satarupa22/MacromolecularLigandDB huggingface dataset:
PanDDA analysis group deposition -- Crystal structure of PTP1B in complex with compound_FMOPL000123a (PDB entry 5QEX)
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): 1.673
R work: 0.1794
R free: 0.2051
Average B factor: 38.4105
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: 3.33
Solvent content (%): 63.03
Ligand: [4-(cyclopropanecarbonyl)piperazin-1-yl](furan-2-yl)methanone (JMM)
Ligand formula: C13 H16 N2 O3
Ligand molecular weight: 248.278
Ligand SMILES: c1cc(oc1)C(=O)N2CCN(CC2)C(=O)C3CC3
Ligand InChI: InChI=1S/C13H16N2O3/c16-12(10-3-4-10)14-5-7-15(8-6-14)13(17)11-2-1-9-18-11/h1-2,9-10H,3-8H2
Release date: 2018-10-10
Human PFKFB3 in complex with a N-Aryl 6-Aminoquinoxaline inhibitor 1 (PDB entry 6HVH)
Macromolecule: 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.1.105
Sequence length: 520 residues
Sequence: MPLELTQSRVQKIWVPVDHRPSLPRSCGPKLTNSPTVIVMVGLPARGKTYISKKLTRYLNWIGVPTKVFNVGEYRREAVKQYSSYNFFRPDNEEAMKVRKQCALAALRDVKSYLAKEGGQIAVFDATNTTRERRHMILHFAKENDFKAFFIESVCDDPTVVASNIMEVKISSPDYKDCNSAEAMDDFMKRISCYEASYQPLDPDKCDRDLSLIKVIDVGRRFLVNRVQDHIQSRIVYYLMNIHVQPRTIYLCRHGENEHNLQGRIGGDSGLSSRGKKFASALSKFVEEQNLKDLRVWTSQLKSTIQTAEALRLPYEQWKALNEIDAGVCEELTYEEIRDTYPEEYALREQDKYYYRYPTGESYQDLVQRLEPVIMELERQENVLVICHQAVLRCLLAYFLDKSAEEMPYLKCPLHTVLKLTPVAYGCRVESIYLNVESVCTHRERSEDAKKGPNPLMRRNSVTPLASPEPTKKPRINSFEEHVASTSAALPSCLPPEVPTQLPGQNMKGSRSSADSSRKH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.36
R work: 0.1953
R free: 0.2375
Average B factor: 39.819
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 277
Crystal growth procedure: 2% Tacsimate, 10% PEG3350, 0.1M MES/imidazole pH 7.0
Matthews coefficient: 3.9
Solvent content (%): 68.47
Ligand: 3-[[8-(1-methylindol-6-yl)quinoxalin-6-yl]amino]-~{N}-(oxan-4-yl)pyridine-4-carboxamide (GV2)
Ligand formula: C28 H26 N6 O2
Ligand molecular weight: 478.545
Ligand SMILES: Cn1ccc2c1cc(cc2)c3cc(cc4c3nccn4)Nc5cnccc5C(=O)NC6CCOCC6
Ligand InChI: InChI=1S/C28H26N6O2/c1-34-11-5-18-2-3-19(14-26(18)34)23-15-21(16-24-27(23)31-10-9-30-24)32-25-17-29-8-4-22(25)28(35)33-20-6-12-36-13-7-20/h2-5,8-11,14-17,20,32H,6-7,12-13H2,1H3,(H,33,35)
Release date: 2018-11-14
Crystal structure of human Fgr tyrosine kinase in complex with TL02-59 (PDB entry 7UY3)
Macromolecule: Tyrosine-protein kinase Fgr
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 456 residues
Sequence: MGHHHHHHTLFIALYDYEARTEDDLTFTKGEKFHILNNTEGDWWEARSLSSGKTGCIPSNYVAPVDSIQAEEWYFGKIGRKDAERQLLSPGNPQGAFLIRESETTKGAYSLSIRDWDQTRGDHVKHYKIRKLDMGGYYITTRVQFNSVQELVQHYMEVNDGLCNLLIAPCTIMKPQTLGLAKDAWEISRSSITLERRLGTGCFGDVWLGTWNGSTKVAVKTLKPGTMSPKAFLEEAQVMKLLRHDKLVQLYAVVSEEPIYIVTEFMCHGSLLDFLKNPEGQDLRLPQLVDMAAQVAEGMAYMERMNYIHRDLRAANILVGERLACKIADFGLARLIKDDEYNPCQGSKFPIKWTAPEAALFGRFTIKSDVWSFGILLTELITKGRIPYPGMNKREVLEQVEQGYHMPCPPGCPASLYEAMEQTWRLDPEERPTFEYLQSFLEDYFTSAEPQYEEIP
