satarupa22/MacromolecularLigandDB huggingface dataset:
HUMAN PI3KDELTA IN COMPLEX WITH COMPOUND 6 (PDB entry 6OCO)
Macromolecule: Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit delta isoform
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.1.153
Sequence length: 1015 residues
Sequence: NQSVVVDFLLPTGVYLNFPVSRNANLSTIKQLLWHRAQYEPLFHMLSGPEAYVFTCINQTAEQQELEDEQRRLCDVQPFLPVLRLVAREGDRVKKLINSQISLLIGKGLHEFDSLCDPEVNDFRAKMCQFCEEAAARRQQLGWEAWLQYSFPLQLEPSAQTWGPGTLRLPNRALLVNVKFEGSEESFTFQVSTKDVPLALMACALRKKATVFRQPLVEQPEDYTLQVNGRHEYLYGSYPLCQFQYICSCLHSGLTPHLTMVHSSSILAMRDEQSNPAPQVQKPRAKPPPIPAKKPSSVSLWSLEQPFRIELIQGSKVNADERMKLVVQAGLFHGNEMLCKTVSSSEVSVCSEPVWKQRLEFDINICDLPRMARLCFALYAVIEKAKKARSTKKKSKKADCPIAWANLMLFDYKDQLKTGERCLYMWPSVPDEKGELLNPTGTVRSNPNTDSAAALLICLPEVAPHPVYYPALEKILELGRHSECVHVTEEEQLQLREILERRGSGELYEHEKDLVWKLRHEVQEHFPEALARLLLVTKWNKHEDVAQMLYLLCSWPELPVLSALELLDFSFPDCHVGSFAIKSLRKLTDDELFQYLLQLVQVLKYESYLDCELTKFLLDRALANRKIGHFLFWHLRSEMHVPSVALRFGLILEAYCRGSTHHMKVLMKQGEALSKLKALNDFVKLSSQKTPKPQTKELMHLCMRQEAYLEALSHLQSPLDPSTLLAEVCVEQCTFMDSKMKPLWIMYSNEEAGSGGSVGIIFKNGDDLRQDMLTLQMIQLMDVLWKQEGLDLRMTPYGCLPTGDRTGLIEVVLRSDTIANIQLNKSNMAATAAFNKDALLNWLKSKNPGEALDRAIEEFTLSCAGYCVATYVLGIGDRHSDNIMIRESGQLFHIDFGHFLGNFKTKFGINRERVPFILTYDFVHVIQQGKTNNSEKFERFRGYCERAYTILRRHGLLFLHLFALMRAAGLPELSCSKDIQYLKDSLALGKTEEEALKHFRVKFNEALRESWKTKV
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.58
R work: 0.2589
R free: 0.296
Average B factor: 61.731
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 293
Crystal growth procedure: 16.60 % PEG6000
0.10 M KCl
0.10 M MES pH=6.00
Matthews coefficient: 2.65
Solvent content (%): 53.59
Ligand: 4-[(1S,4S)-5-(3-chlorophenyl)-2,5-diazabicyclo[2.2.1]heptan-2-yl]-2-(pyridin-3-yl)pyrimidine-5-carbonitrile (M5V)
Ligand formula: C21 H17 Cl N6
Ligand molecular weight: 388.853
Ligand SMILES: c1cc(cc(c1)Cl)N2CC3CC2CN3c4c(cnc(n4)c5cccnc5)C#N
Ligand InChI: InChI=1S/C21H17ClN6/c22-16-4-1-5-17(7-16)27-12-19-8-18(27)13-28(19)21-15(9-23)11-25-20(26-21)14-3-2-6-24-10-14/h1-7,10-11,18-19H,8,12-13H2/t18-,19-/m0/s1
Release date: 2019-12-11
Crystal structure of human TAK1/TAB1 fusion protein in complex with ligand 3 (PDB entry 5GJF)
Macromolecule: TAK1 kinase - TAB1 chimera fusion protein
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.25
Sequence length: 315 residues
Sequence: GPLHMIDYKEIEVEEVVGRGAFGVVCKAKWRAKDVAIKQIESESERKAFIVELRQLSRVNHPNIVKLYGACLNPVCLVMEYAEGGSLYNVLHGAEPLPYYTAAHAMSWCLQCSQGVAYLHSMQPKALIHRDLKPPNLLLVAGGTVLKICDFGTACDIQTHMTNNKGSAAWMAPEVFEGSNYSEKCDVFSWGIILWEVITRRKPFDEIGGPAFRIMWAVHNGTRPPLIKNLPKPIESLMTRCWSKDPSQRPSMEEIVKIMTHLMRYFPGADEPLQYPCQHSLPPGEDGRVEPYVDFAEFYRLWSVDHGEQSVVTAP
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.89
R work: 0.1977
R free: 0.2336
Average B factor: 64.998
