYNCTQTATVKTLVNVKLWAIDRQCFQTIMMRTGLIKHTEY
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.26
R work: 0.1775
R free: 0.197
Average B factor: 23.17
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 4.5
Crystallization temperature (K): 277
Crystal growth procedure: 6% Tacsimate (pH 4.5), 18% PEG 3350
Matthews coefficient: 2.07
Solvent content (%): 40.7
Release date: 2022-05-11
MTH1 in complex with fragment 9 (PDB entry 6EQ3)
Macromolecule: 7,8-dihydro-8-oxoguanine triphosphatase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.1.55
Sequence length: 182 residues
Sequence: MKHHHHHHPMSDYDIPTTENLYFQGAMGASRLYTLVLVLQPQRVLLGMKKRGFGAGRWNGFGGKVQEGETIEDGARRELQEESGLTVDALHKVGQIVFEFVGEPELMDVHVFCTDSIQGTPVESDEMRPCWFQLDQIPFKDMWPDDSYWFPLLLQKKKFHGYFKFQGQDTILDYTLREVDTV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.798
R work: 0.1799
R free: 0.2234
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 4.5
Crystallization temperature (K): 293
Crystal growth procedure: 23 % PEG3350, 0.2 M LI2SO4, 0.1 M SODIUM ACETATE PH 4.5
Ligand: [2-(1~{H}-pyrrolo[2,3-b]pyridin-4-yl)-1,3-thiazol-4-yl]methanol (BU5)
Ligand formula: C11 H9 N3 O S
Ligand molecular weight: 231.274
Ligand SMILES: c1c[nH]c2c1c(ccn2)c3nc(cs3)CO
Ligand InChI: InChI=1S/C11H9N3OS/c15-5-7-6-16-11(14-7)9-2-4-13-10-8(9)1-3-12-10/h1-4,6,15H,5H2,(H,12,13)
Release date: 2018-10-31
Small Molecule inhibitors of IAP (PDB entry 5M6M)
Macromolecule: E3 ubiquitin-protein ligase XIAP
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 6.3.2
Sequence length: 127 residues
Sequence: MGSSHHHHHHSSGLVPRGSHMNFPNSTNLPRNPSMADYEARIFTFGTWIYSVNKEQLARAGFYALGEGDKVKCFHCGGGLTDWKPSEDPWEQHAKWYPGCKYLLEQKGQEYINNIHLTHSLEECLVR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.37
R work: 0.187
R free: 0.233
Average B factor: 42.763
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8
Crystallization temperature (K): 277
Crystal growth procedure: 3.3M NaCl
.1M pH=8 HEPES/NaOH
Matthews coefficient: 4.58
Solvent content (%): 73.16
Ligand: SODIUM ION ()
Ligand formula: Na
Ligand molecular weight: 22.99
Ligand SMILES: [Na+]
Ligand InChI: InChI=1S/Na/q+1
Release date: 2017-05-24
Fragment-based inhibitors of Lipoprotein associated Phospholipase A2 (PDB entry 5LYY)
Macromolecule: Platelet-activating factor acetylhydrolase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.1.47
Sequence length: 388 residues
Sequence: MAAASFGQTKIPRGNGPYSVGCTDLMFDHTNKGTFLRLYYPSQDNDRLDTLWIPNKEYFWGLSKFLGTHWLMGNILRLLFGSMTTPANWNSPLRPGEKYPLVVFSHGLGAFRTLYSAIGIDLASHGFIVAAVEHRDRSASATYYFKDQSAAEIGDKSWLYLRTLKQEEETHIRNEQVRQRAKECSQALSLILDIDHGKPVKNALDLKFDMEQLKDSIDREKIAVIGHSFGGATVIQTLSEDQRFRCGIALDAWMFPLGDEVYSRIPQPLFFINSEYFQYPANIIKMKKCYSPDKERKMITIRGSVHQNFADFTFATGKIIGHMLKLKGDIDSNVAIDLSNKASLAFLQKHLGLHKDFDQWDCLIEGDDENLIPGTNINTTNQHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.17
R work: 0.1773
R free: 0.22523
Average B factor: 40.016
