satarupa22/MacromolecularLigandDB huggingface dataset:
PanDDA analysis group deposition -- Crystal structure of PTP1B in complex with FMOPL000089a (PDB entry 7FRF)
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): 2.15
R work: 0.1763
R free: 0.219
Average B factor: 46.9
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M HEPES, 0.3 M magnesium acetate, 13.5% PEG 8000, 2% ethanol, and 1 mM BME
Matthews coefficient: 3.3
Solvent content (%): 62.68
Ligand: methyl 3-(methylsulfonylamino)benzoate (6SU)
Ligand formula: C9 H11 N O4 S
Ligand molecular weight: 229.253
Ligand SMILES: COC(=O)c1cccc(c1)NS(=O)(=O)C
Ligand InChI: InChI=1S/C9H11NO4S/c1-14-9(11)7-4-3-5-8(6-7)10-15(2,12)13/h3-6,10H,1-2H3
Release date: 2022-11-23
Crystal structure of hDHHS20 bound to palmitoyl CoA (PDB entry 7KHM)
Macromolecule: Isoform 4 of Palmitoyltransferase ZDHHC20
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1.225
Sequence length: 330 residues
Sequence: GPSRATMGAPWTLWRCCQRVVGWVPVLFITFVVVWSYYAYVVELCVFTIFGNEENGKTVVYLVAFHLFFVMFVWSYWMTIFTSPASPSKEFYLSNSEKERYEKEFSQERQQEILRRAARALPIYTTSASKTIRYCEKCQLIKPDRAHHCSACDSCILKMDHHSPWVNNCVGFSNYKFFLLFLLYSLLYCLFVAATVLEYFIKFWTNELTDTRAKFHVLFLFFVSAMFFISVLSLFSYHCWLVGKNRTTIESFRAPTFSYGPDGNGFSLGCSKNWRQVFGDEKKYWLLPIFSSLGDGCSFPTRLVGMDPEQASVTNQNEYARRSKLQRSNS
Oligomeric state: Homo 2-mer
Stoichiometry: A2
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.88
R work: 0.2938
R free: 0.3245
Average B factor: 129.9206
Crystallization method: LIPIDIC CUBIC PHASE
Crystallization temperature (K): 293
Crystal growth procedure: 50mM MES, pH 6.5, 50mM NaH2PO4, 30.3% PEG 300, 50mM DTT, 2.5% 2,5-hexanediol
Matthews coefficient: 3.33
Solvent content (%): 63.06
Ligand: Palmitoyl-CoA (PKZ)
Ligand formula: C37 H66 N7 O17 P3 S
Ligand molecular weight: 1005.943
Ligand SMILES: CCCCCCCCCCCCCCCC(=O)SCCNC(=O)CCNC(=O)C(C(C)(C)COP(=O)(O)OP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)O
Ligand InChI: InChI=1S/C37H66N7O17P3S/c1-4-5-6-7-8-9-10-11-12-13-14-15-16-17-28(46)65-21-20-39-27(45)18-19-40-35(49)32(48)37(2,3)23-58-64(55,56)61-63(53,54)57-22-26-31(60-62(50,51)52)30(47)36(59-26)44-25-43-29-33(38)41-24-42-34(29)44/h24-26,30-32,36,47-48H,4-23H2,1-3H3,(H,39,45)(H,40,49)(H,53,54)(H,55,56)(H2,38,41,42)(H2,50,51,52)/t26-,30-,31-,32+,36-/m1/s1
Release date: 2022-02-02
Apo human biliverdin reductase beta (cryogenic) (PDB entry 8ELL)
Macromolecule: Flavin reductase (NADPH)
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.5.1.30
Sequence length: 206 residues
Sequence: MAVKKIAIFGATGQTGLTTLAQAVQAGYEVTVLVRDSSRLPSEGPRPAHVVVGDVLQAADVDKTVAGQDAVIVLLGTRNDLSPTTVMSEGARNIVAAMKAHGVDKVVACTSAFLLWDPTKVPPRLQAVTDDHIRMHKVLRESGLKYVAVMPPHIGDQPLTGAYTVTLDGRGPSRVISKHDLGHFMLRCLTTDEYDGHSTYPSHQYQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.52
R work: 0.1595
R free: 0.1875
Average B factor: 18.6
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M MES pH 6.5, 1-4% PEG 20000. Equilibrated over 0.25-0.5 M NaCl.