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 294
Crystal growth procedure: 1.94M sodium potassium phosphate, 20%(v/v) Glycerol as cryoprotectant
Matthews coefficient: 3.84
Solvent content (%): 67.99
Ligand: N-(2-isopropoxy-4-(4-methylpiperazine-1-carbonyl)phenyl)-2-(3-(3-phenylureido)phenyl)thiazole-4-carboxamide (6V4)
Ligand formula: C32 H34 N6 O4 S
Ligand molecular weight: 598.715
Ligand SMILES: CC(C)Oc1cc(ccc1NC(=O)c2csc(n2)c3cccc(c3)NC(=O)Nc4ccccc4)C(=O)N5CCN(CC5)C
Ligand InChI: InChI=1S/C32H34N6O4S/c1-21(2)42-28-19-23(31(40)38-16-14-37(3)15-17-38)12-13-26(28)35-29(39)27-20-43-30(36-27)22-8-7-11-25(18-22)34-32(41)33-24-9-5-4-6-10-24/h4-13,18-21H,14-17H2,1-3H3,(H,35,39)(H2,33,34,41)
Release date: 2016-11-16
DNA Polymerase Mu (K438D), 8-oxodGTP:Ct Reaction State Ternary Complex, 50 mM Mn2+ (30min) (PDB entry 7KTM)
Macromolecule: DNA-directed DNA/RNA polymerase mu
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 356 residues
Sequence: GSAAAPLSPAWMPAYACQRPTPLTHHNTGLSEALEILAEAAGFEGSEGRLLTFCRAASVLKALPSPVTTLSQLQGLPHFGEHSSRVVQELLEHGVCEEVERVRRSERYQTMKLFTQIFGVGVKTADRWYREGLRTLDDLREQPQKLTQQQKAGLQHHQDLSTPVLRSDVDALQQVVEEAVGQALPGATVTLTGGFRRGKLQGHDVDFLITHPKEGQEAGLLPRVMCRLQDQGLILYHQHQHSCCESPTRLAQQSHMDAFERSFCIFRLPQPGSWKAVRVDLVVAPVSQFPFALLGWTGSDLFQRELRRFSRKEKGLWLNSHGLFDPEQKTFFQAASEEDIFRHLGLEYLPPEQRNA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.528
R work: 0.1604
R free: 0.1805
Average B factor: 27.3935
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 85-90mM HEPES pH 7.5, 17-18% PEG4000
Matthews coefficient: 2.45
Solvent content (%): 49.74
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: 2022-05-11
Human ADP-ribosylserine hydrolase ARH3 mutant E41A in complex with ADP-ribose dimer (PDB entry 7AKR)
Macromolecule: ADP-ribose glycohydrolase ARH3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.5.1
Sequence length: 349 residues
Sequence: GPGSSLSRFRGCLAGALLGDCVGSFYAAHDTVDLTSVLRHVQSLEPDPGTPGSERTEALYYTDDTAMARALVQSLLAKEAFDEVDMAHRFAQEYKKDPDRGYGAGVVTVFKKLLNPKCRDVFEPARAQFNGKGSYGNGGAMRVAGISLAYSSVQDVQKFARLSAQLTHASSLGYNGAILQALAVHLALQGESSSEHFLKQLLGHMEDLEGDAQSVLDARELGMEERPYSSRLKKIGELLDQASVTREEVVSELGNGIAAFESVPTAIYCFLRCMEPDPEIPSAFNSLQRTLIYSISLGGDTDTIATMAGAIAGAYYGMDQVPESWQQSCEGYEETDILAQSLHRVFQKS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.95
R work: 0.187
R free: 0.2106
Average B factor: 42.84
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293.15
Crystal growth procedure: 100 mM TrisHCl (pH 8.5), 20% (w/v) PEG4000 and 200 mM MgCl2
Matthews coefficient: 2.3
Solvent content (%): 46.61
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: 2021-06-16
GABARAP-L1 ATG4B LIR Complex (PDB entry 5LXI)
