satarupa22/MacromolecularLigandDB huggingface dataset:
Irak4-inhibitor co-structure (PDB entry 4YP8)
Macromolecule: Interleukin-1 receptor-associated kinase 4
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 301 residues
Sequence: VSDTRFHSFSFYELKNVTNNFDERPISVGGNKMGEGGFGVVYKGYVNNTTVAVKKLAAMVDITTEELKQQFDQEIKVMAKCQHENLVELLGFSSDGDDLCLVYVYMPNGSLLDRLSCLDGTPPLSWHMRCKIAQGAANGINFLHENHHIHRDIKSANILLDEAFTAKISDFGLARASEKFAQTVMTSRIVGTTAYMAPEALRGEITPKSDIYSFGVVLLEIITGLPAVDEHREPQLLLDIKEEIEDEEKTIEDYIDKKMNDADSTSVEAMYSVASQCLHEKKNKRPDIKKVQQLLQEMTAS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.641
R work: 0.192
R free: 0.2189
Average B factor: 72.36
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.4
Crystallization temperature (K): 289
Crystal growth procedure: 1.80 to 2.0 M Sodium Malonate, 0.2 M Sodium Acetate, 25 mM Hexamminecobalt(III)chloride, 0.05%w/v Pluronic-F-68
Matthews coefficient: 2.65
Solvent content (%): 53.57
Ligand: N-{1-(4-cyclopropyl-2-fluorophenyl)-3-[1-(propan-2-yl)piperidin-4-yl]-1H-pyrazol-5-yl}pyrazolo[1,5-a]pyrimidine-3-carboxamide (4GF)
Ligand formula: C27 H30 F N7 O
Ligand molecular weight: 487.572
Ligand SMILES: CC(C)N1CCC(CC1)c2cc(n(n2)c3ccc(cc3F)C4CC4)NC(=O)c5cnn6c5nccc6
Ligand InChI: InChI=1S/C27H30FN7O/c1-17(2)33-12-8-19(9-13-33)23-15-25(31-27(36)21-16-30-34-11-3-10-29-26(21)34)35(32-23)24-7-6-20(14-22(24)28)18-4-5-18/h3,6-7,10-11,14-19H,4-5,8-9,12-13H2,1-2H3,(H,31,36)
Release date: 2015-05-20
Crystal Structure of human phosphodiesterase 10 in complex with 4-(azetidine-1-carbonyl)-2-methyl-N-(2-phenyl-[1,2,4]triazolo[1,5-a]pyridin-7-yl)pyrazole-3-carboxamide (PDB entry 5SE7)
Macromolecule: cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.4.17
Sequence length: 343 residues
Sequence: GSSICTSEEWQGLMQFTLPVRLCKEIELFHFDIGPFENMWPGIFVYMVHRSCGTSCFELEKLCRFIMSVKKNYRRVPYHNWKHAVTVAHCMYAILQNNHTLFTDLERKGLLIACLCHDLDHRGFSNSYLQKFDHPLAALYSTSTMEQHHFSQTVSILQLEGHNIFSTLSSSEYEQVLEIIRKAIIATDLALYFGNRKQLEEMYQTGSLNLNNQSHRDRVIGLMMTACDLCSVTKLWPVTKLTANDIYAEFWAEGDEMKKLGIQPIPMMDRDKKDEVPQGQLGFYNAVAIPCYTTLTQILPPTEPLLKACRDNLSQWEKVIRGEETATWISSPSVAQKAAASED
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.17
R work: 0.1794
R free: 0.2322
Average B factor: 40.011
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 295
Crystal growth procedure: 5-20 mg/mL protein in 25mM HEPES/NaOH pH7.5, 150mM NaCl, 50mM BME mixed 1:1 with reservoir 0.1M HEPES/NaOH pH7.5, 30% PEG550MME, 50mM MgCl2
Matthews coefficient: 2.64
Solvent content (%): 53.46
Ligand: 4-(azetidine-1-carbonyl)-1-methyl-N-[(4S)-2-phenyl[1,2,4]triazolo[1,5-a]pyridin-7-yl]-1H-pyrazole-5-carboxamide (IE7)
Ligand formula: C21 H19 N7 O2