BLVRB 18 mg/mL.
Matthews coefficient: 2.27
Solvent content (%): 45.73
Ligand: SODIUM ION ()
Ligand formula: Na
Ligand molecular weight: 22.99
Ligand SMILES: [Na+]
Ligand InChI: InChI=1S/Na/q+1
Release date: 2023-09-06
Structure of BRAF in Complex With Exarafenib (KIN-2787). (PDB entry 8QQG)
Macromolecule: Serine/threonine-protein kinase B-raf
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 275 residues
Sequence: DDWEIPDGQITVGQRIGSGSFGTVYKGKWHGDVAVKMLNVTAPTPQQLQAFKNEVGVLRKTRHVNILLFMGYSTKPQLAIVTQWCEGSSLYHHLHIIETKFEMIKLIDIARQTAQGMDYLHAKSIIHRDLKSNNIFLHEDLTVKIGDFGLATVKSRWSGSHQFEQLSGSILWMAPEVIRMQDKNPYSFQSDVYAFGIVLYELMTGQLPYSNINNRDQIIFMVGRGYLSPDLSKVRSNCPKAMKRLMAECLKKKRDERPLFPQILASIELLARSLP
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.979
R work: 0.2239
R free: 0.2612
Average B factor: 56.222
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M Hepes pH 6.7, 3.9 M NaCl, 0.10 M SCN
Matthews coefficient: 4.39
Solvent content (%): 71.97
Ligand: (3~{S})-~{N}-[4-methyl-3-[2-morpholin-4-yl-6-[[(2~{R})-1-oxidanylpropan-2-yl]amino]pyridin-4-yl]phenyl]-3-[2,2,2-tris(fluoranyl)ethyl]pyrrolidine-1-carboxamide (WJ9)
Ligand formula: C26 H34 F3 N5 O3
Ligand molecular weight: 521.575
Ligand SMILES: Cc1ccc(cc1c2cc(nc(c2)N3CCOCC3)NC(C)CO)NC(=O)N4CCC(C4)CC(F)(F)F
Ligand InChI: InChI=1S/C26H34F3N5O3/c1-17-3-4-21(31-25(36)34-6-5-19(15-34)14-26(27,28)29)13-22(17)20-11-23(30-18(2)16-35)32-24(12-20)33-7-9-37-10-8-33/h3-4,11-13,18-19,35H,5-10,14-16H2,1-2H3,(H,30,32)(H,31,36)/t18-,19+/m1/s1
Release date: 2024-01-24
Crystal structure of CTSB in complex with K777 (PDB entry 8HE9)
Macromolecule: Cathepsin B
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.22.1
Sequence length: 255 residues
Sequence: KLPASFDAREQWPQCPTIKEIRDQGSCGSCWAFGAVEAISDRICIHTNAHVSVEVSAEDLLTCCGSMCGDGCNGGYPAEAWNFWTRKGLVSGGLYESHVGCRPYSIPPCEHHVNGSRPPCTGEGDTPKCSKICEPGYSPTYKQDKHYGYNSYSVSNSEKDIMAEIYKNGPVEGAFSVYSDFLLYKSGVYQHVTGEMMGGHAIRILGWGVENGTPYWLVANSWNTDWGDNGFFKILRGQDHCGIESEVVAGIPRTD
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.55
R work: 0.1794
R free: 0.202
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 17.1 % v/v Polyethylene glycol 600, 50 mM MES pH 5.6, 8.6 % w/v Polyethylene glycol 4,000
Matthews coefficient: 1.86
Solvent content (%): 33.74
Ligand: Nalpha-[(4-methylpiperazin-1-yl)carbonyl]-N-[(3S)-1-phenyl-5-(phenylsulfonyl)pentan-3-yl]-L-phenylalaninamide (0IW)
Ligand formula: C32 H40 N4 O4 S
Ligand molecular weight: 576.749
Ligand SMILES: CN1CCN(CC1)C(=O)NC(Cc2ccccc2)C(=O)NC(CCc3ccccc3)CCS(=O)(=O)c4ccccc4
Ligand InChI: InChI=1S/C32H40N4O4S/c1-35-20-22-36(23-21-35)32(38)34-30(25-27-13-7-3-8-14-27)31(37)33-28(18-17-26-11-5-2-6-12-26)19-24-41(39,40)29-15-9-4-10-16-29/h2-16,28,30H,17-25H2,1H3,(H,33,37)(H,34,38)/t28-,30-/m0/s1