Macromolecule: Gamma-aminobutyric acid receptor-associated protein-like 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 123 residues
Sequence: GPTMGSMKFQYKEDHPFEYRKKEGEKIRKKYPDRVPVIVEKAPKARVPDLDKRKYLVPSDLTVGQFYFLIRKRIHLRPEDALFFFVNNTIPPTSATMGQLYEDNHEEDYFLYVAYSDESVYGK
Oligomeric state: Hetero 4-mer
Stoichiometry: A2, B2
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.44
R work: 0.1969
R free: 0.2299
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M MgCl2, 24.6 % PEG 400, 29.5 % PEG 8000, 0.1M TRIS 8.5
Matthews coefficient: 2.15
Solvent content (%): 42.78
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: 2017-02-08
DYRK1A in complex with JWC-055 (PDB entry 6EIS)
Macromolecule: Dual specificity tyrosine-phosphorylation-regulated kinase 1A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.12.1
Sequence length: 368 residues
Sequence: GASDSSHKKERKVYNDGYDDDNYDYIVKNGEKWMDRYEIDSLIGKGSFGQVVKAYDRVEQEWVAIKIIKNKKAFLNQAQIEVRLLELMNKHDTEMKYYIVHLKRHFMFRNHLCLVFEMLSYNLYDLLRNTNFRGVSLNLTRKFAQQMCTALLFLATPELSIIHCDLKPENILLCNPKRSAIKIVDFGSSCQLGQRIYQYIQSRFYRSPEVLLGMPYDLAIDMWSLGCILVEMHTGEPLFSGANEVDQMNKIVEVLGIPPAHILDQAPKARKFFEKLPDGTWNLKKTKDGKREYKPPGTRKLHNILGVETGGPGGRRAGESGHTVADYLKFKDLILRMLDYDPKTRIQPYYALQHSFFKKTADEGTNTS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.36
R work: 0.221
R free: 0.2615
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M KSCN, 0.1M KCl, 16% PEG 3350
Matthews coefficient: 2.66
Solvent content (%): 53.76
Ligand: 1-[4-fluoranyl-2-(trifluoromethyl)phenyl]-9-(1~{H}-pyrazol-4-yl)benzo[h][1,6]naphthyridin-2-one (B6N)
Ligand formula: C22 H12 F4 N4 O
Ligand molecular weight: 424.35
Ligand SMILES: c1cc2c(cc1c3c[nH]nc3)c4c(cn2)C=CC(=O)N4c5ccc(cc5C(F)(F)F)F
Ligand InChI: InChI=1S/C22H12F4N4O/c23-15-3-5-19(17(8-15)22(24,25)26)30-20(31)6-2-13-9-27-18-4-1-12(7-16(18)21(13)30)14-10-28-29-11-14/h1-11H,(H,28,29)
Release date: 2018-08-29
HsNMT1 in complex with both MyrCoA and Acetylated-GNCFSKPR substrates (PDB entry 6SJZ)
Macromolecule: Glycylpeptide N-tetradecanoyltransferase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1.97
Sequence length: 402 residues
Sequence: GGSEFSVGQGPAKTMEEASKRSYQFWDTQPVPKLGEVVNTHGPVEPDKDNIRQEPYTLPQGFTWDALDLGDRGVLKELYTLLNENYVEDDDNMFRFDYSPEFLLWALRPPGWLPQWHCGVRVVSSRKLVGFISAIPANIHIYDTEKKMVEINFLCVHKKLRSKRVAPVLIREITRRVHLEGIFQAVYTAGVVLPKPVGTCRYWHRSLNPRKLIEVKFSHLSRNMTMQRTMKLYRLPETPKTAGLRPMETKDIPVVHQLLTRYLKQFHLTPVMSQEEVEHWFYPQENIIDTFVVENANGEVTDFLSFYTLPSTIMNHPTHKSLKAAYSFYNVHTQTPLLDLMSDALVLAKMKGFDVFNALDLMENKTFLEKLKFGIGDGNLQYYLYNWKCPSMGAEKVGLVLQ
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.995
R work: 0.1716
R free: 0.2016
Average B factor: 27.1155
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 293
Crystal growth procedure: 22% PEG6K, 100mM Sodium Citrate pH 5.5, 100mM MgCl2, 100mM NaCl.