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.4
Crystallization temperature (K): 293
Crystal growth procedure: 28.0%w/v PEG 3350, 0.1M HEPES/NaOHpH=7.4, 1.3M NaCl
Matthews coefficient: 2.45
Solvent content (%): 49.88
Ligand: 3-[2-(4-fluoranylphenoxy)ethyl]-1,3-diazaspiro[4.5]decane-2,4-dione (7BJ)
Ligand formula: C16 H19 F N2 O3
Ligand molecular weight: 306.332
Ligand SMILES: c1cc(ccc1OCCN2C(=O)C3(CCCCC3)NC2=O)F
Ligand InChI: InChI=1S/C16H19FN2O3/c17-12-4-6-13(7-5-12)22-11-10-19-14(20)16(18-15(19)21)8-2-1-3-9-16/h4-7H,1-3,8-11H2,(H,18,21)
Release date: 2016-12-21
Crystal structure of PTP1B D181A/Q262A phosphatase domain with a JAK3 activation loop phosphopeptide (PDB entry 8EXM)
Macromolecule: Tyrosine-protein phosphatase non-receptor type 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 299 residues
Sequence: MEMEKEFEQIDKSGSWAAIYEDIRHEASDFPCRVAKLPKNKNRNRYRDVSPFDHSRIKLHQEDNDYINASLIKMEEAQRSYILTQGPLPNTCGHFWEMVWEQKSRGVVMLNRVMEKGSLKCAQYWPQKEEKEMIFEDTNLKLTLISEDIKSYYTVRQLELENLTTQETREILHFHYTTWPAFGVPESPASFLNFLFKVRESGSLSPEHGPVVVHCSAGIGRSGTFCLADTCLLLMDKRKDPSSVDIKKVLLEMRKFRMGLIATADQLRFSYLAVIEGAKFIMGDSSVQDQWKELSHEDL
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.349
R work: 0.206
R free: 0.2475
Average B factor: 61.5873
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 281.15
Crystal growth procedure: 12% Peg 4K, 0.15 M Calcium acetate, 0.05 M MES (pH 6.5)
Matthews coefficient: 3.67
Solvent content (%): 66.52
Ligand: PHOSPHATE ION (PO4)
Ligand formula: O4 P
Ligand molecular weight: 94.971
Ligand SMILES: [O-]P(=O)([O-])[O-]
Ligand InChI: InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4)/p-3
Release date: 2023-07-05
Crystal structures of spleen tyrosine kinase in complex with a novel inhibitor (PDB entry 5Y5T)
Macromolecule: Tyrosine-protein kinase SYK
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 293 residues
Sequence: MALEEIRPKEVYLDRKLLTLEDKELGSGNFGTVKKGYYQMKKVVKTVAVKILKNEANDPALKDELLAEANVMQQLDNPYIVRMIGICEAESWMLVMEMAELGPLNKYLQQNRHVKDKNIIELVHQVSMGMKYLEESNFVHRDLAARNVLLVTQHYAKISDFGLSKALRADENYYKAQTHGKWPVKWYAPECINYYKFSSKSDVWSFGVLMWEAFSYGQKPYRGMKGSEVTAMLEKGERMGCPAGCPREMYDLMNLCWTYDVENRPGFAAVELRLRNYYYDVVNLEHHHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.19391
R free: 0.2344
Average B factor: 41.174
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 10-20% PEG 3350, 100mM Tris-HCl, pH 8.5
Matthews coefficient: 2.08
Solvent content (%): 40.77
Ligand: 2-[[(1S,2S)-2-azanylcyclohexyl]amino]-4-[(4-methylsulfonylphenyl)amino]-6H-pyrido[4,3-d]pyrimidin-5-one (8OR)
Ligand formula: C20 H24 N6 O3 S
Ligand molecular weight: 428.508
Ligand SMILES: CS(=O)(=O)c1ccc(cc1)Nc2c3c(nc(n2)NC4CCCCC4N)C=CNC3=O
Ligand InChI: InChI=1S/C20H24N6O3S/c1-30(28,29)13-8-6-12(7-9-13)23-18-17-16(10-11-22-19(17)27)25-20(26-18)24-15-5-3-2-4-14(15)21/h6-11,14-15H,2-5,21H2,1H3,(H,22,27)(H2,23,24,25,26)/t14-,15-/m0/s1
Release date: 2018-06-27