Release date: 2023-12-13
dAb3/HOIP-RBR-Ligand2 (PDB entry 6SC5)
Macromolecule: E3 ubiquitin-protein ligase RNF31
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2.31
Sequence length: 376 residues
Sequence: QECAVCGWALPHNRMQALTSCECTICPDCFRQHFTIALKEKHITDMVCPACGRPDLTDDTQLLSYFSTLDIQLRESLEPDAYALFHKKLTEGVLMRDPKFLWCAQCSFGFIYEREQLEATCPQCHQTFCVRCKRQWEEQHRGRSCEDFQNWKRMNDPEYQAQGLAMYLQENGIDCPKCKFSYALARGGCMHFHCTQCRHQFCSGCYNAFYAKNKCPEPNCRVKKSLHGHHPRDCLFYLRDWTALRLQKLLQDNNVMFNTEPPAGARAVPGGGCRVIEQKEVPNGLRDEACGKETPAGYAGLCQAHYKEYLVSLINAHSLDPATLYEVEELETATERYLHVRPQPLAGEDPPAYQARLLQKLTEEVPLGQSIPRRRK
Oligomeric state: Hetero 3-mer
Stoichiometry: A2, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.1
R work: 0.2191
R free: 0.2518
Average B factor: 56.86
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: Ammonium sulfate, sodium chloride, HEPES
Matthews coefficient: 2.54
Solvent content (%): 51.54
Ligand: methyl 4-[(2-oxidanylidene-5,6,7,8-tetrahydro-1~{H}-quinolin-3-yl)carbonylamino]but-3-enoate (L6B)
Ligand formula: C15 H18 N2 O4
Ligand molecular weight: 290.314
Ligand SMILES: COC(=O)CC=CNC(=O)C1=CC2=C(CCCC2)NC1=O
Ligand InChI: InChI=1S/C15H18N2O4/c1-21-13(18)7-4-8-16-14(19)11-9-10-5-2-3-6-12(10)17-15(11)20/h4,8-9H,2-3,5-7H2,1H3,(H,16,19)(H,17,20)/b8-4+
Release date: 2019-11-27
Crystal structure of human apo MTH1 (PDB entry 6JVF)
Macromolecule: 7,8-dihydro-8-oxoguanine triphosphatase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.1.55
Sequence length: 156 residues
Sequence: MGASRLYTLVLVLQPQRVLLGMKKRGFGAGRWNGFGGKVQEGETIEDGARRELQEESGLTVDALHKVGQIVFEFVGEPELMDVHVFCTDSIQGTPVESDEMRPCWFQLDQIPFKDMWPDDSYWFPLLLQKKKFHGYFKFQGQDTILDYTLREVDTV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.73
R work: 0.1864
R free: 0.2174
Average B factor: 20.2542
Crystallization method: EVAPORATION
Crystallization pH: 3.75
Crystallization temperature (K): 298
Crystal growth procedure: 30% PEG6 000, 200 mM Lithium sulphate, 100 mM Sodium acetate pH 3.75
Matthews coefficient: 2.26
Solvent content (%): 45.52
Release date: 2020-10-28
FGFR-1 in complex with ligand tasurgratinib (PDB entry 8YKI)
Macromolecule: Fibroblast growth factor receptor 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 317 residues
Sequence: GGSSEYELPEDPRWELPRDRLVLGKPLGEGAFGQVVLAEAIGLDKDKPNRVTKVAVKMLKSDATEKDLSDLISEMEMMKMIGKHKNIINLLGACTQDGPLYVIVEYASKGNLREYLQARRPPGLEYCYNPSHNPEEQLSSKDLVSCAYQVARGMEYLASKKCIHRDLAARNVLVTEDNVMKIADFGLARDIHHIDYYKKTTNGRLPVKWMAPEALFDRIYTHQSDVWSFGVLLWEIFTLGGSPYPGVPVEELFKLLKEGHRMDKPSNCTNELYMMMRDCWHAVPSQRPTFKQLVEDLDRIVALTSNQEYLDLSMPLD
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.79
