satarupa22/MacromolecularLigandDB huggingface dataset:
Human Xylosyltransferase 1 in complex with peptide PAAEGSGEQDFT (PDB entry 6EJE)
Macromolecule: Xylosyltransferase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.4.2.26
Sequence length: 751 residues
Sequence: APLVHHHHHHALDENLYFQGALADVSRPPHARKTGGSSPETKYDQPPKCDISGKEAISALSRAKSKHCRQEIGETYCRHKLGLLMPEKVTRFCPLEGKANKNVQWDEDSVEYMPANPVRIAFVLVVHGRASRQLQRMFKAIYHKDHFYYIHVDKRSNYLHRQVLQVSRQYSNVRVTPWRMATIWGGASLLSTYLQSMRDLLEMTDWPWDFFINLSAADYPIRTNDQLVAFLSRYRDMNFLKSHGRDNARFIRKQGLDRLFLECDAHMWRLGDRRIPEGIAVDGGSDWFLLNRRFVEYVTFSTDDLVTKMKQFYSYTLLPAESFFHTVLENSPHCDTMVDNNLRITNWNRKLGCKCQYKHIVDWCGCSPNDFKPQDFHRFQQTARPTFFARKFEAVVNQEIIGQLDYYLYGNYPAGTPGLRSYWENVYDEPDGIHSLSDVTLTLYHSFARLGLRRAETSLHTDGENSCRYYPMGHPASVHLYFLADRFQGFLIKHHATNLAVSKLETLETWVMPKKVFKIASPPSDFGRLQFSEVGTDWDAKERLFRNFGGLLGPMDEPVGMQKWGKGPNVTVTVIWVDPVNVIAATYDILIESTAEFTHYKPPLNLPLRPGVWTVKILHHWVPVAETKFLVAPLTFSNRQPIKPEEALKLHNGPLRNAYMEQSFQSLNPVLSLPINPAQVEQARRNAASTGTALEGWLDSLVGGMWTAMDICATGPTACPVMQTCSQTAWSSFSPDPKSELGAVKPDGRLR
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.43
R work: 0.1972
R free: 0.2349
Average B factor: 50.0257
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: 55-65% Morpheus Precipitant mix 2 (PEG8000 and Ethylene glycol)
0.1M Bicine/Tris buffer at pH 7.5
0.1M of NPS mix (0.033M of each)
Matthews coefficient: 2.56
Solvent content (%): 52.02
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: 2018-05-02
Structure of CREBBP bromodomain with compound 2 bound (PDB entry 6QST)
Macromolecule: CREB-binding protein
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1.48
Sequence length: 119 residues
Sequence: SMRKKIFKPEELRQALMPTLEALYRQDPESLPFRQPVDPQLLGIPDYFDIVKNPMDLSTIKRKLDTGQYQEPWQYVDDVWLMFNNAWLYNRKTSRVYKFCSKLAEVFEQEIDPVMQSLG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.1
R work: 0.1871
R free: 0.2189
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 0.1 M Bis-Tris propane pH 7.5, 0.02 M Sodium/potassium phosphate, 20% w/v PEG 3350
Matthews coefficient: 2.78
Solvent content (%): 55.8
Ligand: ~{N}-[3-(3-azanyl-5-methyl-1,2-oxazol-4-yl)-5-(5-ethanoyl-2-ethoxy-phenyl)phenyl]furan-2-carboxamide (JGK)
Ligand formula: C25 H23 N3 O5
Ligand molecular weight: 445.467
Ligand SMILES: CCOc1ccc(cc1c2cc(cc(c2)NC(=O)c3ccco3)c4c(onc4N)C)C(=O)C
Ligand InChI: InChI=1S/C25H23N3O5/c1-4-31-21-8-7-16(14(2)29)13-20(21)17-10-18(23-15(3)33-28-24(23)26)12-19(11-17)27-25(30)22-6-5-9-32-22/h5-13H,4H2,1-3H3,(H2,26,28)(H,27,30)
Release date: 2020-03-18
PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with FMOPL000631a (PDB entry 7GS9)
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): 1.96
R work: 0.2226
R free: 0.263
Average B factor: 41.915
