satarupa22/MacromolecularLigandDB huggingface dataset:
Crystal structure of the Angiotensin-1 converting enzyme N-domain in complex with amyloid-beta 1-16 (PDB entry 5AMA)
Macromolecule: ANGIOTENSIN-CONVERTING ENZYME
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.15.1
Sequence length: 629 residues
Sequence: LDPGLQPGQFSADEAGAQLFAQSYQSSAEQVLFQSVAASWAHDTNITAENARRQEEAALLSQEFAEAWGQKAKELYEPIWQQFTDPQLRRIIGAVRTLGSANLPLAKRQQYNALLSQMSRIYSTAKVCLPQKTATCWSLDPDLTNILASSRSYAMLLFAWEGWHNAAGIPLKPLYEDFTALSNEAYKQDGFTDTGAYWRSWYNSPTFEDDLEHLYQQLEPLYLNLHAFVRRALHRRYGDRYINLRGPIPAHLLGDMWAQSWENIYDMVVPFPDKPNLDVTSTMLQQGWQATHMFRVAEEFFTSLELSPMPPEFWEGSMLEKPADGREVVCHASAWDFYNRKDFRIKQCTRVTMDQLSTVHHEMGHIQYYLQYKDLPVSLRRGANPGFHEAIGDVLALSVSTPEHLHKIGLLDRVTNDTESDINYLLKMALEKIAFLPFGYLVDQWRWGVFSGRTPPSRYNFDWWYLRTKYQGICPPVTRNETHFDAGAKFHVPNVTPYIRYFVSFVLQFQFHEALCKEAGYEGPLHQCDIYRSTKAGAKLRKVLRAGSSRPWQEVLKDMVGLDALDAQPLLKYFQLVTQWLQEQNQQNGEVLGWPEYQWHPPLPDNYPEGIDLVTDEAEASKFVEEYDL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.18675
R free: 0.21764
Average B factor: 23.805
Crystallization pH: 8.5
Crystal growth procedure: 0.06 M DIVALENT CATIONS, 0.1 M TRIS/BICINE PH 8.5, 30 % PEG550MME/PEG20000
Matthews coefficient: 2.95
Solvent content (%): 58
Ligand: ASPARTIC ACID (ASP)
Ligand formula: C4 H7 N O4
Ligand molecular weight: 133.103
Ligand SMILES: C(C(C(=O)O)N)C(=O)O
Ligand InChI: InChI=1S/C4H7NO4/c5-2(4(8)9)1-3(6)7/h2H,1,5H2,(H,6,7)(H,8,9)/t2-/m0/s1
Release date: 2016-01-13
Non-receptor Protein Tyrosine Phosphatase SHP2 in Complex with Allosteric Inhibitor Compound 24 (PDB entry 7JVN)
Macromolecule: Tyrosine-protein phosphatase non-receptor type 11
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 525 residues
Sequence: MTSRRWFHPNITGVEAENLLLTRGVDGSFLARPSKSNPGDFTLSVRRNGAVTHIKIQNTGDYYDLYGGEKFATLAELVQYYMEHHGQLKEKNGDVIELKYPLNCADPTSERWFHGHLSGKEAEKLLTEKGKHGSFLVRESQSHPGDFVLSVRTGDDKGESNDGKSKVTHVMIRCQELKYDVGGGERFDSLTDLVEHYKKNPMVETLGTVLQLKQPLNTTRINAAEIESRVRELSKLAETTDKVKQGFWEEFETLQQQECKLLYSRKEGQRQENKNKNRYKNILPFDHTRVVLHDGDPNEPVSDYINANIIMPEFETKCNNSKPKKSYIATQGCLQNTVNDFWRMVFQENSRVIVMTTKEVERGKSKCVKYWPDEYALKEYGVMRVRNVKESAAHDYTLRELKLSKVGQGNTERTVWQYHFRTWPDHGVPSDPGGVLDFLEEVHHKQESIMDAGPVVVHCSAGIGRTGTFIVIDILIDIIREKGVDCDIDVPKTIQMVRSQRSGMVQTEAQYRFIYMAVQHYIETL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.917
R work: 0.181
R free: 0.214
Average B factor: 29.49
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277.15
Crystal growth procedure: 17% PEG 3350 and 200 mM ammonium phosphate