Matthews coefficient: 2.2
Solvent content (%): 44.16
Ligand: TETRADECANOYL-COA (MYA)
Ligand formula: C35 H62 N7 O17 P3 S
Ligand molecular weight: 977.89
Ligand SMILES: CCCCCCCCCCCCCC(=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/C35H62N7O17P3S/c1-4-5-6-7-8-9-10-11-12-13-14-15-26(44)63-19-18-37-25(43)16-17-38-33(47)30(46)35(2,3)21-56-62(53,54)59-61(51,52)55-20-24-29(58-60(48,49)50)28(45)34(57-24)42-23-41-27-31(36)39-22-40-32(27)42/h22-24,28-30,34,45-46H,4-21H2,1-3H3,(H,37,43)(H,38,47)(H,51,52)(H,53,54)(H2,36,39,40)(H2,48,49,50)/t24-,28-,29-,30+,34-/m1/s1
Release date: 2020-03-18
PRMT5:MEP50 Complexed with Allosteric Inhibitor Compound 8 (PDB entry 6UXY)
Macromolecule: Protein arginine N-methyltransferase 5
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1.320
Sequence length: 645 residues
Sequence: MDYKDDDDKAAMAVGGAGGSRVSSGRDLNCVPEIADTLGAVAKQGFDFLCMPVFHPRFKREFIQEPAKNRPGPQTRSDLLLSGRDWNTLIVGKLSPWIRPDSKVEKIRRNSEAAMLQELNFGAYLGLPAFLLPLNQEDNTNLARVLTNHIHTGHHSSMFWMRVPLVAPEDLRDDIIENAPTTHTEEYSGEEKTWMWWHNFRTLCDYSKRIAVALEIGADLPSNHVIDRWLGEPIKAAILPTSIFLTNKKGFPVLSKMHQRLIFRLLKLEVQFIITGTNHHSEKEFCSYLQYLEYLSQNRPPPNAYELFAKGYEDYLQSPLQPLMDNLESQTYEVFEKDPIKYSQYQQAIYKCLLDRVPEEEKDTNVQVLMVLGAGRGPLVNASLRAAKQADRRIKLYAVEKNPNAVVTLENWQFEEWGSQVTVVSSDMREWVAPEKADIIVSELLGSFADNELSPECLDGAQHFLKDDGVSIPGEYTSFLAPISSSKLYNEVRACREKDRDPEAQFEMPYVVRLHNFHQLSAPQPCFTFSHPNRDPMIDNNRYCTLEFPVEVNTVLHGFAGYFETVLYQDITLSIRPETHSPGMFSWFPILFPIKQPITVREGQTICVRFWRCSNSKKVWYEWAVTAPVCSAIHNPTGRSYTIGL
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.57
R work: 0.246
R free: 0.275
Average B factor: 82.81
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6
Crystallization temperature (K): 277
Crystal growth procedure: 0.1 M sodium citrate pH 6.0, 0.2 M sodium acetate, 10-12% PEG 4000
Matthews coefficient: 2.88
Solvent content (%): 57.29
Ligand: (5R)-2-amino-5-(2-cyclohexylethyl)-3-methyl-5-phenyl-3,5-dihydro-4H-imidazol-4-one (QKY)
Ligand formula: C18 H25 N3 O
Ligand molecular weight: 299.411
Ligand SMILES: CN1C(=O)C(N=C1N)(CCC2CCCCC2)c3ccccc3
Ligand InChI: InChI=1S/C18H25N3O/c1-21-16(22)18(20-17(21)19,15-10-6-3-7-11-15)13-12-14-8-4-2-5-9-14/h3,6-7,10-11,14H,2,4-5,8-9,12-13H2,1H3,(H2,19,20)/t18-/m1/s1
Release date: 2020-08-19
Binary DNA Polymerase Beta bound to DNA containing primer terminal dC base-paired with FapydG (PDB entry 8VF8)
Macromolecule: DNA polymerase beta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 335 residues
Sequence: MSKRKAPQETLNGGITDMLTELANFEKNVSQAIHKYNAYRKAASVIAKYPHKIKSGAEAKKLPGVGTKIAEKIDEFLATGKLRKLEKIRQDDTSSSINFLTRVSGIGPSAARKFVDEGIKTLEDLRKNEDKLNHHQRIGLKYFGDFEKRIPREEMLQMQDIVLNEVKKVDSEYIATVCGSFRRGAESSGDMDVLLTHPSFTSESTKQPKLLHQVVEQLQKVHFITDTLSKGETKFMGVCQLPSKNDEKEYPHRRIDIRLIPKDQYYCGVLYFTGSDIFNKNMRAHALEKGFTINEYTIRPLGVTGVAGEPLPVDSEKDIFDYIQWKYREPKDRSE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.98
R work: 0.1919
R free: 0.2216
Average B factor: 30.61
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 14-22% PEG 3350
0.05 M Imidazole pH 8.0
0.35 M Sodium Acetate
Matthews coefficient: 2.39
Solvent content (%): 48.58
Ligand: SODIUM ION ()
Ligand formula: Na
Ligand molecular weight: 22.99