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.99
R work: 0.2031
R free: 0.2473
Average B factor: 104.6638
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: For co-crystallization with TL02-59, Fgr (3.2 mg/mL in 20 mM Tris-HCl, pH 8.3, 100 mM NaCl, and 2 mM TCEP) was mixed with 10 mM TL02-59 (in 100% DMSO) to a final concentration of 120 microM (0.6% DMSO final) and incubated for thirty minutes at 298 K.  Diffraction quality crystals were grown by sitting- and hanging-drop vapor diffusion at 277 K by mixing Fgr/TL02-59 in a 1:1 ratio with the mother liquor (0.1 M HEPES, pH 7.5, 0.8 M sodium phosphate, 0.8 M potassium phosphate and 1% 1,2-butanediol)
Matthews coefficient: 4.2
Solvent content (%): 70.7
Ligand: 3-[(6,7-dimethoxyquinazolin-4-yl)oxy]-N-{4-[(4-ethylpiperazin-1-yl)methyl]-3-(trifluoromethyl)phenyl}-4-methylbenzamide (OJL)
Ligand formula: C32 H34 F3 N5 O4
Ligand molecular weight: 609.639
Ligand SMILES: CCN1CCN(CC1)Cc2ccc(cc2C(F)(F)F)NC(=O)c3ccc(c(c3)Oc4c5cc(c(cc5ncn4)OC)OC)C
Ligand InChI: InChI=1S/C32H34F3N5O4/c1-5-39-10-12-40(13-11-39)18-22-8-9-23(15-25(22)32(33,34)35)38-30(41)21-7-6-20(2)27(14-21)44-31-24-16-28(42-3)29(43-4)17-26(24)36-19-37-31/h6-9,14-17,19H,5,10-13,18H2,1-4H3,(H,38,41)
Release date: 2022-12-28
Crystal Structure of human cyclic GMP-AMP synthase in complex with cGAMP (PDB entry 7FTH)
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): 2.55
R work: 0.1908
R free: 0.2559
Average B factor: 88.903
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: 2.12
Solvent content (%): 42.04
Ligand: cGAMP (1SY)
Ligand formula: C20 H24 N10 O13 P2
Ligand molecular weight: 674.411
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C4C(O3)COP(=O)(OC5C(C(COP(=O)(O4)O)OC5n6cnc7c6NC(=NC7=O)N)O)O)O)N
Ligand InChI: InChI=1S/C20H24N10O13P2/c21-14-8-15(24-3-23-14)29(4-25-8)18-11(32)12-7(41-18)2-39-45(36,37)43-13-10(31)6(1-38-44(34,35)42-12)40-19(13)30-5-26-9-16(30)27-20(22)28-17(9)33/h3-7,10-13,18-19,31-32H,1-2H2,(H,34,35)(H,36,37)(H2,21,23,24)(H3,22,27,28,33)/t6-,7-,10-,11-,12-,13-,18-,19-/m1/s1
Release date: 2024-02-21
chimera of ExoY Nucleotidyl Cyclase domain from Vibrio nigripulchritudo fused to a proline-Rich-Domain (PRD) and profilin, bound to ADP-Mg-actin and a sulfate ion (PDB entry 8BJI)
Macromolecule: Actin, alpha skeletal muscle, intermediate form
Type: Protein, polypeptide(L)
Source organism: Oryctolagus cuniculus
Sequence length: 375 residues
Sequence: DEDETTALVCDNGSGLVKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYPIEHGIITNWDDMEKIWHHTFYNELRVAPEEHPTLLTEAPLNPKANREKMTQIMFETFNVPAMYVAIQAVLSLYASGRTTGIVLDSGDGVTHNVPIYEGYALPHAIMRLDLAGRDLTDYLMKILTERGYSFVTTAEREIVRDIKEKLCYVALDFENEMATAASSSSLEKSYELPDGQVITIGNERFRCPETLFQPSFIGMESAGIHETTYNSIMKCDIDIRKDLYANNVMSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWITKQEYDEAGPSIVHRKCF
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.75
R work: 0.1753
R free: 0.2121
Average B factor: 30.28
Crystallization method: EVAPORATION
Crystallization pH: 8.5
Crystallization temperature (K): 293
Crystal growth procedure: 30% peg 4000, 0.2 M Lithium Sulfate (LiSO4), 0.1 M TrisHCl pH8.5
Matthews coefficient: 2.25
Solvent content (%): 45.36
Ligand: ADENOSINE-5'-DIPHOSPHATE (ADP)
Ligand formula: C10 H15 N5 O10 P2
Ligand molecular weight: 427.201
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
Ligand InChI: InChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
Release date: 2023-09-20
Notum Fragment 705 (PDB entry 7BCC)
Macromolecule: Palmitoleoyl-protein carboxylesterase NOTUM
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.1.98
Sequence length: 383 residues
Sequence: ETGSAQQLNEDLRLHLLLNTSVTCNDGSPAGYYLKESRGSRRWLLFLEGGWYCFNRENCDSRYDTMRRLMSSRDWPRTRTGTGILSSQPEENPYWWNANMVFIPYCSSDVWSGASSKSEKNEYAFMGALIIQEVVRELLGRGLSGAKVLLLAGSSAGGTGVLLNVDRVAEQLEKLGYPAIQVRGLADSGWFLDNKQYRHTDCVDTITCAPTEAIRRGIRYWNGVVPERCRRQFQEGEEWNCFFGYKVYPTLRSPVFVVQWLFDEAQLTVDNVHLTGQPVQEGLRLYIQNLGRELRHTLKDVPASFAPACLSHEIIIRSHWTDVQVKGTSLPRALHCWDRSLHDSHKASKTPLKGCPVHLVDSCPWPHCNPSCPTGTKHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.58
R work: 0.2177
R free: 0.2346
Average B factor: 25.0381
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 296
Crystal growth procedure: 1.5 M Ammonium Sulphate
0.1 M Sodium Citrate, pH4.2
Matthews coefficient: 1.98
Solvent content (%): 38.02
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: 2022-01-12
Human Sterol Carrier Protein with unnatural amino acid 2,2'-bipyridine alanine incorporated at position 111 (PDB entry 8AF2)
Macromolecule: Enoyl-CoA hydratase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.107
Sequence length: 128 residues
Sequence: MEGGKLQSTFVFEEIGRRLKDIGPEVVKKVNAVFEWHITKGGNIGAKWTIDLKSGSGKVYQGPAKGAADTTIILSDEDFMEVVLGKLDPQKAFFSGRLKARGNIMLSQKLXMILKDYAKLGSENLYFQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.51
R work: 0.2338
R free: 0.2997
Average B factor: 48.14
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 281
Crystal growth procedure: well solution 2.3M ammonium sulphate, 100 mM citric acid pH 5.6 and 200 mM NaCl
Solvent content (%): 35.13