Matthews coefficient: 2.27
Solvent content (%): 45.9
Ligand: 6-(4-amino-4-methylpiperidin-1-yl)-3-[(2,3-dichlorophenyl)sulfanyl]pyrazin-2-amine (VKP)
Ligand formula: C16 H19 Cl2 N5 S
Ligand molecular weight: 384.327
Ligand SMILES: CC1(CCN(CC1)c2cnc(c(n2)N)Sc3cccc(c3Cl)Cl)N
Ligand InChI: InChI=1S/C16H19Cl2N5S/c1-16(20)5-7-23(8-6-16)12-9-21-15(14(19)22-12)24-11-4-2-3-10(17)13(11)18/h2-4,9H,5-8,20H2,1H3,(H2,19,22)
Release date: 2020-09-23
Crystal structure of FGFR1 kinase domain in complex with a novel inhibitor (PDB entry 5Z0S)
Macromolecule: Fibroblast growth factor receptor 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 308 residues
Sequence: AGVSEYELPEDPRWELPRDRLVLGKPLGEGAFGQVVLAEAIGLDKDKPNRVTKVAVKMLKSDATEKDLSDLISEMEMMKMIGKHKNIINLLGACTQDGPLYVIVEYASKGNLREYLQARRPPGLEYSYNPSHNPEEQLSSKDLVSCAYQVARGMEYLASKKCIHRDLAARNVLVTEDNVMKIADFGLARDIHHIDYYKKTTNGRLPVKWMAPEALFDRIYTHQSDVWSFGVLLWEIFTLGGSPYPGVPVEELFKLLKEGHRMDKPSNCTNELYMMMRDCWHAVPSQRPTFKQLVEDLDRIVALTSNQE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.45
R work: 0.2252
R free: 0.2747
Average B factor: 41.6378
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.1M Bis-Tris pH 6.5, 0.3M (NH4)2SO4, 15-20% PEG10000, 5% EG
Matthews coefficient: 2.71
Solvent content (%): 54.58
Ligand: 1-[(6-chloroimidazo[1,2-b]pyridazin-3-yl)sulfonyl]-6-(1-methyl-1H-pyrazol-4-yl)-1H-pyrazolo[4,3-b]pyridine (960)
Ligand formula: C16 H11 Cl N8 O2 S
Ligand molecular weight: 414.829
Ligand SMILES: Cn1cc(cn1)c2cc3c(cnn3S(=O)(=O)c4cnc5n4nc(cc5)Cl)nc2
Ligand InChI: InChI=1S/C16H11ClN8O2S/c1-23-9-11(6-20-23)10-4-13-12(18-5-10)7-21-25(13)28(26,27)16-8-19-15-3-2-14(17)22-24(15)16/h2-9H,1H3
Release date: 2018-12-26
IDO1 in complex with compound 4 (PDB entry 6X5Y)
Macromolecule: Indoleamine 2,3-dioxygenase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.13.11.52
Sequence length: 394 residues
Sequence: MISKEYHIDEEVGFALPNPQENLPDFYNDWMFIAKHLPDLIESGQLRERVEKLNMLSIDHLTDHKSQRLARLVLGCITMAYVWGKGHGDVRKVLPRNIAVPYCQLSKKLELPPILVYADCVLANWKKKDPNKPLTYENMDVLFSFRDGDCSKGFFLVSLLVEIAAASAIKVIPTVFKAMQMQERDTLLKALLEIASCLEKALQVFHQIHDHVNPKAFFSVLRIYLSGWKGNPQLSDGLVYEGFWEDPKEFAGGSAGQSSVFQCFDVLLGIQQTAGGGHAAQFLQDMRRYMPPAHRNFLCSLESNPSVREFVLSKGDAGLREAYDACVKALVSLRSYHLQIVTKYILIPASQQPKENKTSEDPSKLEAKGTGGTDLMNFLKTVRSTTEKSLLKEG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.65
R work: 0.2399
R free: 0.2723
Average B factor: 83.571
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 mM Tris pH 8.0, 20% (w/v) PEG 6000