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.3 M magnesium acetate, 0.1 M HEPES pH 7.5, 0.1% beta-mercaptoethanol, 13-14% PEG 8000, 2% ethanol
Matthews coefficient: 3.38
Solvent content (%): 63.66
Ligand: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL (TRS)
Ligand formula: C4 H12 N O3
Ligand molecular weight: 122.143
Ligand SMILES: C(C(CO)(CO)[NH3+])O
Ligand InChI: InChI=1S/C4H11NO3/c5-4(1-6,2-7)3-8/h6-8H,1-3,5H2/p+1
Release date: 2024-01-24
EED in complex with PRC2 allosteric inhibitor compound 8 (PDB entry 5H24)
Macromolecule: Polycomb protein EED
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 367 residues
Sequence: GKKCKYSFKCVNSLKEDHNQPLFGVQFNWHSKEGDPLVFATVGSNRVTLYECHSQGEIRLLQSYVDADADENFYTCAWTYDSNTSHPLLAVAGSRGIIRIINPITMQCIKHYVGHGNAINELKFHPRDPNLLLSVSKDHALRLWNIQTDTLVAIFGGVEGHRDEVLSADYDLLGEKIMSCGMDHSLKLWRINSKRMMNAIKESYDYNPNKTNRPFISQKIHFPDFSTRDIHRNYVDCVRWLGDLILSKSCENAIVCWKPGKMEDDIDKIKPSESNVTILGRFDYSQCDIWYMRFSMDFWQKMLALGNQVGKLYVWDLEVEDPHKAKCTTLTHHKCGAAIRQTSFSRDSSILIAVCDDASIWRWDRLR
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.5
R work: 0.187
R free: 0.255
Average B factor: 34.99
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M Tris, 16% PEG 8000, 10 mM beta-Nicotinamide mononucleotide
Matthews coefficient: 2.28
Solvent content (%): 46.07
Ligand: 5-(furan-2-ylmethylamino)-[1,2,4]triazolo[4,3-a]pyridine-6-carbonitrile (LQG)
Ligand formula: C12 H9 N5 O
Ligand molecular weight: 239.233
Ligand SMILES: c1cc(oc1)CNc2c(ccc3n2cnn3)C#N
Ligand InChI: InChI=1S/C12H9N5O/c13-6-9-3-4-11-16-15-8-17(11)12(9)14-7-10-2-1-5-18-10/h1-5,8,14H,7H2
Release date: 2017-01-25
The crystal structure of coexpressed SDS22:PP1 complex (PDB entry 6OBN)
Macromolecule: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.16
Sequence length: 305 residues
Sequence: GHMGSMSDSEKLNLDSIIGRLLEVQGSRPGKNVQLTENEIRGLCLKSREIFLSQPILLELEAPLKICGDIHGQYYDLLRLFEYGGFPPESNYLFLGDYVDRGKQSLETICLLLAYKIKYPENFFLLRGNHECASINRIYGFYDECKRRYNIKLWKTFTDCFNCLPIAAIVDEKIFCCHGGLSPDLQSMEQIRRIMRPTDVPDQGLLCDLLWSDPDKDVQGWGENDRGVSFTFGAEVVAKFLHKHDLDLICRAHQVVEDGYEFFAKRQLVTLFSAPNYCGEFDNAGAMMSVDETLMCSFQILKPAD
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.7
R work: 0.2023
R free: 0.2458
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.2
Crystallization temperature (K): 289
Crystal growth procedure: 14% PEG4000, 6% MPD, sodium/potassium phosphate
Matthews coefficient: 2.46
Solvent content (%): 50.03
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: 2019-09-18
Structure of human cGAS (PDB entry 8SHZ)
Macromolecule: Cyclic GMP-AMP synthase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.86
Sequence length: 369 residues