Ligand molecular weight: 401.421
Ligand SMILES: Cn1c(c(cn1)C(=O)N2CCC2)C(=O)Nc3ccn4c(c3)nc(n4)c5ccccc5
Ligand InChI: InChI=1S/C21H19N7O2/c1-26-18(16(13-22-26)21(30)27-9-5-10-27)20(29)23-15-8-11-28-17(12-15)24-19(25-28)14-6-3-2-4-7-14/h2-4,6-8,11-13H,5,9-10H2,1H3,(H,23,29)
Release date: 2022-10-12
Crystal structure of human exonuclease 1 Exo1 (WT) in complex with 5' flap DNA (f5I) (PDB entry 5V0E)
Macromolecule: Exonuclease 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1
Sequence length: 358 residues
Sequence: MGIQGLLQFIKEASEPIHVRKYKGQVVAVDTYCWLHKGAIACAEKLAKGEPTDRYVGFCMKFVNMLLSHGIKPILVFDGCTLPSKKEVERSRRERRQANLLKGKQLLREGKVSEARECFTRSINITHAMAHKVIKAARSQGVDCLVAPYEADAQLAYLNKAGIVQAIITEDSDLLAFGCKKVILKMDQFGNGLEIDQARLGMCRQLGDVFTEEKFRYMCILSGCDYLSSLRGIGLAKACKVLRLANNPDIVKVIKKIGHYLKMNITVPEDYINGFIRANNTFLYQLVFDPIKRKLIPLNAYEDDVDPETLSYAGQYVDDSIALQIALGNKDINTFEQIDDYNPDTAMPAHSRENLYFQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.744
R work: 0.2038
R free: 0.2467
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: 2.45
Solvent content (%): 49.9
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
BTK in complex with LOU064, a potent and highly selective covalent inhibitor (PDB entry 6TFP)
Macromolecule: Tyrosine-protein kinase BTK
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 276 residues
Sequence: GPSTAGLGYGSWEIDPKDLTFLKELGTGQFGVVKYGKWRGQYDVAIKMIKEGSMSEDEFIEEAKVMMNLSHEKLVQLYGVCTKQRPIFIITEYMANGCLLNYLREMRHRFQTQQLLEMCKDVCEAMEYLESKQFLHRDLAARNCLVNDQGVVKVSDFGLSRYVLDDEYTSSVGSKFPVRWSPPEVLMYSKFSSKSDIWAFGVLMWEIYSLGKMPYERFTNSETAEHIAQGLRLYRPHLASEKVYTIMYSCWHEKADERPTFKILLSNILDVMDEES
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2
R work: 0.186
R free: 0.204
Average B factor: 58.88
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 3.5 M sodium formate
Matthews coefficient: 3.45
Solvent content (%): 64.31
Ligand: SODIUM ION ()
Ligand formula: Na
Ligand molecular weight: 22.99
Ligand SMILES: [Na+]
Ligand InChI: InChI=1S/Na/q+1
Release date: 2020-03-04
A fragment-based inhibitor of SHP2 (PDB entry 8S0H)
Macromolecule: Tyrosine-protein phosphatase non-receptor type 11
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 537 residues
Sequence: HMTSRRWFHPNITGVEAENLLLTRGVDGSFLARPSKSNPGDFTLSVRRNGAVTHIKIQNTGDYYDLYGGEKFATLAELVQYYMEHHGQLKEKNGDVIELKYPLNCADPTSERWFHGHLSGKEAEKLLTEKGKHGSFLVRESQSHPGDFVLSVRTGDDKGESNDGKSKVTHVMIRCQELKYDVGGGERFDSLTDLVEHYKKNPMVETLGTVLQLKQPLNTTRINAAEIESRVRELSKLAETTDKVKQGFWEEFETLQQQECKLLYSRKEGQRQENKNKNRYKNILPFDHTRVVLHDGDPNEPVSDYINANIIMPEFETKCNNSKPKKSYIATQGCLQNTVNDFWRMVFQENSRVIVMTTKEVERGKSKCVKYWPDEYALKEYGVMRVRNVKESAAHDYTLRELKLSKVGQGNTERTVWQYHFRTWPDHGVPSDPGGVLDFLEEVHHKQESIMDAGPVVVHCSAGIGRTGTFIVIDILIDIIREKGVDCDIDVPKTIQMVRSQRSGMVQTEAQYRFIYMAVQHYIETLQRRLEHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.99