Ligand SMILES: [Na+]
Ligand InChI: InChI=1S/Na/q+1
Release date: 2024-05-08
Crystal structure of oncogenic KRAS Q61E GMPPCP-bound (PDB entry 7LZ5)
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: MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGEEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKSDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQGVDDAFYTLVREIRKHKEK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.5
R work: 0.1639
R free: 0.1791
Average B factor: 17.24
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: PEG 3350, 0.2 M ammonium sulfate, 0.1 M HEPES
Matthews coefficient: 2.66
Solvent content (%): 53.72
Ligand: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER (GCP)
Ligand formula: C11 H18 N5 O13 P3
Ligand molecular weight: 521.208
Ligand SMILES: c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(CP(=O)(O)O)O)O)O)N=C(NC2=O)N
Ligand InChI: InChI=1S/C11H18N5O13P3/c12-11-14-8-5(9(19)15-11)13-2-16(8)10-7(18)6(17)4(28-10)1-27-32(25,26)29-31(23,24)3-30(20,21)22/h2,4,6-7,10,17-18H,1,3H2,(H,23,24)(H,25,26)(H2,20,21,22)(H3,12,14,15,19)/t4-,6-,7-,10-/m1/s1
Release date: 2022-03-16
Carbonic anhydrase IX-mimic in complex with 4-(phenyl)-benzenesulfonamide (PDB entry 5SZ4)
Macromolecule: Carbonic anhydrase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 257 residues
Sequence: HWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHSFQVTFDDSQDKAVLKGGPLDGTYRLLQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDVGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTEGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLAECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.6
R work: 0.1831
R free: 0.217
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 296
Crystal growth procedure: 1.6M Sodium Citrate, 50mM Tris pH 7.8
Matthews coefficient: 2.12
Solvent content (%): 41.84
Ligand: DIMETHYL SULFOXIDE (DMS)
Ligand formula: C2 H6 O S
Ligand molecular weight: 78.133
Ligand SMILES: CS(=O)C
Ligand InChI: InChI=1S/C2H6OS/c1-4(2)3/h1-2H3
Release date: 2016-12-21
Crystal structure of human Sirt3 in complex with an acetylated HIV1 Tat-46-54 substrate peptide (PDB entry 8CCW)
Macromolecule: NAD-dependent protein deacetylase sirtuin-3, mitochondrial
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1.286
Sequence length: 282 residues
Sequence: SDKGKLSLQDVAELIRARACQRVVVMVGAGISTPSGIPDFRSPGSGLYSNLQQYDLPYPEAIFELPFFFHNPKPFFTLAKELYPGNYKPNVTHYFLRLLHDKGLLLRLYTQNIDGLERVSGIPASKLVEAHGTFASATCTVCQRPFPGEDIRADVMADRVPRCPVCTGVVKPDIVFFGEPLPQRFLLHVVDFPMADLLLILGTSLEVEPFASLTEAVRSSVPRLLINRDLVGPLAWHPRSRDVAQLGDVVHGVESLVELLGWTEEMRDLVQRETGKLDGPDK
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.65
R work: 0.1807
R free: 0.2089
Average B factor: 36.94
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293.15
Crystal growth procedure: 10 mg/ml human Sirt3-(118-399) in 20 mM Tris/HCl, pH 8.0, 150 mM NaCl, 5% (v/v) glycerol, 1 mM TCEP were incubated with 2 mM ac-Tat-46-54 for 60 min at 293.15 K. The complex was crystallized using the sitting-drop vapor-diffusion method at 293.15 K with 100 mM MES, pH 6.0, 30% (w/v) PEG 200, 5% (w/v) PEG 3000 as reservoir solution.