Sequence: GTGDAAPGASKLRAVLEKLKLSRDDISTAAGMVKGVVDHLLLRLKCDSAFRGVGLLNTGSYYEHVKISAPNEFDVMFKLEVPRIQLEEYSNTRAYYFVKFKRNPKENPLSQFLEGEILSASKMLSKFRKIIKEEINDIKDTDVIMKRKRGGSPAVTLLISEKISVDITLALESKSSWPASTQEGLRIQNWLSAKVRKQLRLKPFYLVPKHAKEGNGFQEETWRLSFSHIEKEILNNHGKSKTCCENKEEKCCRKDCLKLMKYLLEQLKERFKDKKHLDKFSSYHVKTAFFHVCTQNPQDSQWDRKDLGLCFDNCVTYFLQCLRTEKLENYFIPEFNLFSSNLIDKRSKEFLTKQIEYERNNEFPVFDEF
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.4
R work: 0.2118
R free: 0.2581
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 298.15
Crystal growth procedure: 0.1 M Tris, pH 8.5, 8% w/v PEG8000
Matthews coefficient: 2.07
Solvent content (%): 40.62
Ligand: ZINC ION (ZN)
Ligand formula: Zn
Ligand molecular weight: 65.409
Ligand SMILES: [Zn+2]
Ligand InChI: InChI=1S/Zn/q+2
Release date: 2024-04-24
Human DNA Polymerase Beta With Gapped DNA Containing an 8-oxo-7,8-dihydro-Guanine (8-oxoG)and dATP soaked with MgCl2 for 60 s (PDB entry 4RQ5)
Macromolecule: DNA polymerase beta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 343 residues
Sequence: MGMSKRKAPQETLNGGITDMLTELANFEKNVSQAIHKYNAYRKAASVIAKYPHKIKSGAEAKKLPGVGTKIAEKIDEFLATGKLRKLEKIRQDDTSSSINFLTRVSGIGPSAARKFVDEGIKTLEDLRKNEDKLNHHQRIGLKYFGDFEKRIPREEMLQMQDIVLNEVKKVDSEYIATVCGSFRRGAESSGDMDVLLTHPSFTSESTKQPKLLHQVVEQLQKVHFITDTLSKGETKFMGVCQLPSKNDEKEYPHRRIDIRLIPKDQYYCGVLYFTGSDIFNKNMRAHALEKGFTINEYTIRPLGVTGVAGEPLPVDSEKDIFDYIQWKYREPKDRSEHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.32
R work: 0.19644
R free: 0.26586
Average B factor: 39.173
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8
Crystallization temperature (K): 295
Crystal growth procedure: 50 MM IMIDAZOLE, 350 MM SODIUM Acetate, 17% PEG3350, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Matthews coefficient: 2.12
Solvent content (%): 42.02
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: 2015-04-15
Crystal structure of human Pim-1 kinase in complex with a consensus peptide and fragment like molecule 2-(4-chlorophenyl)sulfanylacetohydrazide (PDB entry 5N50)
Macromolecule: Serine/threonine-protein kinase pim-1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 313 residues
Sequence: MLLSKINSLAHLRAAPCNDLHATKLAPGKEKEPLESQYQVGPLLGSGGFGSVYSGIRVSDNLPVAIKHVEKDRISDWGELPNGTRVPMEVVLLKKVSSGFSGVIRLLDWFERPDSFVLILERPEPVQDLFDFITERGALQEELARSFFWQVLEAVRHCHNCGVLHRDIKDENILIDLNRGELKLIDFGSGALLKDTVYTDFDGTRVYSPPEWIRYHRYHGRSAAVWSLGILLYDMVCGDIPFEHDEEIIGGQVFFRQRVSSECQHLIRWCLALRPSDRPTFEEIQNHPWMQDVLLPQETAEIHLHSLSPGPSK
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.92
R work: 0.1584
R free: 0.18
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 277
Crystal growth procedure: HEPES
CaCl2
Glycerol
DTT
BIS-TRIS-propane
PEG3350
Ethylene-glycol
DMSO
Matthews coefficient: 3.15
Solvent content (%): 61
Ligand: 2-(4-chlorophenyl)sulfanylethanehydrazide (8MN)
Ligand formula: C8 H9 Cl N2 O S