Matthews coefficient: 2.89
Solvent content (%): 57.42
Ligand: 4-fluoro-N-{1-[5-(2-methylpyrimidin-4-yl)-5,6,7,8-tetrahydro-1,5-naphthyridin-2-yl]cyclopropyl}benzamide (URJ)
Ligand formula: C23 H22 F N5 O
Ligand molecular weight: 403.452
Ligand SMILES: Cc1nccc(n1)N2CCCc3c2ccc(n3)C4(CC4)NC(=O)c5ccc(cc5)F
Ligand InChI: InChI=1S/C23H22FN5O/c1-15-25-13-10-21(26-15)29-14-2-3-18-19(29)8-9-20(27-18)23(11-12-23)28-22(30)16-4-6-17(24)7-5-16/h4-10,13H,2-3,11-12,14H2,1H3,(H,28,30)
Release date: 2021-06-02
Crystal structure of human PLU-1 (JARID1B) in complex with Pyridine-2, 6-dicarboxylic Acid (PDCA) (PDB entry 5A3W)
Macromolecule: LYSINE-SPECIFIC DEMETHYLASE 5B
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11
Sequence length: 481 residues
Sequence: SMFLPPPECPVFEPSWEEFADPFAFIHKIRPIAEQTGICKVRPPPDWQPPFACDVDKLHFTPRIQRLNELEAQTRVKLGGGGARDYTLRTFGEMADAFKSDYFNMPVHMVPTELVEKEFWRLVSTIEEDVTVEYGADIASKEFGSGFPVRDGKIKLSPEEEEYLDSGWNLNNMPVMEQSVLAHITADICGMKLPWLYVGMCFSSFCWHIEDHWSYSINYLHWGEPKTWYGVPGYAAEQLENVMKKLAPELFVSQPDLLHQLVTIMNPNTLMTHEVPVYRTNQCAGEFVITFPRAYHSGFNQGFNFAEAVNFCTVDWLPLGRQCVEHYRLLHRYCVFSHDEMICKMASKADVLDVVVASTVQKDMAIMIEDEKALRETVRKLGVIDSERMDFELLPDDERQCVKCKTTCFMSAISCSCKPGLLVCLHHVKELCSCPPYKYKLRYRYTLDDLYPMMNALKLRAESYNEWALNVNEALEAKINK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2
R work: 0.1842
R free: 0.2161
Crystallization pH: 8
Crystal growth procedure: 0.1M HEPES PH 8.0, 0.8M POTASSIUM PHOSPHATE-DIBASIC, 0.8M SODIUM PHOSPHATE MONOBASIC
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: 2015-06-17
Carbonic Anhydrase IX like mutant in Complex with Steriod_Sulphamoyl inhibitor AKI_13 (PDB entry 8OKG)
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): 1.45
R work: 0.16824
R free: 0.18121
Average B factor: 19.829
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: 2.08
Solvent content (%): 40.85
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: 2024-04-24
Crystal structure of HMCES SRAP domain in complex with longer 3' overhang DNA (PDB entry 6OEA)
Macromolecule: Embryonic stem cell-specific 5-hydroxymethylcytosine-binding protein
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4
Sequence length: 276 residues
Sequence: CGRTSCHLPRDVLTRACAYQDRRGQQRLPEWRDPDKYCPSYNKSPQSNSPVLLSRLHFEKDADSSERIIAPMRWGLVPSWFKESDPSKLQFNTTNCRSDTVMEKRSFKVPLGKGRRCVVLADGFYEWQRCQGTNQRQPYFIYFPQIKTEKSGSIGAADSPENWEKVWDNWRLLTMAGIFDCWEPPEGGDVLYSYTIITVDSCKGLSDIHHRMPAILDGEEAVSKWLDFGEVSTQEALKLIHPTENITFHAVSSVVNNSRNNTPECLAPVAENLYFQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.1