Ligand: FRAGMENT OF TRITON X-100 (TRT)
Ligand formula: C21 H36 O4
Ligand molecular weight: 352.508
Ligand SMILES: CC(C)(C)CC(C)(C)c1ccc(cc1)OCCOCCOCCOC
Ligand InChI: InChI=1S/C21H36O4/c1-20(2,3)17-21(4,5)18-7-9-19(10-8-18)25-16-15-24-14-13-23-12-11-22-6/h7-10H,11-17H2,1-6H3
Release date: 2023-08-16
Crystal structure of human ALK2 kinase domain with R206H mutation in complex with a bicyclic pyrazole inhibitor RK-73134 (PDB entry 7C3G)
Macromolecule: Activin receptor type-1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.30
Sequence length: 301 residues
Sequence: SMQRTVAHQITLLECVGKGRYGEVWRGSWQGENVAVKIFSSRDEKSWFRETELYNTVMLRHENILGFIASDMTSRHSSTQLWLITHYHEMGSLYDYLQLTTLDTVSCLRIVLSIASGLAHLHIEIFGTQGKPAIAHRDLKSKNILVKKNGQCCIADLGLAVMHSQSTNQLDVGNNPRVGTKRYMAPEVLDETIQVDCFDSYKRVDIWAFGLVLWEVARRMVSNGIVEDYKPPFYDVVPNDPSFEDMRKVVCVDQQRPNIPNRWFSDPTLTSLAKLMKECWYQNPSARLTALRIKKTLTKID
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.802
R work: 0.1851
R free: 0.2266
Average B factor: 32.697
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 100 mM HEPES pH 7.6-8.0, 1.5-1.6 M ammonium sulfate
Matthews coefficient: 2.56
Solvent content (%): 51.9
Ligand: ~{N}-[4-(4-methylpiperazin-1-yl)phenyl]-4-(2-pyridin-3-yl-6,7-dihydro-4~{H}-pyrazolo[5,1-c][1,4]oxazin-3-yl)pyrimidin-2-amine (FH0)
Ligand formula: C26 H28 N8 O
Ligand molecular weight: 468.554
Ligand SMILES: CN1CCN(CC1)c2ccc(cc2)Nc3nccc(n3)c4c5n(nc4c6cccnc6)CCOC5
Ligand InChI: InChI=1S/C26H28N8O/c1-32-11-13-33(14-12-32)21-6-4-20(5-7-21)29-26-28-10-8-22(30-26)24-23-18-35-16-15-34(23)31-25(24)19-3-2-9-27-17-19/h2-10,17H,11-16,18H2,1H3,(H,28,29,30)
Release date: 2021-03-03
human dihydrofolate reductase complex with NADPH and 5-methyl-6-(2',3',4'-trifluorophenylthio)thieno[2,3-d]pyrimidine-2,4-diamine (PDB entry 5HQY)
Macromolecule: Dihydrofolate reductase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.5.1.3
Sequence length: 186 residues
Sequence: VGSLNCIVAVSQNMGIGKNGDLPWPPLRNEFRYFQRMTTTSSVEGKQNLVIMGKKTWFSIPEKNRPLKGRINLVLSRELKEPPQGAHFLSRSLDDALKLTEQPELANKVDMVWIVGGSSVYKEAMNHPGHLKLFVTRIMQDFESDTFFPEIDLEKYKLLPEYPGVLSDVQEEKGIKYKFEVYEKND
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.46
R work: 0.23284
R free: 0.27118
Average B factor: 29.382
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.9
Crystallization temperature (K): 287
Crystal growth procedure: 100 mM KP04, 60% AmSO4, 3%v/v ETOH
Matthews coefficient: 2.59
Solvent content (%): 52.43
Ligand: 5-methyl-6-[(2,3,4-trifluorophenyl)sulfanyl]thieno[2,3-d]pyrimidine-2,4-diamine (63Y)
Ligand formula: C13 H9 F3 N4 S2
Ligand molecular weight: 342.363
Ligand SMILES: Cc1c2c(nc(nc2sc1Sc3ccc(c(c3F)F)F)N)N