Matthews coefficient: 2.99
Solvent content (%): 58.93
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: 2023-05-10
Co-crystal structure of PERK with compound 24 (PDB entry 8EQD)
Macromolecule: Eukaryotic translation initiation factor 2-alpha kinase 3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 317 residues
Sequence: GSSSWNDIKNSGYISRYLTDFEPIQCLGRGGFGVVFEAKNKVDDCNYAIKRIRLPNRELAREKVMREVKALAKLEHPGIVRYFNAWLEAPPEKWQEKLQPSSPKVYLYIQMQLCRKENLKDWMNGRCTIEERERSVCLHIFLQIAEAVEFLHSKGLMHRNLKPSNIFFTMDDVVKVGDFGLVTAMDQDEEEQTVLTPMPAYARHTGQVGTKLYMSPEQIHGNSYSHKVDIFSLGLILFELLYPFSTQMERVRTLTDVRNLKFPPLFTQKYPCEYVMVQDMLSPSPMERPEAINIIENAVFEDLDFPGKTVLRQRSRS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.92
R work: 0.246
R free: 0.2796
Average B factor: 93.984
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 100 mM HEPES pH 7.0, 180 mM Na/K tartrate, 9% PEG3350
Matthews coefficient: 3.43
Solvent content (%): 64.15
Ligand: (2R)-N-[(4M)-4-(4-amino-2,7-dimethyl-7H-pyrrolo[2,3-d]pyrimidin-5-yl)-3-methylphenyl]-2-(3-fluorophenyl)-2-hydroxyacetamide (WPX)
Ligand formula: C23 H22 F N5 O2
Ligand molecular weight: 419.451
Ligand SMILES: Cc1cc(ccc1c2cn(c3c2c(nc(n3)C)N)C)NC(=O)C(c4cccc(c4)F)O
Ligand InChI: InChI=1S/C23H22FN5O2/c1-12-9-16(28-23(31)20(30)14-5-4-6-15(24)10-14)7-8-17(12)18-11-29(3)22-19(18)21(25)26-13(2)27-22/h4-11,20,30H,1-3H3,(H,28,31)(H2,25,26,27)/t20-/m1/s1
Release date: 2022-11-30
AGF271 and GAR in complex with human recombinant GARFTase, ligase, purine biosynthesis, transfers formyl group from 10-formyl tetrahydrofolate to glycinamide ribonucleotide (GAR) to form tetrahydrofolate and formyl GAR (PDB entry 8FDX)
Macromolecule: Trifunctional purine biosynthetic protein adenosine-3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 6.3.4.13
Sequence length: 210 residues
Sequence: MARVAVLISGTGSNLQALIDSTREPNSSAQIDIVISNKAAVAGLDKAERAGIPTRVINHKLYKNRVEFDSAIDLVLEEFSIDIVCLAGFMRILSGPFVQKWNGKMLNIHPSLLPSFKGSNAHEQALETGVTVTGCTVHFVAEDVDAGQIILQEAVPVKRGDTVATLSERVKLAEHKIFPAALQLVASGTVQLGENGKICWVKEEHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.07
R work: 0.2016
R free: 0.2404
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.1 M Tris-HCl, pH 7.5, 0.33 M sodium chloride, 16-21% PEG4000, 2% PEG400
Matthews coefficient: 3.47
Solvent content (%): 64.54
Ligand: GLYCINAMIDE RIBONUCLEOTIDE (GAR)
Ligand formula: C7 H13 N2 O8 P
Ligand molecular weight: 284.16
Ligand SMILES: C(C1C(C(C(O1)NC(=O)CN)O)O)OP(=O)([O-])[O-]
Ligand InChI: InChI=1S/C7H15N2O8P/c8-1-4(10)9-7-6(12)5(11)3(17-7)2-16-18(13,14)15/h3,5-7,11-12H,1-2,8H2,(H,9,10)(H2,13,14,15)/p-2/t3-,5-,6-,7-/m1/s1
Release date: 2023-05-10
PanDDA analysis group deposition -- Crystal Structure of human NUDT22 in complex with N13589a (PDB entry 5R5L)
Macromolecule: Uridine diphosphate glucose pyrophosphatase NUDT22
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.1.45
Sequence length: 304 residues