R work: 0.2081
R free: 0.242
Average B factor: 55.262
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 293
Crystal growth procedure: 20% PEG3350, 0.1 M potassium chloride, 0.1 M Bis-Tris, 0.05 M magnesium chloride
Matthews coefficient: 3.02
Solvent content (%): 59.23
Ligand: 1,2-ETHANEDIOL (EDO)
Ligand formula: C2 H6 O2
Ligand molecular weight: 62.068
Ligand SMILES: C(CO)O
Ligand InChI: InChI=1S/C2H6O2/c3-1-2-4/h3-4H,1-2H2
Release date: 2019-04-10
Crystal Structure of Drosophila DHX36 helicase in complex with AGGGTTTTTT (PDB entry 5N96)
Macromolecule: CG9323, isoform A
Type: Protein, polypeptide(L)
Source organism: Drosophila melanogaster
EC number: 3.6.1.3
Sequence length: 944 residues
Sequence: MQRDRDSSGSNARKGNRPPGLRGKDIGLYYRNLARQQKKDRGENAESKEPQIRLGCNVSAPSGVLERVKELMEDYSRAPSRQNVDDKNVDAKFQQQFRHLLSVNFEEFVAETKERNADLDWVNPKLDERLQLELGQRQLEENAKKRLEARKKLPTMKYADDIIQAVRENQVILIVGSTGCGKTTQVPQILLDDAISRGCASSCRIICTQPRRISAIAIAEWVSYERCESLGNSVGYQIRLESRKARERASITYCTTGVLLQQLQSDPLMHNLSVLILDEIHERSVETDLLMGLLKVILPHRPDLKVILMSATVREQDFCDYFNNCPMFRIEGVMFPVKMLYLEDVLSKTNYEFQKFRDRRPKRDPPERRMKHEAMIEPYLRRIRNSYDSRVLDKLRLPESEGCEDIDFIADLVYYICENEPEGAILVFLPGYDKISQLYNILDKPKTSKGQRWRDHMAVFPLHSLMQSGEQQAVFRRPPAGQRKVIISTIIAETSVTIDDVVYVINSGRTKATNYDIETNIQSLDEVWVTKANTQQRRGRAGRVRPGICYNLFSRAREDRMDDIPTPEILRSKLESIILSLKLLHIDDPYRFLQTLINAPNPEAIKMGVELLKRIEALDQTGTLTPLGMHLAKLPIDPQMGKMILMSALFCCLDPITSAAAALSFKSPFYSPLGKESRVDEIKRRMARNMRSDHLMVHNTIIAYRDSRYSHAERDFCYKNFLSSMTLQQLERMKNQFSELLYNYKFLASSNCKDAASNKNSEKIPLLRAIIGAGLYPNMAHLRKSRQIKNRVRAIHTMATDDGRRVNFHPSSVNSGESGFDSAYFVYFQRQKSTDLFLLDSTMVFPMALIIFGDGVEAGVTQNTPYLCVAKTYYFKCNRETADVVIQLRSNLEKLLLKKALYPAPIEENGYEKQLIKAIELLLSLDERLGEDYISSDEIDDIVD
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.716
R work: 0.1797
R free: 0.2481
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 298
Crystal growth procedure: 0.1M MES monohydrate-imidazole
20mM sodium formate
20mM ammonium acetate
20mM sodium citrate tribasic hydrate
20mM sodium oxamate
20mM potassium sodium tartrate tetrahydrate
Matthews coefficient: 2.69
Solvent content (%): 52.93
Ligand: MAGNESIUM ION (MG)
Ligand formula: Mg
Ligand molecular weight: 24.305
Ligand SMILES: [Mg+2]
Ligand InChI: InChI=1S/Mg/q+2
Release date: 2018-03-14
Crystal Structure of human cyclic GMP-AMP synthase in complex with 2-benzyl-6-(2-chloro-4-methylphenyl)indazole-4-carboxylic acid (PDB entry 7FU6)
Macromolecule: Cyclic GMP-AMP synthase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.86