R work: 0.2403
R free: 0.2879
Average B factor: 88.27
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 18% w/v PEG 3350, 0.2M (NH4)2 TARTRATE
Matthews coefficient: 2.31
Solvent content (%): 46.86
Ligand: Tasurgratinib (A1LY1)
Ligand formula: C32 H37 N5 O6
Ligand molecular weight: 587.666
Ligand SMILES: CNC(=O)n1ccc2c1cc(c(c2)Oc3ccnc(c3)NC(=O)c4ccc(cc4)C5CCN(CC5)CCO)OCCOC
Ligand InChI: InChI=1S/C32H37N5O6/c1-33-32(40)37-14-10-25-19-29(28(21-27(25)37)42-18-17-41-2)43-26-7-11-34-30(20-26)35-31(39)24-5-3-22(4-6-24)23-8-12-36(13-9-23)15-16-38/h3-7,10-11,14,19-21,23,38H,8-9,12-13,15-18H2,1-2H3,(H,33,40)(H,34,35,39)
Release date: 2024-06-12
APE1 Mn-bound product complex with abasic ribonucleotide DNA (PDB entry 7LPH)
Macromolecule: DNA-(apurinic or apyrimidinic site) lyase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1
Sequence length: 276 residues
Sequence: ALYEDPPDQKTSPSGKPATLKICSWNVDGLRAWIKKKGLDWVKEEAPDILCLQETKCSENKLPAELQELPGLSHQYWSAPSDKEGYSGVGLLSRQAPLKVSYGIGDEEHDQEGRVIVAEFDSFVLVTAYVPNAGRGLVRLEYRQRWDEAFRKFLKGLASRKPLVLCGDLNVAHEEIDLRNPKGNKKNAGFTPQERQGFGELLQAVPLADSFRHLYPNTPYAYTFWTYMMNARSKNVGWRLDYFLLSHSLLPALCDSKIRSKALGSDHCPITLYLAL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.99
R work: 0.1919
R free: 0.2366
Average B factor: 33.67
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 200 mM MgCl2, 100 mM Sodium Citrate (pH 5), 10-15% PEG 20,000
Matthews coefficient: 2.58
Solvent content (%): 52.27
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: 2021-08-04
Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor NPD-1439 (PDB entry 6FET)
Macromolecule: cAMP-specific 3',5'-cyclic phosphodiesterase 4D
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.4.53
Sequence length: 364 residues
Sequence: GSHMIPRFGVKTEQEDVLAKELEDVNKWGLHVFRIAELSGNRPLTVIMHTIFQERDLLKTFKIPVDTLITYLMTLEDHYHADVAYHNNIHAADVVQSTHVLLSTPALEAVFTDLEILAAIFASAIHDVDHPGVSNQFLINTNSELALMYNDSSVLENHHLAVGFKLLQEENCDIFQNLTKKQRQSLRKMVIDIVLATDMSKHMNLLADLKTMVETKKVTSSGVLLLDNYSDRIQVLQNMVHCADLSNPTKPLQLYRQWTDRIMEEFFRQGDRERERGMEISPMCDKHNASVEKSQVGFIDYIVHPLWETWADLVHPDAQDILDTLEDNREWYQSTIPQSPSPAPDDPEEGRQGQTEKFQFELTL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.88
R work: 0.17148
R free: 0.19932
Average B factor: 40.058
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: 24% PEG 3350, 30% Ethylene Glycol, 0.1 M HEPES
Matthews coefficient: 2.6
Solvent content (%): 52.73
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: 2019-04-24
Structure of C1156Y,L1198F Mutant Human Anaplastic Lymphoma Kinase in Complex with PF-06463922 ((10R)-7-amino-12-fluoro-2,10,16-trimethyl- 15-oxo-10,15,16,17-tetrahydro-2H-8,4-(metheno)pyrazolo(4,3-h)(2,5,11) benzoxadiazacyclotetradecine-3-carbonitrile). (PDB entry 5AA8)