Ligand molecular weight: 216.688
Ligand SMILES: c1cc(ccc1SCC(=O)NN)Cl
Ligand InChI: InChI=1S/C8H9ClN2OS/c9-6-1-3-7(4-2-6)13-5-8(12)11-10/h1-4H,5,10H2,(H,11,12)
Release date: 2018-02-28
Crystal structure of double mutant Y115E Y117E human Glutaminyl Cyclase in apo-state (PDB entry 9FXG)
Macromolecule: Glutaminyl-peptide cyclotransferase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2.5
Sequence length: 341 residues
Sequence: MRGSHHHHHHGSASAWPEEKNYHQPAILNSSALRQIAEGTSISEMWQNDLQPLLIERYPGSPGSYAARQHIMQRIQRLQADWVLEIDTFLSQTPEGERSFSNIISTLNPTAKRHLVLACHYDSKYFSHWNNRVFVGATDSAVPCAMMLELARALDKKLLSLKTVSDSKPDLSLQLIFFDGEEAFLHWSPQDSLYGSRHLAAKMASTPHPPGARGTSQLHGMDLLVLLDLIGAPNPTFPNFFPNSARWFERLQAIEHELHELGLLKDHSLEGRYFQNYSYGGVIQDDHIPFLRRGVPVLHLIPSPFPEVWHTMDDNEENLDESTIDNLNKILQVFVLEYLHL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.96
R work: 0.20804
R free: 0.25717
Average B factor: 22.516
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6
Crystallization temperature (K): 281
Crystal growth procedure: 0.2 M ammonium sulphate and 0.1 M MES, pH 6.0
Matthews coefficient: 2.76
Solvent content (%): 55.39
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
KRAS 1-169 G12C Mutant at 310k (PDB entry 8TY8)
Macromolecule: Isoform 2B of GTPase KRas
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.5.2
Sequence length: 169 residues
Sequence: MTEYKLVVVGACGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKCDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQGVDDAFYTLVREIRKHKEK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.4
R work: 0.1824
R free: 0.206
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 200mM Na Acetate pH 3.6
100mM Tris pH 8.5
20% PEG 3350
1mM DTT
Matthews coefficient: 1.96
Solvent content (%): 37.38
Ligand: GUANOSINE-5'-DIPHOSPHATE (GDP)
Ligand formula: C10 H15 N5 O11 P2
Ligand molecular weight: 443.201
Ligand SMILES: c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
Ligand InChI: InChI=1S/C10H15N5O11P2/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(25-9)1-24-28(22,23)26-27(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1
Release date: 2024-08-28
Crystal structure of MUS81-EME1 bound by compound 10. (PDB entry 9F99)
Macromolecule: Crossover junction endonuclease MUS81
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.22
Sequence length: 308 residues
Sequence: GSSAELASEAGVQQQPLELRPGEYRVLLCVDIGETRGGGHRPELLRELQRLHVTHTVRKLHVGDFVWVAQETNPRDPANPGELVLDHIVERKRLDDLCSSIIDGRFREQKFRLKRCGLERRVYLVEEHGSVHNLSLPESTLLQAVTNTQVIDGFFVKRTADIKESAAYLALLTRGLQRLYQGHTLRSRPWGTPGNPESGAMTSPNPLCSLLTFSDFNAGAIKNKAQSVREVFARQLMQVRGVSGEKAAALVDRYSTPASLLAAYDACATPKEQETLLSTIKCGRLQRNLGPALSRTLSQLYCSYGPLT
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.803
R work: 0.2401
R free: 0.2804