R work: 0.20397
R free: 0.25397
Average B factor: 44.227
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8
Crystallization temperature (K): 293
Crystal growth procedure: 0.5M K formate
15% PEG 3350
0.1M pH=8 Bis-Tris propane/HCl
Matthews coefficient: 2.25
Solvent content (%): 45.42
Ligand: 5-(aminomethyl)-N-(3-chloranyl-1-methyl-indol-7-yl)-1,3-dihydroisoindole-2-sulfonamide (A1H4Q)
Ligand formula: C18 H19 Cl N4 O2 S
Ligand molecular weight: 390.887
Ligand SMILES: Cn1cc(c2c1c(ccc2)NS(=O)(=O)N3Cc4ccc(cc4C3)CN)Cl
Ligand InChI: InChI=1S/C18H19ClN4O2S/c1-22-11-16(19)15-3-2-4-17(18(15)22)21-26(24,25)23-9-13-6-5-12(8-20)7-14(13)10-23/h2-7,11,21H,8-10,20H2,1H3
Release date: 2024-03-20
Crystal structure of APOBEC3G Catalytic domain complex with ssDNA containing 2'-deoxy Zebularine. (PDB entry 7UXD)
Macromolecule: DNA dC->dU-editing enzyme APOBEC-3G
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.5.4.38
Sequence length: 199 residues
Sequence: GPLGSEILRHSMDPATFTFNFNNEPWVRGRHETYLCYEVERMHNDTWVKLAQRRGFLANQAKHKHGFLEGRHAELCFLDVIPFWKLDLDQDYRVTCFTSWSPCFSCAQEMAKFISKNKHVSLCIKTARIYDDKGRAAEGLRTLAEAGAKISIMTYSEFKHCWDTFVDHQGAPFQPWDGLDEHSQDLSGRLRAILQNQEN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.5
R work: 0.1725
R free: 0.1944
Average B factor: 36.7548
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 20% PEG6000, 50 mM di-Sodium L-Malate; pH5.0, 30 mM CACL2
Matthews coefficient: 2.2
Solvent content (%): 43.99
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: 2022-12-14
Discovery and Optimisation of Potent, Efficacious and Selective Inhibitors Targeting EGFR Exon20 Insertion Mutations. Compound 12 bound to EGFRinsNPG (PDB entry 8PO0)
Macromolecule: Epidermal growth factor receptor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 332 residues
Sequence: GSGEAPNQALLRILKETEFKKIKVLGSGAFGTVYKGLWIPEGEKVKIPVAIKELREATSPKANKEILDEAYVMASVDNPGNPHVCRLLGICLTSTVQLITQLMPFGCLLDYVREHKDNIGSQYLLNWCVQIAKGMNYLEDRRLVHRDLAARNVLVKTPQHVKITDFGLAKLLGAEEKEYHAEGGKVPIKWMALESILHRIYTHQSDVWSYGVTVWELMTFGSKPYDGIPASEISSILEKGERLPQPPICTIDVYMIMVKCWMIDADSRPKFRELIIEFSKMARDPQRYLVIQGDERMHLPSPTDSNFYRALMDEEDMDDVVDADEYLIPQQG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.523
R work: 0.3151
R free: 0.3755
Average B factor: 96.52
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293.15
Crystal growth procedure: Sodium Citrate
Matthews coefficient: 3.79
Solvent content (%): 67.51
Ligand: 1-[3-[7-methoxy-4-[3-(3-methoxyphenyl)-1~{H}-pyrazol-4-yl]quinazolin-6-yl]oxyazetidin-1-yl]propan-1-one (2I6)
Ligand formula: C25 H25 N5 O4