Macromolecule: ALK TYROSINE KINASE RECEPTOR
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 327 residues
Sequence: MAHHHHHHNPNYCFAGKTSSISDLKEVPRKNITLIRGLGHGAFGEVYEGQVSGMPNDPSPLQVAVKTLPEVYSEQDELDFLMEALIISKFNHQNIVRCIGVSLQSLPRFILLEFMAGGDLKSFLRETRPRPSQPSSLAMLDLLHVARDIACGCQYLEENHFIHRDIAARNCLLTCPGPGRVAKIGDFGMARDIYRASYYRKGGCAMLPVKWMPPEAFMEGIFTSKTDTWSFGVLLWEIFSLGYMPYPSKSNQEVLEFVTSGGRMDPPKNCPGPVYRIMTQCWQHQPEDRPNFAIILERIEYCTQDPDVINTALPIEYGPLVEEEEKV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.86
R work: 0.209
R free: 0.233
Average B factor: 33.9
Crystallization pH: 8
Crystal growth procedure: pH 8
Matthews coefficient: 2.1
Solvent content (%): 41.35
Ligand: (10R)-7-amino-12-fluoro-2,10,16-trimethyl-15-oxo-10,15,16,17-tetrahydro-2H-8,4-(metheno)pyrazolo[4,3-h][2,5,11]benzoxadiazacyclotetradecine-3-carbonitrile (5P8)
Ligand formula: C21 H19 F N6 O2
Ligand molecular weight: 406.413
Ligand SMILES: CC1c2cc(ccc2C(=O)N(Cc3c(c(n(n3)C)C#N)-c4cc(c(nc4)N)O1)C)F
Ligand InChI: InChI=1S/C21H19FN6O2/c1-11-15-7-13(22)4-5-14(15)21(29)27(2)10-16-19(17(8-23)28(3)26-16)12-6-18(30-11)20(24)25-9-12/h4-7,9,11H,10H2,1-3H3,(H2,24,25)/t11-/m1/s1
Release date: 2016-06-08
Crystal structure of Syk catalytic domain in complex with a furo[3,2-d]pyrimidine (PDB entry 5T68)
Macromolecule: Tyrosine-protein kinase SYK
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 291 residues
Sequence: MALEEIRPKEVYLDRKLLTLEDKELGSGNFGTVKKGYYQMKKVVKTVAVKILKNEANDPALKDELLAEANVMQQLDNPYIVRMIGICEAESWMLVMEMAELGPLNKYLQQNRHVKDKNIIELVHQVSMGMKYLEESNFVHRDLAARNVLLVTQHYAKISDFGLSKALRADENYYKAQTHGKWPVKWYAPECINYYKFSSKSDVWSFGVLMWEAFSYGQKPYRGMKGSEVTAMLEKGERMGCPAGCPREMYDLMNLCWTYDVENRPGFAAVELRLRNYYYDVVNEGHHHHHH
Oligomeric state: Homo 2-mer
Stoichiometry: A2
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.93
R work: 0.183
R free: 0.281
Average B factor: 60.04
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 293
Crystal growth procedure: 14-18% PEG3350, 100 mM Tris pH 8.5 using a seed stock that was grown in PEG 3350 13-20% and 100 mM Tris pH 8.5
Matthews coefficient: 1.89
Solvent content (%): 34.87
Ligand: N~4~-cyclopropyl-N~2~-(3-methyl-1H-indazol-6-yl)furo[3,2-d]pyrimidine-2,4-diamine (77V)
Ligand formula: C17 H16 N6 O
Ligand molecular weight: 320.349
Ligand SMILES: Cc1c2ccc(cc2[nH]n1)Nc3nc4ccoc4c(n3)NC5CC5
Ligand InChI: InChI=1S/C17H16N6O/c1-9-12-5-4-11(8-14(12)23-22-9)19-17-20-13-6-7-24-15(13)16(21-17)18-10-2-3-10/h4-8,10H,2-3H2,1H3,(H,22,23)(H2,18,19,20,21)
Release date: 2016-10-26
PanDDA analysis group deposition -- Crystal structure of PTP1B in complex with compound_FMOOA000491a (PDB entry 5QFQ)
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): 1.621