Ligand InChI: InChI=1S/C13H9F3N4S2/c1-4-7-10(17)19-13(18)20-11(7)22-12(4)21-6-3-2-5(14)8(15)9(6)16/h2-3H,1H3,(H4,17,18,19,20)
Release date: 2017-01-25
DHODH in complex with Ligand 16 (PDB entry 9BKN)
Macromolecule: Dihydroorotate dehydrogenase (quinone), mitochondrial
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.3.5.2
Sequence length: 367 residues
Sequence: GATGDERFYAEHLMPTLQGLLDPESAHRLAVRFTSLGLLPRARFQDSDMLEVRVLGHKFRNPVGIAAGFDKHGEAVDGLYKMGFGFVEIGSVTPKPQEGNPRPRVFRLPEDQAVINRYGFNSHGLSVVEHRLRARQQKQAKLTEDGLPLGVNLGKNKTSVDAAEDYAEGVRVLGPLADYLVVNVSSPNTAGLRSLQGKAELRRLLTKVLQERDGLRRVHRPAVLVKIAPDLTSQDKEDIASVVKELGIDGLIVTNTTVSRPAGLQGALRSETGGLSGKPLRDLSTQTIREMYALTQGRVPIIGVGGVSSGQDALEKIRAGASLVQLYTALTFWGPPVVGKVKRELEALLKEQGFGGVTDAIGADHRR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.3
R work: 0.12884
R free: 0.15205
Average B factor: 22.771
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 293
Crystal growth procedure: 0.10 M NaAcetate pH=4.8, 2.0 M (NH4)2SO4, 30 % Glycerol
Matthews coefficient: 3.66
Ligand: FLAVIN MONONUCLEOTIDE (FMN)
Ligand formula: C17 H21 N4 O9 P
Ligand molecular weight: 456.344
Ligand SMILES: Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)CC(C(C(COP(=O)(O)O)O)O)O
Ligand InChI: InChI=1S/C17H21N4O9P/c1-7-3-9-10(4-8(7)2)21(15-13(18-9)16(25)20-17(26)19-15)5-11(22)14(24)12(23)6-30-31(27,28)29/h3-4,11-12,14,22-24H,5-6H2,1-2H3,(H,20,25,26)(H2,27,28,29)/t11-,12+,14-/m0/s1
Release date: 2024-07-03
Fragment-based screening of HSP70 sheds light on the functional role of ATP-binding site residues (PDB entry 5AQO)
Macromolecule: BAG FAMILY MOLECULAR CHAPERONE REGULATOR 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 118 residues
Sequence: GPLGSNSPQEEVELKKLKHLEKSVEKIADQLEELNKELTGIQQGFLPKDLQAEALCKLDRRVKATIEQFMKILEEIDTLILPENFKDSRLKRKGLVKKVQAFLAECDTVEQNICQETE
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.12
R work: 0.1797
R free: 0.2101
Average B factor: 51.16
Crystallization pH: 8.5
Crystal growth procedure: 16-26% (W/V) PEG3350, 0.1 M K-NA TARTRATE, 0.1 M TRIS.HCL PH 8.5 AND 25% (V/V) GLYCEROL
Matthews coefficient: 2.45
Solvent content (%): 49.79
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: 2016-10-05
HUMAN PRMT5:MEP50 Crystal Structure With MTA and Fragment Bound (PDB entry 7ZUY)
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): 2.0
R work: 0.222
R free: 0.2698
Average B factor: 31.269
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 281
Crystal growth procedure: 13 % PEG3350, 100 mM Na citrate, pH 5.4, 4% Tacsimate pH 7.0
Matthews coefficient: 2.92
Solvent content (%): 57.94
Ligand: 5'-DEOXY-5'-METHYLTHIOADENOSINE (MTA)
Ligand formula: C11 H15 N5 O3 S