Average B factor: 70
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 15% ethanol
Matthews coefficient: 3.12
Solvent content (%): 60.63
Ligand: 2-(4-chlorophenyl)-5-oxidanyl-6-oxidanylidene-1H-pyrimidine-4-carboxylic acid (A1IA5)
Ligand formula: C11 H7 Cl N2 O4
Ligand molecular weight: 266.637
Ligand SMILES: c1cc(ccc1C2=NC(=C(C(=O)N2)O)C(=O)O)Cl
Ligand InChI: InChI=1S/C11H7ClN2O4/c12-6-3-1-5(2-4-6)9-13-7(11(17)18)8(15)10(16)14-9/h1-4,15H,(H,17,18)(H,13,14,16)
Release date: 2024-06-19
Crystal structure of SYK in complex with compound 2 (PDB entry 5C27)
Macromolecule: Tyrosine-protein kinase SYK
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 299 residues
Sequence: MDTEVYESPYADPEEIRPKEVYLDRKLLTLEDKELGSGNFGTVKKGYYQMKKVVKTVAVKILKNEANDPALKDELLAEANVMQQLDNPYIVRMIGICEAESWMLVMEMAELGPLNKYLQQNRHVKDKNIIELVHQVSMGMKYLEESNFVHRDLAARNVLLVTQHYAKISDFGLSKALRADENYYKAQTHGKWPVKWYAPECINYYKFSSKSDVWSFGVLMWEAFSYGQKPYRGMKGSEVTAMLEKGERMGCPAGCPREMYDLMNLCWTYDVENRPGFAAVELRLRNYYYDVVNHHHHHH
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.15
R work: 0.1772
R free: 0.2251
Average B factor: 40.54
Crystallization method: EVAPORATION
Crystallization pH: 5.5
Crystallization temperature (K): 298
Crystal growth procedure: 1.75 M ammonium sulfate, 0.1 M sodium citrate, 0.1 M sodium acetate pH 5.5
Matthews coefficient: 2.13
Solvent content (%): 42.13
Ligand: 3-{8-[(3,4-dimethoxyphenyl)amino]imidazo[1,2-a]pyrazin-6-yl}-N-[4-(methylcarbamoyl)phenyl]benzamide (50J)
Ligand formula: C29 H26 N6 O4
Ligand molecular weight: 522.555
Ligand SMILES: CNC(=O)c1ccc(cc1)NC(=O)c2cccc(c2)c3cn4ccnc4c(n3)Nc5ccc(c(c5)OC)OC
Ligand InChI: InChI=1S/C29H26N6O4/c1-30-28(36)18-7-9-21(10-8-18)33-29(37)20-6-4-5-19(15-20)23-17-35-14-13-31-27(35)26(34-23)32-22-11-12-24(38-2)25(16-22)39-3/h4-17H,1-3H3,(H,30,36)(H,32,34)(H,33,37)
Release date: 2015-10-07
Room-temperature Human Hsp90a-NTD bound to adenine (PDB entry 7S95)
Macromolecule: Heat shock protein HSP 90-alpha
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.4.10
Sequence length: 237 residues
Sequence: HMPEETQTQDQPMEEEEVETFAFQAEIAQLMSLIINTFYSNKEIFLRELISNSSDALDKIRYESLTDPSKLDSGKELHINLIPNKQDRTLTIVDTGIGMTKADLINNLGTIAKSGTKAFMEALQAGADISMIGQFGVGFYSAYLVAEKVTVITKHNDDEQYAWESSAGGSFTVRTDTGEPMGRGTKVILHLKEDQTEYLEERRIKEIVKKHSQFIGYPITLFVEKERDKEVSDDEAE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.71
R work: 0.16
R free: 0.191
Average B factor: 46.01
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 1.8 M Malic acid, pH 7
Matthews coefficient: 2.8
Solvent content (%): 56.08
Ligand: ADENINE (ADE)
Ligand formula: C5 H5 N5
Ligand molecular weight: 135.127
Ligand SMILES: c1[nH]c2c(n1)c(ncn2)N
Ligand InChI: InChI=1S/C5H5N5/c6-4-3-5(9-1-7-3)10-2-8-4/h1-2H,(H3,6,7,8,9,10)
Release date: 2022-08-03