Sequence: SMDPEVTLLLQCPGGGLPQEQIQAELSPAHDRRPLPGGDEAITAIWETRLKAQPWLFDAPKFRLHSATLAPIGSRGPQLLLRLGLTSYRDFLGTNWSSSAAWLRQQGATDWGDTQAYLADPLGVGAALATADDFLVFLRRSRQVAEAPGLVDVPGGHPEPQALCPGGSPQHQDLAGQLVVHELFSSVLQEICDEVNLPLLTLSQPLLLGIARNETSAGRASAEFYVQCSLTSEQVRKHYLSGGPEAHESTGIFFVETQNVRRLPETEMWAELCPSAKGAIILYNRVQGSPTGAALGSPALLPPL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.63
R work: 0.1849
R free: 0.219
Average B factor: 29.275
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.1M HEPES pH 7.5, 0.3M sodium/potassium phosphate, 15% PEG Smear High, 20% ethylene glycol
Matthews coefficient: 2.02
Solvent content (%): 39.09
Ligand: 4-(methylsulfonylamino)benzamide (S2S)
Ligand formula: C8 H10 N2 O3 S
Ligand molecular weight: 214.242
Ligand SMILES: CS(=O)(=O)Nc1ccc(cc1)C(=O)N
Ligand InChI: InChI=1S/C8H10N2O3S/c1-14(12,13)10-7-4-2-6(3-5-7)8(9)11/h2-5,10H,1H3,(H2,9,11)
Release date: 2020-07-01
Human glucokinase in complex with novel indazole activator. (PDB entry 5V4W)
Macromolecule: Glucokinase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.1.2
Sequence length: 458 residues
Sequence: MLPQPNSQVEQILAEFQLQEEDLKKVMRRMQKEMDRGLRLETHEEASVKMLPTYVRSTPEGSEVGDFLSLDLGGTNFRVMLVKVGEGEEGQWSVKTKHQMYSIPEDAMTGTAEMLFDYISECISDFLDKHQMKHKKLPLGFTFSFPVRHEDIDKGILLNWTKGFKASGAEGNNVVGLLRDAIKRRGDFEMDVVAMVNDTVATMISCYYEDHQCEVGMIVGTGCNACYMEEMQNVELVEGDEGRMCVNTEWGAFGDSGELDEFLLEYDRLVDESSANPGQQLYEKLIGGKYMGELVRLVLLRLVDENLLFHGEASEQLRTRGAFETRFVSQVESDTGDRKQIYNILSTLGLRPSTTDCDIVRRACESVSTRAAHMCSAGLAGVINRMRESRSEDVMRITVGVDGSVYKLHPSFKERFHASVRRLTPSCEITFIESEEGSGRGAALVSAVACKKACMLGQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.39
R work: 0.198
R free: 0.261
Average B factor: 30.88
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 277
Crystal growth procedure: 15% PEG3350, 200 mM ammonium iodide, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Matthews coefficient: 2.3
Solvent content (%): 46.42
Ligand: alpha-D-glucopyranose (GLC)
Ligand formula: C6 H12 O6
Ligand molecular weight: 180.156
Ligand SMILES: C(C1C(C(C(C(O1)O)O)O)O)O
Ligand InChI: InChI=1S/C6H12O6/c7-1-2-3(8)4(9)5(10)6(11)12-2/h2-11H,1H2/t2-,3-,4+,5-,6+/m1/s1
Release date: 2017-05-31
Human carboanhydrase F131C_C206S double mutant in complex with 2 (PDB entry 5T72)
Macromolecule: Carbonic anhydrase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 260 residues
Sequence: MSHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHAFNVEFDDSQDKAVLKGGPLDGTYRLIQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDCGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTKGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLLESVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.3
R work: 0.14779
R free: 0.16634
Average B factor: 14.517
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 293
Crystal growth procedure: 3 M (NH4)2SO4, 50 mM Tris-HCl
Matthews coefficient: 2.09
Solvent content (%): 41.16
Ligand: 4-(HYDROXYMERCURY)BENZOIC ACID (HGB)
Ligand formula: C7 H6 Hg O3
Ligand molecular weight: 338.711
Ligand SMILES: c1cc(ccc1C(=O)O)[Hg]O
Ligand InChI: InChI=1S/C7H5O2.Hg.H2O/c8-7(9)6-4-2-1-3-5-6;;/h2-5H,(H,8,9);;1H2/q;+1;/p-1
Release date: 2017-09-06