Ligand molecular weight: 459.497
Ligand SMILES: CCC(=O)N1CC(C1)Oc2cc3c(cc2OC)ncnc3c4c[nH]nc4c5cccc(c5)OC
Ligand InChI: InChI=1S/C25H25N5O4/c1-4-23(31)30-12-17(13-30)34-22-9-18-20(10-21(22)33-3)26-14-27-25(18)19-11-28-29-24(19)15-6-5-7-16(8-15)32-2/h5-11,14,17H,4,12-13H2,1-3H3,(H,28,29)
Release date: 2024-06-05
Diphosphoinositol polyphosphate phosphohydrolase 1 (DIPP1/NUDT3) in complex with 5-diphosphoinositol pentakisphosphate and Mg, presoaked with 5-IP7, Mg and Fluoride, soaking 1min in the absence of Fluoride. (PDB entry 6WOC)
Macromolecule: Diphosphoinositol polyphosphate phosphohydrolase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.1.52
Sequence length: 169 residues
Sequence: HHHHHHSSGVDLGTENLYFQSMMKLKSNQTRTYDGDGYKKRAACLCFRSESEEEVLLVSSSRHPDRWIVPGGGMEPEEEPSVAAVREVCEEAGVKGTLGRLVGIFENQERKHRTYVYVLIVTEVLEDWEDSVNIGRKREWFKIEDAIKVLQYHKPVQASYFETLRQGYS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.35
R work: 0.138
R free: 0.1638
Average B factor: 16.805
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7
Crystallization temperature (K): 293
Crystal growth procedure: 10% (w/v) PEG 8000, 10% (v/v) isopropanol, 200 mM Li2SO4, 75 mM NaAc, pH 5.5 and 25 mM HEPES, pH 7.0 and soaking in solution of 200 mM LiCl, 20% (w/v) PEG 8000, 20% (v/v) isopropanol, 100 mM HEPES, pH 7.0, 80 mM NaF, 20 mM MgCl2 in present of 2mM 5-IP7 for 2 days, and transferred into 200 mM LiCl, 20% (w/v) PEG 8000, 20% (v/v) isopropanol, 100 mM HEPES, pH 7.0, 20 mM MgCl2 for 1min.
Matthews coefficient: 2.18
Solvent content (%): 43.61
Ligand: (1r,2R,3S,4s,5R,6S)-2,3,4,5,6-pentakis(phosphonooxy)cyclohexyl trihydrogen diphosphate (I7P)
Ligand formula: C6 H19 O27 P7
Ligand molecular weight: 740.015
Ligand SMILES: C1(C(C(C(C(C1OP(=O)(O)O)OP(=O)(O)O)OP(=O)(O)OP(=O)(O)O)OP(=O)(O)O)OP(=O)(O)O)OP(=O)(O)O
Ligand InChI: InChI=1S/C6H19O27P7/c7-34(8,9)27-1-2(28-35(10,11)12)4(30-37(16,17)18)6(32-40(25,26)33-39(22,23)24)5(31-38(19,20)21)3(1)29-36(13,14)15/h1-6H,(H,25,26)(H2,7,8,9)(H2,10,11,12)(H2,13,14,15)(H2,16,17,18)(H2,19,20,21)(H2,22,23,24)/t1-,2+,3-,4-,5+,6+
Release date: 2021-03-03
Pre-catalytic synaptic complex of DNA Polymerase Lambda with gapped DSB substrate and incoming dUMPNPP (PDB entry 7M0E)
Macromolecule: DNA polymerase lambda
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 348 residues
Sequence: GSAAAPAVLDKWVCAQPSSQKATNHNLHITEKLEVLAKAYSVQGDKWRALGYAKAINALKSFHKPVTSYQEACSIPGIGKRMAEKIIEILESGHLRKLDHISESVPVLELFSNIWGAGTKTAQMWYQQGFRSLEDIRSQASLTTQQAIGLKHYSDFLERMPREEATEIEQTVQKAAQAFNSGLLCVACGSYRRGKATCGDVDVLITHPDGRSHRGIFSRLLDSLRQEGFLTDDLVSQEENGQQQKYLGVCRLPGPGRRHRRLDIIVVPYSEFACALLYFTGSAHFNRSMRALAKTKGMSLSEHALSTAVVRNTHGCKVGPGRVLPTPTEKDVFRLLGLPYREPAERDW