Human cytosolic 5' nucleotidase IIIB in complex with 3,4-diF-Bn7GMP (PDB entry 7ZEG)
Macromolecule: 7-methylguanosine phosphate-specific 5'-nucleotidase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.91
Sequence length: 302 residues
Sequence: RSMAEEVSTLMKATVLMRQPGRVQEIVGALRKGGGDRLQVISDFDMTLSRFAYNGKRCPSSYNILDNSKIISEECRKELTALLHHYYPIEIDPHRTVKEKLPHMVEWWTKAHNLLCQQKIQKFQIAQVVRESNAMLREGYKTFFNTLYHNNIPLFIFSAGIGDILEEIIRQMKVFHPNIHIVSNYMDFNEDGFLQGFKGQLIHTYNKNSSACENSGYFQQLEGKTNVILLGDSIGDLTMADGVPGVQNILKIGFLNDKVEERRERYMDSYDIVLEKDETLDVVNGLLQHILCQGVQLEMQGP
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.56
R work: 0.2396
R free: 0.273
Average B factor: 37.89
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 6.2
Crystallization temperature (K): 277.15
Crystal growth procedure: 22% PEG 3350, 0.1M MES pH 6.2
Matthews coefficient: 2.19
Solvent content (%): 43.92
Ligand:  N7-(3,4-difluorobenzyl) guanosine 5'-monophosphate (IOO)
Ligand formula: C17 H19 F2 N5 O8 P
Ligand molecular weight: 490.332
Ligand SMILES: c1cc(c(cc1C[n+]2cn(c3c2C(=O)NC(=N3)N)C4C(C(C(O4)COP(=O)(O)O)O)O)F)F
Ligand InChI: InChI=1S/C17H18F2N5O8P/c18-8-2-1-7(3-9(8)19)4-23-6-24(14-11(23)15(27)22-17(20)21-14)16-13(26)12(25)10(32-16)5-31-33(28,29)30/h1-3,6,10,12-13,16,25-26H,4-5H2,(H4-,20,21,22,27,28,29,30)/p+1/t10-,12-,13-,16-/m1/s1
Release date: 2022-04-13
Crystal structure of EGFR 696-1022 T790M/C797S in complex with D3003 (PDB entry 5ZTO)
Macromolecule: Epidermal growth factor receptor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 331 residues
Sequence: GAMGGEAPNQALLRILKETEFKKIKVLGSGAFGTVYKGLWIPEGEKVKIPVAIKELREATSPKANKEILDEAYVMASVDNPHVCRLLGICLTSTVQLIMQLMPFGSLLDYVREHKDNIGSQYLLNWCVQIAKGMNYLEDRRLVHRDLAARNVLVKTPQHVKITDFGLAKLLGAEEKEYHAEGGKVPIKWMALESILHRIYTHQSDVWSYGVTVWELMTFGSKPYDGIPASEISSILEKGERLPQPPICTIDVYMIMVKCWMIDADSRPKFRELIIEFSKMARDPQRYLVIQGDERMHLPSPTDSNFYRALMDEEDMDDVVDADEYLIPQQG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.649
R work: 0.2314
R free: 0.2724
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8
Crystallization temperature (K): 298
Crystal growth procedure: 0.05M HEPES pH 8.0, 0.2M ZnSO4, 25% PEG 600
Matthews coefficient: 3.64
Solvent content (%): 66.23
Ligand: N-{trans-4-[3-(2-chlorophenyl)-7-{[3-methyl-4-(4-methylpiperazin-1-yl)phenyl]amino}-2-oxo-3,4-dihydropyrimido[4,5-d]pyrimidin-1(2H)-yl]cyclohexyl}propanamide (9JO)
Ligand formula: C33 H41 Cl N8 O2
Ligand molecular weight: 617.184
Ligand SMILES: CCC(=O)NC1CCC(CC1)N2c3c(cnc(n3)Nc4ccc(c(c4)C)N5CCN(CC5)C)CN(C2=O)c6ccccc6Cl
Ligand InChI: InChI=1S/C33H41ClN8O2/c1-4-30(43)36-24-9-12-26(13-10-24)42-31-23(21-41(33(42)44)29-8-6-5-7-27(29)34)20-35-32(38-31)37-25-11-14-28(22(2)19-25)40-17-15-39(3)16-18-40/h5-8,11,14,19-20,24,26H,4,9-10,12-13,15-18,21H2,1-3H3,(H,36,43)(H,35,37,38)/t24-,26-