Sequence length: 362 residues
Sequence: GASKLRAVLEKLKLSRDDISTAAGMVKGVVDHLLLRLKCDSAFRGVGLLNTGSYYEHVKISAPNEFDVMFKLEVPRIQLEEYSNTRAYYFVKFKRNPKENPLSQFLEGEILSASKMLSKFRKIIKEEINDIKDTDVIMKRKRGGSPAVTLLISEKISVDITLALESKSSWPASTQEGLRIQNWLSAKVRKQLRLKPFYLVPKHAKEGNGFQEETWRLSFSHIEKEILNNHGKSKTCCENKEEKCCRKDCLKLMKYLLEQLKERFKDKKHLDKFSSYHVKTAFFHVCTQNPQDSQWDRKDLGLCFDNCVTYFLQCLRTEKLENYFIPEFNLFSSNLIDKRSKEFLTKQIEYERNNEFPVFDEF
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.37
R work: 0.233
R free: 0.263
Average B factor: 123.27
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 293
Crystal growth procedure: 10-12 mg/mL protein in 25 mM Tris/HCl pH7.5, 500mM NaCl, 2mM TCEP, supplemented with 10x molar excess of ligand and, if needed, with 10 mM MgCl2 and 5mM ATP, then mixed 1:1 with reservoir of the Procomplex screen. Several conditions resulted in crystals
Matthews coefficient: 2.53
Solvent content (%): 51.47
Ligand: (6M)-2-benzyl-6-(2-chloro-4-methylphenyl)-2H-indazole-4-carboxylic acid (YMT)
Ligand formula: C22 H17 Cl N2 O2
Ligand molecular weight: 376.836
Ligand SMILES: Cc1ccc(c(c1)Cl)c2cc(c3cn(nc3c2)Cc4ccccc4)C(=O)O
Ligand InChI: InChI=1S/C22H17ClN2O2/c1-14-7-8-17(20(23)9-14)16-10-18(22(26)27)19-13-25(24-21(19)11-16)12-15-5-3-2-4-6-15/h2-11,13H,12H2,1H3,(H,26,27)
Release date: 2024-02-21
Post-catalytic nicked complex of DNA Polymerase Lambda with bound 1-nt gapped SSB substrate and incoming dUMPNPP (PDB entry 7M08)
Macromolecule: DNA polymerase lambda
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 346 residues
Sequence: GSAAAVLDKWVCAQPSSQKATNHNLHITEKLEVLAKAYSVQGDKWRALGYAKAINALKSFHKPVTSYQEACSIPGIGKRMAEKIIEILESGHLRKLDHISESVPVLELFSNIWGAGTKTAQMWYQQGFRSLEDIRSQASLTTQQAIGLKHYSDFLERMPREEATEIEQTVQKAAQAFNSGLLCVACGSYRRGKATCGDVDVLITHPDGRSHRGIFSRLLDSLRQEGFLTDDLVSQEENGQQQKYLGVCRLPGPGRRHRRLDIIVVPYSEFACALLYFTGSAHFNRSMRALAKTKGMSLSEHALSTAVVRNTHGCKVGPGRVLPTPTEKDVFRLLGLPYREPAERDW
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.7
R work: 0.1855
R free: 0.2093
Average B factor: 31.17
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 37.5mM Na cacodylate pH 6.5, 150mM KCl, 75mM magnesium acetate, 7.5% (w/v) PEG8000
Matthews coefficient: 2.6
Solvent content (%): 52.78
Ligand: CHLORIDE ION (CL)
Ligand formula: Cl
Ligand molecular weight: 35.453
Ligand SMILES: [Cl-]
Ligand InChI: InChI=1S/ClH/h1H/p-1
Release date: 2022-03-16
PanDDA analysis group deposition -- Crystal Structure of DCP2 (NUDT20) in complex with YW-FY-378 (PDB entry 5QOY)