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.25
R work: 0.1835
R free: 0.2221
Average B factor: 48.64
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 0.138M sodium sulfate, 20% (w/v) PEG 3350
Matthews coefficient: 2.58
Solvent content (%): 52.38
Ligand: 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE (DUP)
Ligand formula: C9 H16 N3 O13 P3
Ligand molecular weight: 467.157
Ligand SMILES: C1C(C(OC1N2C=CC(=O)NC2=O)COP(=O)(NP(=O)(O)OP(=O)(O)O)O)O
Ligand InChI: InChI=1S/C9H16N3O13P3/c13-5-3-8(12-2-1-7(14)10-9(12)15)24-6(5)4-23-26(16,17)11-27(18,19)25-28(20,21)22/h1-2,5-6,8,13H,3-4H2,(H,10,14,15)(H2,20,21,22)(H3,11,16,17,18,19)/t5-,6+,8+/m0/s1
Release date: 2022-03-16
Linked KDM5A Jmj Domain Bound to the Inhibitor N8 ( 5-methyl-7-oxo-6-(propan-2-yl)-4,7-dihydropyrazolo[1,5-a]pyrimidine-3-carbonitrile) (PDB entry 5IVE)
Macromolecule: Lysine-specific demethylase 5A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11
Sequence length: 330 residues
Sequence: HNMAGVGPGGYAAEFVPPPECPVFEPSWEEFTDPLSFIGRIRPLAEKTGICKIRPPKDWQPPFACEVKSFRFTPRVQRLNELEAMTRVRPREAFGFEQAVREYTLQSFGEMADNFKSDYFNMPVHMVPTELVEKEFWRLVSSIEEDVIVEYGADISSKDFGSGFPVKDGRRKILPEEEEYALSGWNLNNMPVLEQSVLAHINVDISGMKVPWLYVGMCFSSFCWHIEDHWSYSINYLHWGEPKTWYGVPSHAAEQLEEVMRELAPELFESQPDLLHQLVTIMNPNVLMEHGVPVYRTNQCAGEFVVTFPRAYHSGFNQGYNFAEAVNFCT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.783
R work: 0.1747
R free: 0.2055
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 289
Crystal growth procedure: 1.2-1.35 M (NH4)2SO4,
0.1 M Tris-HCl (pH 8.6-9.2)
0-20% glycerol 
25 mM (Na/K) dibasic/monobasic phosphate
Matthews coefficient: 2.24
Solvent content (%): 45.15
Ligand: 5-methyl-7-oxo-6-(propan-2-yl)-4,7-dihydropyrazolo[1,5-a]pyrimidine-3-carbonitrile (6E8)
Ligand formula: C11 H12 N4 O
Ligand molecular weight: 216.239
Ligand SMILES: CC1=C(C(=O)n2c(c(cn2)C#N)N1)C(C)C
Ligand InChI: InChI=1S/C11H12N4O/c1-6(2)9-7(3)14-10-8(4-12)5-13-15(10)11(9)16/h5-6,14H,1-3H3
Release date: 2016-07-27
X-ray structure of human furin in complex with the competitive inhibitor para-guanidinomethyl-Phac-R-Tle-R-Amba (PDB entry 4RYD)
Macromolecule: Furin
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.75
Sequence length: 482 residues
Sequence: DVYQEPTDPKFPQQWYLSGVTQRDLNVKAAWAQGYTGHGIVVSILDDGIEKNHPDLAGNYDPGASFDVNDQDPDPQPRYTQMNDNRHGTRCAGEVAAVANNGVCGVGVAYNARIGGVRMLDGEVTDAVEARSLGLNPNHIHIYSASWGPEDDGKTVDGPARLAEEAFFRGVSQGRGGLGSIFVWASGNGGREHDSCNCDGYTNSIYTLSISSATQFGNVPWYSEACSSTLATTYSSGNQNEKQIVTTDLRQKCTESHTGTSASAPLAAGIIALTLEANKNLTWRDMQHLVVQTSKPAHLNANDWATNGVGRKVSHSYGYGLLDAGAMVALAQNWTTVAPQRKCIIDILTEPKDIGKRLEVRKTVTACLGEPNHITRLEHAQARLTLSYNRRGDLAIHLVSPMGTRSTLLAARPHDYSADGFNDWAFMTTHSWDEDPSGEWVLEIENTSEANNYGTLTKFTLVLYGTASGSLVPRGSHHHHHH