Ligand molecular weight: 297.334
Ligand SMILES: CSCC1C(C(C(O1)n2cnc3c2ncnc3N)O)O
Ligand InChI: InChI=1S/C11H15N5O3S/c1-20-2-5-7(17)8(18)11(19-5)16-4-15-6-9(12)13-3-14-10(6)16/h3-5,7-8,11,17-18H,2H2,1H3,(H2,12,13,14)/t5-,7-,8-,11-/m1/s1
Release date: 2022-10-19
CDK8-CYCC IN COMPLEX WITH COMPOUND 17:3-chloro-4-(4-pyridyl)-1H-pyrrole-2-carboxamide (PDB entry 5XS2)
Macromolecule: Cyclin-dependent kinase 8
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.22
Sequence length: 380 residues
Sequence: GAMGSHMEFMDYDFKVKLSSERERVEDLFEYEGCKVGRGTYGHVYKAKRKDGKDDKDYALKQIEGTGISMSACREIALLRELKHPNVISLQKVFLSHADRKVWLLFDYAEHDLWHIIKFHRASKANKKPVQLPRGMVKSLLYQILDGIHYLHANWVLHRDLKPANILVMGEGPERGRVKIADMGFARLFNSPLKPLADLDPVVVTFWYRAPELLLGARHYTKAIDIWAIGCIFAELLTSEPIFHCRQEDIKTSNPYHHDQLDRIFNVMGFPADKDWEDIKKMPEHSTLMKDFRRNTYTNCSLIKYMEKHKVKPDSKAFHLLQKLLTMDPIKRITSEQAMQDPYFLEDPLPTSDVFAGCQIPYPKREFLTEEEPDDKGDKK
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.04
R work: 0.19566
R free: 0.22512
Average B factor: 29.166
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.05M MgCl, 0.1M MES
pH 6.5, 10% Iso-propanol, 5% PEG4K
Matthews coefficient: 2.99
Solvent content (%): 58.82
Ligand: GLYCEROL (GOL)
Ligand formula: C3 H8 O3
Ligand molecular weight: 92.094
Ligand SMILES: C(C(CO)O)O
Ligand InChI: InChI=1S/C3H8O3/c4-1-3(6)2-5/h3-6H,1-2H2
Release date: 2017-08-09
Nucleotide-binding domain 1 of the human cystic fibrosis transmembrane conductance regulator (CFTR) with UTP (PDB entry 5TFF)
Macromolecule: Cystic fibrosis transmembrane conductance regulator
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.3.49
Sequence length: 229 residues
Sequence: SLTTTEVVMENVTAFWEEGGTPVLKDINFKIERGQLLAVAGSTGAGKTSLLMMIMGELEPSEGKIKHSGRISFCSQFSWIMPGTIKENIIFGVSYDEYRYRSVIKACQLEEDISKFAEKDNIVLGEGGITLSGGQRARISLARAVYKDADLYLLDSPFGYLDVLTEKEIFESCVCKLMANKTRILVTSKMEHLKKADKILILHEGSSYFYGTFSELQNLQPDFSSKLMG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.891
R work: 0.1595
R free: 0.1897
Crystallization method: MICROBATCH
Crystallization pH: 7.5
Crystallization temperature (K): 279
Crystal growth procedure: Protein buffer: 150 mM NaCl, 30% (v/v) glycerol, 1 mM TCEP, and 20 mM Na-HEPES, pH 7.5;
Precipitant buffer: 40% (v/v) PEG 400, 100 mM NH4Cl, and 100 mM MES, pH 6
Matthews coefficient: 2.38
Solvent content (%): 48.36
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: 2018-05-09
Human Cyclophilin D Complexed with Inhibitor. (PDB entry 5CBW)
Macromolecule: Peptidyl-prolyl cis-trans isomerase F, mitochondrial
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 5.2.1.8
Sequence length: 165 residues