Macromolecule: DCP2 (NUDT20)
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.1.62
Sequence length: 167 residues
Sequence: SMGVPTYGAIILDETLENVLLVQGYLAKSGWGFPKGKVNKEEAPHDCAAREVFEETGFDIKDYICKDDYIELRINDQLARLYIIPGIPKDTKFNPKTRREIRNIEWFSIEKLPCHRNDMTPKSKLGLAPNKFFMAIPFIRPLRDWLSRRFGDSSDSDNGFSSTGSTP
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.69
R work: 0.1981
R free: 0.2538
Average B factor: 34.21
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 4.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.1 M acetate, pH 4.5, 5-25% PEG3350
Matthews coefficient: 2.49
Solvent content (%): 50.65
Ligand: 1,2-ETHANEDIOL (EDO)
Ligand formula: C2 H6 O2
Ligand molecular weight: 62.068
Ligand SMILES: C(CO)O
Ligand InChI: InChI=1S/C2H6O2/c3-1-2-4/h3-4H,1-2H2
Release date: 2019-05-08
Peptide RLSAKP in complex with human cathepsin V C25S mutant (PDB entry 7Q8Q)
Macromolecule: Cathepsin L2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.22.43
Sequence length: 221 residues
Sequence: LPKSVDWRKKGYVTPVKNQKQCGSSWAFSATGALEGQMFRKTGKLVSLSEQNLVDCSRPQGNQGCNGGFMARAFQYVKENGGLDSEESYPYVAVDEICKYRPENSVAQDTGFTVVAPGKEKALMKAVATVGPISVAMDAGHSSFQFYKSGIYFEPDCSSKNLDHGVLVVGYGFEGANSQNSKYWLVKNSWGPEWGSNGYVKIAKDKNNHCGIATAASYPNV
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.13
R work: 0.2114
R free: 0.2392
Average B factor: 42.6
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 278
Crystal growth procedure: 77 % MPD, 23 % of 60 mM TRIS, pH 8
Matthews coefficient: 2.79
Solvent content (%): 55.87
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: 2022-11-23
Crystal structure of human cathepsin S produced in insect cells in complex with ketoamide 13b (PDB entry 9GJ2)
Macromolecule: Cathepsin S
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.22.27
Sequence length: 242 residues
Sequence: ILPDSVDWREKGCVTEVKYQGSCGACWAFSAVGALEAQLKLKTGKLVSLSAQNLVDCSTEKYGNKGCNGGFMTTAFQYIIDNKGIDSDASYPYKAMDQKCQYDSKYRAATCSKYTELPYGREDVLKEAVANKGPVSVGVDARHPSFFLYRSGVYYEPSCTQNVNHGVLVVGYGDLNGKEYWLVKNSWGHNFGEEGYIRMARNKGNHCGIASFPSYPEIAAAENLYFQSSSGVDLGTHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.15
R work: 0.1513
R free: 0.1618
Average B factor: 16.47
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: Cathepsin S (7 mg/ml) was mixed with an equal volume of reservoir and equilibrated against 20% (w/v) PEG4000, 0.2 M ammonium sulfate, 0.1 M sodium citrate pH 4.6. Crystals were soaked with ketoamide 13b in the presence of 5% (v/v) DMSO.