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.15
R work: 0.1862
R free: 0.2186
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 293
Crystal growth procedure: 50mM Tris, 2.8M sodium formate, 15mM Cymal-7, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Matthews coefficient: 2.86
Solvent content (%): 56.93
Ligand: FORMIC ACID (FMT)
Ligand formula: C H2 O2
Ligand molecular weight: 46.025
Ligand SMILES: C(=O)O
Ligand InChI: InChI=1S/CH2O2/c2-1-3/h1H,(H,2,3)
Release date: 2015-05-27
NMR-guided design of potent and selective EphA4 agonistic ligands (PDB entry 7OFV)
Macromolecule: Ephrin type-A receptor 4
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 185 residues
Sequence: GSHMNEVTLLDSRSVQGELGWIASPLEGGWEEVSIMDEKNTPIRTYQVCNVMEPSQNNWLRTDWITREGAQRVYIEIKFTLRDCNSLPGVMGTCKETFNLYYYESDNDKERFIRENQFVKIDTIAADESFTQVDIGDRIMKLNTEIRDVGPLSKKGFYLAFQDVGACIALVSVRVFYKKAPLTVR
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.43
R work: 0.149
R free: 0.2065
Average B factor: 20.129
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 4.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.10 M Na Acet, pH 4.50, 1.20 M K2HPO4, 0.80 M NaH2PO4
Matthews coefficient: 2.47
Solvent content (%): 50.11
Ligand: ACETATE ION (ACT)
Ligand formula: C2 H3 O2
Ligand molecular weight: 59.044
Ligand SMILES: CC(=O)[O-]
Ligand InChI: InChI=1S/C2H4O2/c1-2(3)4/h1H3,(H,3,4)/p-1
Release date: 2021-08-11
Wildtype PTP1b in complex with DES4799 (PDB entry 8G65)
Macromolecule: Tyrosine-protein phosphatase non-receptor type 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 298 residues
Sequence: MEMEKEFEQIDKSGSWAAIYQDIRHEASDFPCRVAKLPKNKNRNRYRDVSPFDHSRIKLHQEDNDYINASLIKMEEAQRSYILTQGPLPNTCGHFWEMVWEQKSRGVVMLNRVMEKGSLKCAQYWPQKEEKEMIFEDTNLKLTLISEDIKSYYTVRQLELENLTTQETREILHFHYTTWPDFGVPESPASFLNFLFKVRESGSLSPEHGPVVVHCSAGIGRSGTFCLADTCLLLMDKRKDPSSVDIKKVLLEMRKFRMGLIQTADQLRFSYLAVIEGAKFIMGDSSVQDQWKELSHED
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.45
R work: 0.13438
R free: 0.18836
Average B factor: 24.011
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 6.2
Crystallization temperature (K): 278
Crystal growth procedure: Reservoir solution: 50 mM MES (pH 6.2), 14% PEG6000, 50 mM MgCl2;
Protein solution: 10.3 mg/ml PTP-1B 1-298 in 25 mM Hepes pH 7.2, 150 mM NaCl, 1 mM EDTA, 2 mM DTT
Matthews coefficient: 2.39
Solvent content (%): 48.47
Ligand: 4-(3,5-dimethyl-1H-pyrazol-1-yl)aniline (YW9)
Ligand formula: C11 H13 N3
Ligand molecular weight: 187.241
Ligand SMILES: Cc1cc(n(n1)c2ccc(cc2)N)C
Ligand InChI: InChI=1S/C11H13N3/c1-8-7-9(2)14(13-8)11-5-3-10(12)4-6-11/h3-7H,12H2,1-2H3