Release date: 2019-06-12
PanDDA analysis group deposition -- Crystal structure of PTP1B in complex with compound_FMSOA000272b (PDB entry 5QF1)
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): 1.844
R work: 0.1876
R free: 0.2184
Average B factor: 46.6814
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: 3.37
Solvent content (%): 63.45
Ligand: 4-(2-hydroxyethyl)benzonitrile (JMD)
Ligand formula: C9 H9 N O
Ligand molecular weight: 147.174
Ligand SMILES: c1cc(ccc1CCO)C#N
Ligand InChI: InChI=1S/C9H9NO/c10-7-9-3-1-8(2-4-9)5-6-11/h1-4,11H,5-6H2
Release date: 2018-10-10
C2 crystal form of APE1 with Mg2+ (PDB entry 5CFG)
Macromolecule: DNA-(apurinic or apyrimidinic site) lyase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1
Sequence length: 275 residues
Sequence: LYEDPPDQKTSPSGKPATLKICSWNVDGLRAWIKKKGLDWVKEEAPDILCLQETKCSENKLPAELQELPGLSHQYWSAPSDKEGYSGVGLLSRQCPLKVSYGIGDEEHDQEGRVIVAEFDSFVLVTAYVPNAGRGLVRLEYRQRWDEAFRKFLKGLASRKPLVLCGDLNVAHEEIDLRNPKGNKKNAGFTPQERQGFGELLQAVPLADSFRHLYPNTPYAYTFWTYMMNARSKNVGWRLDYFLLSHSLLPALCDSKIRSKALGSDHCPITLYLAL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.1846
R free: 0.2041
Average B factor: 29.63
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 295
Crystal growth procedure: 20% PEG 8000, 0.2 M MgAc and 0.1 M Cacodylate
Matthews coefficient: 2.36
Solvent content (%): 47.9
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: 2016-07-06
FGFR1 kinase domain (residues 458-765) with mutations C488A, C584S in complex with 19. (PDB entry 7OZF)
Macromolecule: Fibroblast growth factor receptor 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 309 residues
Sequence: GAGVSEYELPEDPRWELPRDRLVLGKPLGEGAFGQVVLAEAIGLDKDKPNRVTKVAVKMLKSDATEKDLSDLISEMEMMKMIGKHKNIINLLGACTQDGPLYVIVEYASKGNLREYLQARRPPGLEYSYNPSHNPEEQLSSKDLVSCAYQVARGMEYLASKKCIHRDLAARNVLVTEDNVMKIADFGLARDIHHIDYYKKTTNGRLPVKWMAPEALFDRIYTHQSDVWSFGVLLWEIFTLGGSPYPGVPVEELFKLLKEGHRMDKPSNCTNELYMMMRDCWHAVPSQRPTFKQLVEDLDRIVALTSNQE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.82
R work: 0.204
R free: 0.2425
Average B factor: 46.193
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.7
Crystallization temperature (K): 291
Crystal growth procedure: 0.185M ammonium sulfate, 20% v/v ethylene glycol, 17% w/v PEG 8000, 0.1M PCPT
Matthews coefficient: 2.7
Solvent content (%): 54.4
Ligand: N-[6-(3-ethoxyphenyl)-1H-indazol-3-yl]benzamide (466)
Ligand formula: C22 H19 N3 O2
Ligand molecular weight: 357.405
Ligand SMILES: CCOc1cccc(c1)c2ccc3c(c2)[nH]nc3NC(=O)c4ccccc4
Ligand InChI: InChI=1S/C22H19N3O2/c1-2-27-18-10-6-9-16(13-18)17-11-12-19-20(14-17)24-25-21(19)23-22(26)15-7-4-3-5-8-15/h3-14H,2H2,1H3,(H2,23,24,25,26)
Release date: 2021-12-01