Matthews coefficient: 2.9
Solvent content (%): 57.58
Ligand: 1,2-ETHANEDIOL (EDO)
Ligand formula: C2 H6 O2
Ligand molecular weight: 62.068
Ligand SMILES: C(CO)O
Ligand InChI: InChI=1S/C2H6O2/c3-1-2-4/h3-4H,1-2H2
Release date: 2024-09-04
X-ray structure of human PPAR gamma ligand binding domain-lanifibranor-SRC1 coactivator peptide co-crystals obtained by co-crystallization (PDB entry 8HUM)
Macromolecule: Isoform 1 of Peroxisome proliferator-activated receptor gamma
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 279 residues
Sequence: GSHMQLNPESADLRALAKHLYDSYIKSFPLTKAKARAILTGKTTDKSPFVIYDMNSLMMGEDKIKFKHITPLQEQSKEVAIRIFQGCQFRSVEAVQEITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQGFMTREFLKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQDNLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLLQVIKKTETDMSLHPLLQEIYKDLY
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.29
R work: 0.2057
R free: 0.2504
Average B factor: 60.6091
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M HEPES (pH 7.5), 1.0 M trisodium citrate
Matthews coefficient: 2.91
Solvent content (%): 57.73
Ligand: 4-[1-(1,3-benzothiazol-6-ylsulfonyl)-5-chloro-indol-2-yl]butanoic acid (BJB)
Ligand formula: C19 H15 Cl N2 O4 S2
Ligand molecular weight: 434.916
Ligand SMILES: c1cc2c(cc1S(=O)(=O)n3c4ccc(cc4cc3CCCC(=O)O)Cl)scn2
Ligand InChI: InChI=1S/C19H15ClN2O4S2/c20-13-4-7-17-12(8-13)9-14(2-1-3-19(23)24)22(17)28(25,26)15-5-6-16-18(10-15)27-11-21-16/h4-11H,1-3H2,(H,23,24)
Release date: 2023-08-09
Human Argonaute2-miR-27a bound to HSUR1 target RNA (PDB entry 6MFN)
Macromolecule: Protein argonaute-2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.26
Sequence length: 859 residues
Sequence: MYSGAGPALAPPAPPPPIQGYAFKPPPRPDFGTSGRTIKLQANFFEMDIPKIDIYHYELDIKPEKCPRRVNREIVEHMVQHFKTQIFGDRKPVFDGRKNLYTAMPLPIGRDKVELEVTLPGEGKDRIFKVSIKWVSCVSLQALHDALSGRLPSVPFETIQALDVVMRHLPSMRYTPVGRSFFTASEGCSNPLGGGREVWFGFHQSVRPSLWKMMLNIDVSATAFYKAQPVIEFVCEVLDFKSIEEQQKPLTDSQRVKFTKEIKGLKVEITHCGQMKRKYRVCNVTRRPASHQTFPLQQESGQTVECTVAQYFKDRHKLVLRYPHLPCLQVGQEQKHTYLPLEVCNIVAGQRCIKKLTDNQTSTMIRATARSAPDRQEEISKLMRSADFNTDPYVREFGIMVKDEMTDVTGRVLQPPSILYGGRNKAIATPVQGVWDMRNKQFHTGIEIKVWAIACFAPQRQCTEVHLKSFTEQLRKISRDAGMPIQGQPCFCKYAQGADSVEPMFRHLKNTYAGLQLVVVILPGKTPVYAEVKRVGDTVLGMATQCVQMKNVQRTTPQTLSNLCLKINVKLGGVNNILLPQGRPPVFQQPVIFLGADVTHPPAGDGKKPSIAAVVGSMDAHPNRYCATVRVQQHRQEIIQDLAAMVRELLIQFYKSTRFKPTRIIFYRAGVSEGQFQQVLHHELLAIREACIKLEKDYQPGITFIVVQKRHHTRLFCTDKNERVGKSGNIPAGTTVDTKITHPTEFDFYLCSHAGIQGTSRPSHYHVLWDDNRFSSDELQILTYQLCHTYVRCTRSVSIPAPAYYAHLVAFRARYHLVDKEHDAAEGDHTDGQANGRDHQALAKAVQVHQDTLRTMYFA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.5