Release date: 2023-04-26
Aurora A kinase in complex with TPX2-inhibitor CAM2602 (PDB entry 8C1K)
Macromolecule: Aurora kinase A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 273 residues
Sequence: MGRQWALEDFEIGRPLGKGKFGNVYLAREKQSKFILALKVLFKAQLEKAGVEHQLRREVEIQSHLRHPNILRLYGYFHDATRVYLILEYAPLGTVYRELQKLSKFDEQRTATYITELANALSYCHSKRVIHRDIKPENLLLGSAGELKIADFGWSVHAPSSRRTTLAGTLDYLPPEMIEGRMHDEKVDLWSLGVLCYEFLVGKPPFEANTYQETYKRISRVEFTFPDFVTEGARDLISRLLKHNPSQRPMLREVLEHPWITANSSKPHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.43
R work: 0.217
R free: 0.242
Average B factor: 82.17
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 6.5
Crystallization temperature (K): 298
Crystal growth procedure: 30% PEG5000 MME, 0.1M (NH4)2SO4, 0.1 M MES 6.5: soaking: 31.5% PEG5000 MME, 0.09M (NH4)2SO4, 0.09 M MES 6.5, 10% DMSO, 5 mM compound
Matthews coefficient: 2.59
Solvent content (%): 52.51
Ligand: 4-(4-chloranyl-3-pyridin-2-yloxy-phenyl)-~{N}-(dimethylsulfamoyl)-7-methyl-1~{H}-indole-6-carboxamide (T4O)
Ligand formula: C23 H21 Cl N4 O4 S
Ligand molecular weight: 484.955
Ligand SMILES: Cc1c(cc(c2c1[nH]cc2)c3ccc(c(c3)Oc4ccccn4)Cl)C(=O)NS(=O)(=O)N(C)C
Ligand InChI: InChI=1S/C23H21ClN4O4S/c1-14-17(23(29)27-33(30,31)28(2)3)13-18(16-9-11-26-22(14)16)15-7-8-19(24)20(12-15)32-21-6-4-5-10-25-21/h4-13,26H,1-3H3,(H,27,29)
Release date: 2024-01-10
ERAP2 bound to Aryl Sulfonamide Uncompetitive Inhibitor (PDB entry 6EA4)
Macromolecule: Endoplasmic reticulum aminopeptidase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.11
Sequence length: 911 residues
Sequence: FPVATNGERFPWQELRLPSVVIPLHYDLFVHPNLTSLDFVASEKIEVLVSNATQFIILHSKDLEITNATLQSEEDSRYMKPGKELKVLSYPAHEQIALLVPEKLTPHLKYYVAMDFQAKLGDGFEGFYKSTYRTLGGETRILAVTDFEPTQARMAFPCFDEPLFKANFSIKIRRESRHIALSNMPKVKTIELEGGLLEDHFETTVKMSTYLVAYIVCDFHSLSGFTSSGVKVSIYASPDKRNQTHYALQASLKLLDFYEKYFDIYYPLSKLDLIAIPDFAPGAMENWGLITYRETSLLFDPKTSSASDKLWVTRVIAHELAHQWFGNLVTMEWWNDIWLNEGFAKYMELIAVNATYPELQFDDYFLNVCFEVITKDSLNSSRPISKPAETPTQIQEMFDEVSYNKGACILNMLKDFLGEEKFQKGIIQYLKKFSYRNAKNDDLWSSLSNSCLESDFTSGGVCHSDPKMTSNMLAFLGENAEVKEMMTTWTLQKGIPLLVVKQDGCSLRLQQERFLQGVFQEDPEWRALQERYLWHIPLTYSTSSSNVIHRHILKSKTDTLDLPEKTSWVKFNVDSNGYYIVHYEGHGWDQLITQLNQNHTLLRPKDRVGLIHDVFQLVGAGRLTLDKALDMTYYLQHETSSPALLEGLSYLESFYHMMDRRNISDISENLKRYLLQYFKPVIDRQSWSDKGSVWDRMLRSALLKLACDLNHAPCIQKAAELFSQWMESSGKLNIPTDVLKIVYSVGAQTTAGWNYLLEQYELSMSSAEQNKILYALSTSKHQEKLLKLIELGMEGKVIKTQNLAALLHAIARRPKGQQLAWDFVRENWTHLLKKFDLGSYDIRMIISGTTAHFSSKDKLQEVKLFFESLEAQGSHLDIFQTVLETITKNIKWLEKNLPTLRTWLMVNTRHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.45
R work: 0.208
R free: 0.2361
Average B factor: 82.35