R work: 0.1906
R free: 0.2146
Average B factor: 39.4005
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: 3.31
Solvent content (%): 62.9
Ligand: N-[(1S,2S,3S,4R)-3-hydroxy-1,2,3,4-tetrahydro-1,4-epoxynaphthalen-2-yl]cyclobutanecarboxamide (JK7)
Ligand formula: C15 H17 N O3
Ligand molecular weight: 259.3
Ligand SMILES: c1ccc2c(c1)C3C(C(C2O3)O)NC(=O)C4CCC4
Ligand InChI: InChI=1S/C15H17NO3/c17-12-11(16-15(18)8-4-3-5-8)13-9-6-1-2-7-10(9)14(12)19-13/h1-2,6-8,11-14,17H,3-5H2,(H,16,18)/t11-,12-,13-,14+/m0/s1
Release date: 2018-10-10
Structure of human PARP1 catalytic domain bound to a quinazoline-2,4(1H,3H)-dione inhibitor (PDB entry 5KPQ)
Macromolecule: Poly [ADP-ribose] polymerase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.4.2.30
Sequence length: 350 residues
Sequence: KSKLPKPVQDLIKMIFDVESMKKAMVEYEIDLQKMPLGKLSKRQIQAAYSILSEVQQAVSQGSSDSQILDLSNRFYTLIPHDFGMKKPPLLNNADSVQAKAEMLDNLLDIEVAYSLLRGGSDDSSKDPIDVNYEKLKTDIKVVDRDSEEAEIIRKYVKNTHATTHNAYDLEVIDIFKIEREGECQRYKPFKQLHNRRLLWHGSRTTNFAGILSQGLRIAPPEAPVTGYMFGKGIYFADMVSKSANYCHTSQGDPIGLILLGEVALGNMYELKHASHISKLPKGKHSVKGLGKTTPDPSANISLDGVDVPLGTGISSGVNDTSLLYNEYIVYDIAQVNLKYLLKLKFNFKT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.55
R work: 0.23289
R free: 0.28195
Average B factor: 58.227
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 298
Crystal growth procedure: 2.5M AMMONIUM SULFATE, 100mM TRIS
Matthews coefficient: 2.35
Solvent content (%): 47.71
Ligand: 1-[[4-fluoranyl-3-[(3R)-3-methyl-4-propyl-piperazin-1-yl]carbonyl-phenyl]methyl]quinazoline-2,4-dione (6X2)
Ligand formula: C24 H27 F N4 O3
Ligand molecular weight: 438.495
Ligand SMILES: CCCN1CCN(CC1C)C(=O)c2cc(ccc2F)CN3c4ccccc4C(=O)NC3=O
Ligand InChI: InChI=1S/C24H27FN4O3/c1-3-10-27-11-12-28(14-16(27)2)23(31)19-13-17(8-9-20(19)25)15-29-21-7-5-4-6-18(21)22(30)26-24(29)32/h4-9,13,16H,3,10-12,14-15H2,1-2H3,(H,26,30,32)/t16-/m1/s1
Release date: 2016-12-14
Crystal Structure of Human NEIL1 bound to duplex DNA containing THF (PDB entry 5ITT)
Macromolecule: Endonuclease 8-like 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.2.2
Sequence length: 400 residues
Sequence: MPEGPELHLASQFVNEACRALVFGGCVEKSSVSRNPEVPFESSAYRISASARGKELRLILSPLPGAQPQQEPLALVFRFGMSGSFQLVPREELPRHAHLRFYTAPPGPRLALCFVDIRRFGRWDLGGKWQPGRGPCVLQEYQQFRENVLRNLADKAFDRPICEALLDQRFFNGIGNYLRAEILYRLKIPPFEKARSVLEALQQHRPSPELTLSQKIRTKLQNPDLLELCHSVPKEVVQLGGRGYGSESGEEDFAAFRAWLRCYGMPGMSSLQDRHGRTIWFQGDPGPLAPKGRKSRKKKSKATQLSPEDRVEDALPPSKAPSRTRRAKRDLPKRTATQRPEGTSLQQDPEAPTVPKKGRRKGRQAASGHCRPRKVKADIPSLEPEGTSASAALGHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.53
R work: 0.21016
R free: 0.27788
Crystallization method: EVAPORATION
Crystallization pH: 6.5