R work: 0.209
R free: 0.2468
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8
Crystallization temperature (K): 293
Crystal growth procedure: 10% PEG3350, 50 mM Tris, pH 8.0, 20 mM magnesium chloride, 75 mM phenol
Matthews coefficient: 2.58
Solvent content (%): 52.32
Ligand: PHENOL (IPH)
Ligand formula: C6 H6 O
Ligand molecular weight: 94.111
Ligand SMILES: c1ccc(cc1)O
Ligand InChI: InChI=1S/C6H6O/c7-6-4-2-1-3-5-6/h1-5,7H
Release date: 2019-08-07
Structure of DDR1 receptor tyrosine kinase in complex with inhibitor SR159 (PDB entry 7BE6)
Macromolecule: Epithelial discoidin domain-containing receptor 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 315 residues
Sequence: SMPRVDFPRSRLRFKEKLGEGQFGEVHLCEVDSPQDLVSLDFPLNVRKGHPLLVAVKILRPDATKNARNDFLKEVKIMSRLKDPNIIRLLGVCVQDDPLCMITDYMENGDLNQFLSAHQLEDKAAEGAPGDGQAAQGPTISYPMLLHVAAQIASGMRYLATLNFVHRDLATRNCLVGENFTIKIADFGMSRNLYAGDYYRVQGRAVLPIRWMAWECILMGKFTTASDVWAFGVTLWEVLMLCRAQPFGQLTDEQVIENAGEFFRDQGRQVYLSRPPACPQGLYELMLRCWSRESEQRPPFSQLHRFLAEDALNTV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.87081933411
R work: 0.186795116458
R free: 0.230440082701
Average B factor: 33.7961154469
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 293
Crystal growth procedure: 20% PEG 3350, 10% ethylene glycol, 0.1 M BisTrisPropane pH 6.5, 0.2 M sodium sulfate (50 nL protein and 100 nL reservoir)
Matthews coefficient: 2.55
Solvent content (%): 51.71
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: 2021-03-03
Human TET2 in complex with favourable DNA substrate. (PDB entry 7NE3)
Macromolecule: Methylcytosine dioxygenase TET2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11
Sequence length: 463 residues
Sequence: GGSDFPSCRCVEQIIEKDEGPFYTHLGAGPNVAAIREIMEERFGQKGKAIRIERVIYTGKEGKSSQGCPIAKWVVRRSSSEEKLLCLVRERAGHTCEAAVIVILILVWEGIPLSLADKLYSELTETLRKYGTLTNRRCALNEERTCACQGLDPETCGASFSFGCSWSMYYNGCKFARSKIPRKFKLLGDDPKEEEKLESHLQNLSTLMAPTYKKLAPDAYNNQIEYEHRAPECRLGLKEGRPFSGVTACLDFCAHAHRDLHNMQNGSTLVCTLTREDNREFGGKPEDEQLHVLPLYKVSDVDEFGSVEAQEEKKRSGAIQVLSSFRRKVRMLAEPVKTCRQRKLEAKKAAAEKLSGGGGSGGGGSGGGGSDEVWSDSEQSFLDPDIGGVAVAPTHGSILIECAKRELHATTPLKNPNRNHPTRISLVFYQHKSMNEPKHGLALWEAKMAEKAREKEEECEKYG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.26
R work: 0.1749
R free: 0.2263
Average B factor: 63.02
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.3
Crystallization temperature (K): 278
Crystal growth procedure: 0.1M MES pH6.3, 23% PEG2000MME
Matthews coefficient: 2.63
Solvent content (%): 53.3
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: 2022-03-02