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 297
Crystal growth procedure: 10% PEG 8000, 20% ethylene glycol, 61 mM MES, 39 mM imidazole, 20 mM sodium-L-glutamate, 20 mM D-L-alanine, 20 mM glycine, 20 mM D-L-lysine, 20 mM D-L-serine (Morpheus H2)
Matthews coefficient: 3.19
Solvent content (%): 61.38
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: 2019-12-18
Complex of XLF and heterodimer Ku bound to DNA (PDB entry 6ERG)
Macromolecule: X-ray repair cross-complementing protein 6
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.4
Sequence length: 544 residues
Sequence: MSGWESYYKTEGDEEAEEEQEENLEASGDYKYSGRDSLIFLVDASKAMFESQSEDELTPFDMSIQCIQSVYISKIISSDRDLLAVVFYGTEKDKNSVNFKNIYVLQELDNPGAKRILELDQFKGQQGQKRFQDMMGHGSDYSLSEVLWVCANLFSDVQFKMSHKRIMLFTNEDNPHGNDSAKASRARTKAGDLRDTGIFLDLMHLKKPGGFDISLFYRDIISIAEDEDLRVHFEESSKLEDLLRKVRAKETRKRALSRLKLKLNKDIVISVGIYNLVQKALKPPPIKLYRETNEPVKTKTRTFNTSTGGLLLPSDTKRSQIYGSRQIILEKEETEELKRFDDPGLMLMGFKPLVLLKKHHYLRPSLFVYPEESLVIGSSTLFSALLIKCLEKEVAALCRYTPRRNIPPYFVALVPQEEELDDQKIQVTPPGFQLVFLPFADDKRKMPFTEKIMATPEQVGKMKAIVEKLRFTYRSDSFENPVLQQHFRNLEALALDLMEPEQAVDLTLPKVEAMNKRLGSLVDEFKELVYPPDYNPEGKVTKRK
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.9
R work: 0.218
R free: 0.244
Average B factor: 100.04
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 293
Crystal growth procedure: 18% PEG 3350, 150 mM Na sulfate , 100 mM Bis-Tris-Propane
Matthews coefficient: 2.75
Solvent content (%): 55.35
Ligand: SULFATE ION (SO4)
Ligand formula: O4 S
Ligand molecular weight: 96.063
Ligand SMILES: [O-]S(=O)(=O)[O-]
Ligand InChI: InChI=1S/H2O4S/c1-5(2,3)4/h(H2,1,2,3,4)/p-2
Release date: 2018-10-17
Human DNA polymerase eta-DNA-dGMPNPP ternary mismatch complex in 0.1 mM Mg2+ for 600s (PDB entry 7U7U)
Macromolecule: DNA polymerase eta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 435 residues
Sequence: GPHMATGQDRVVALVDMDCFFVQVEQRQNPHLRNKPCAVVQYKSWKGGGIIAVSYEARAFGVTRSMWADDAKKLCPDLLLAQVRESRGKANLTKYREASVEVMEIMSRFAVIERASIDEAYVDLTSAVQERLQKLQGQPISADLLPSTYIEGLPQGPTTAEETVQKEGMRKQGLFQWLDSLQIDNLTSPDLQLTVGAVIVEEMRAAIERETGFQCSAGISHNKVLAKLACGLNKPNRQTLVSHGSVPQLFSQMPIRKIRSLGGKLGASVIEILGIEYMGELTQFTESQLQSHFGEKNGSWLYAMCRGIEHDPVKPRQLPKTIGCSKNFPGKTALATREQVQWWLLQLAQELEERLTKDRNDNDRVATQLVVSIRVQGDKRLSSLRRCCALTRYDAHKMSHDAFTVIKNCNTSGIQTEWSPPLTMLFLCATKFSAS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.54
R work: 0.1936
R free: 0.2214
Average B factor: 32.9643
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6
Crystallization temperature (K): 298
Crystal growth procedure: 10% PEG 2000MME, 0.1 M MES
Matthews coefficient: 2.1
Solvent content (%): 41.45
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: 2022-05-04