Crystallization temperature (K): 288
Crystal growth procedure: 0.1 M cacodylic acid (pH 7.0), 0.1 M NaCl, 0.05 M MgCl2 and 24% (w/v) PEG 8000
Matthews coefficient: 2.22
Solvent content (%): 44.55
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: 2016-07-06
PanDDA analysis group deposition -- Crystal structure of PTP1B in complex with compound_PKOOA000283c (PDB entry 5QFB)
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): 1.851
R work: 0.1811
R free: 0.2087
Average B factor: 41.8054
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: 3.31
Solvent content (%): 62.82
Ligand: 6-ethylthieno[2,3-d]pyrimidin-4(3H)-one (JND)
Ligand formula: C8 H8 N2 O S
Ligand molecular weight: 180.227
Ligand SMILES: CCc1cc2c(s1)N=CNC2=O
Ligand InChI: InChI=1S/C8H8N2OS/c1-2-5-3-6-7(11)9-4-10-8(6)12-5/h3-4H,2H2,1H3,(H,9,10,11)
Release date: 2018-10-10
LSD1-CoREST in complex with 4-[5-(piperidin-4-ylmethoxy)-2-(p-tolyl)pyridin-3-yl]benzonitrile (PDB entry 5YJB)
Macromolecule: Lysine-specific histone demethylase 1A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1
Sequence length: 669 residues
Sequence: GPLGSHMSGVEGAAFQSRLPHDRMTSQEAACFPDIISGPQQTQKVFLFIRNRTLQLWLDNPKIQLTFEATLQQLEAPYNSDTVLVHRVHSYLERHGLINFGIYKRIKPLPTKKTGKVIIIGSGVSGLAAARQLQSFGMDVTLLEARDRVGGRVATFRKGNYVADLGAMVVTGLGGNPMAVVSKQVNMELAKIKQKCPLYEANGQAVPKEKDEMVEQEFNRLLEATSYLSHQLDFNVLNNKPVSLGQALEVVIQLQEKHVKDEQIEHWKKIVKTQEELKELLNKMVNLKEKIKELHQQYKEASEVKPPRDITAEFLVKSKHRDLTALCKEYDELAETQGKLEEKLQELEANPPSDVYLSSRDRQILDWHFANLEFANATPLSTLSLKHWDQDDDFEFTGSHLTVRNGYSCVPVALAEGLDIKLNTAVRQVRYTASGCEVIAVNTRSTSQTFIYKCDAVLCTLPLGVLKQQPPAVQFVPPLPEWKTSAVQRMGFGNLNKVVLCFDRVFWDPSVNLFGHVGSTTASRGELFLFWNLYKAPILLALVAGEAAGIMENISDDVIVGRCLAILKGIFGSSAVPQPKETVVSRWRADPWARGSYSYVAAGSSGNDYDLMAQPITPGPSIPGAPQPIPRLFFAGEHTIRNYPATVHGALLSGLREAGRIADQFLGAM
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.96
R work: 0.189
R free: 0.219
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M N-(2-ACETAMIDO)IMINODIACETIC ACID (PH 5.5), 1.23M POTASSIUM SODIUM TARTRATE TETRAHYDRATE
Matthews coefficient: 7.09
Solvent content (%): 82.64
Ligand: FLAVIN-ADENINE DINUCLEOTIDE (FAD)
Ligand formula: C27 H33 N9 O15 P2
Ligand molecular weight: 785.55
Ligand SMILES: Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)CC(C(C(COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)n5cnc6c5ncnc6N)O)O)O)O)O
Ligand InChI: InChI=1S/C27H33N9O15P2/c1-10-3-12-13(4-11(10)2)35(24-18(32-12)25(42)34-27(43)33-24)5-14(37)19(39)15(38)6-48-52(44,45)51-53(46,47)49-7-16-20(40)21(41)26(50-16)36-9-31-17-22(28)29-8-30-23(17)36/h3-4,8-9,14-16,19-21,26,37-41H,5-7H2,1-2H3,(H,44,45)(H,46,47)(H2,28,29,30)(H,34,42,43)/t14-,15+,16+,19-,20+,21+,26+/m0/s1
Release date: 2018-07-04