Sequence: MGNPLVYLDVDANGKPLGRVVLELKADVVPKTAENFRALCTGEKGFGYKGSTFHRVIPSFMCQAGDFTNHNGTGGKSIYGSRFPDENFTLKHVGPGVLSMANAGPNTNGSQFFICTIKTDWLDGKHVVFGHVIEGMDVVKKIESFGSKSGRTSKKIVITDCGQLS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.17362
R free: 0.20816
Average B factor: 19.684
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 9
Crystallization temperature (K): 294
Crystal growth procedure: 4M potassium formate, 0.1M BIS-TRIS propane pH 9, 2% w/v PEG2000mme
Matthews coefficient: 2.66
Solvent content (%): 53.74
Ligand: TETRAETHYLENE GLYCOL (PG4)
Ligand formula: C8 H18 O5
Ligand molecular weight: 194.226
Ligand SMILES: C(COCCOCCOCCO)O
Ligand InChI: InChI=1S/C8H18O5/c9-1-3-11-5-7-13-8-6-12-4-2-10/h9-10H,1-8H2
Release date: 2016-07-20
Crystal structure of the tandem bromodomain (BD1 and BD2) of human TAF1 bound to ATR kinase inhibitor AZD6738 (PDB entry 7K03)
Macromolecule: Transcription initiation factor TFIID subunit 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1.48
Sequence length: 265 residues
Sequence: SMSIHRRRTDPMVTLSSILESIINDMRDLPNTYPFHTPVNAKVVKDYYKIITRPMDLQTLRENVRKRLYPSREEFREHLELIVKNSATYNGPKHSLTQISQSMLDLCDEKLKEKEDKLARLEKAINPLLDDDDQVAFSFILDNIVTQKMMAVPDSWPFHHPVNKKFVPDYYKVIVNPMDLETIRKNISKHKYQSRESFLDDVNLILANSVKYNGPESQYTKTAQEIVNVCYQTLTEYDEHLTQLEKDICTAKEAALEEAELESLD
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.6
R work: 0.1523
R free: 0.1805
Average B factor: 22.5989
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 291
Crystal growth procedure: 0.2 M Magnesium acetate tetrahydrate, 0.1 M Sodium cacodylate trihydrate, 20% Polyethylene glycol 8,000
Matthews coefficient: 2.45
Solvent content (%): 49.76
Ligand: 4-(4-{1-[(R)-amino(hydroxy)methyl-lambda~4~-sulfanyl]cyclopropyl}-6-[(3R)-3-methylmorpholin-4-yl]pyrimidin-2-yl)-1H-pyrrolo[2,3-b]pyridine (VJM)
Ligand formula: C20 H26 N6 O2 S
Ligand molecular weight: 414.524
Ligand SMILES: CC1COCCN1c2cc(nc(n2)c3ccnc4c3cc[nH]4)C5(CC5)S(C)(N)O
Ligand InChI: InChI=1S/C20H26N6O2S/c1-13-12-28-10-9-26(13)17-11-16(20(5-6-20)29(2,21)27)24-19(25-17)15-4-8-23-18-14(15)3-7-22-18/h3-4,7-8,11,13,27H,5-6,9-10,12,21H2,1-2H3,(H,22,23)/t13-/m1/s1
Release date: 2021-09-22
Diphosphoinositol polyphosphate phosphohydrolase 1 (DIPP1/NUDT3) in complex with 5-methylenebisphosphonate inositol pentakisphosphate (5-PCP-IP5) (PDB entry 6WOG)
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): 1.5
R work: 0.1506
R free: 0.1873
Average B factor: 17.211
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 4.5
Crystallization temperature (K): 293
Crystal growth procedure: 200 mM Li2SO4, 18% (w/v) PEG 8000, 5% (v/v) isopropanol, 100mM NaAc, pH 4.5
Matthews coefficient: 2.13
Solvent content (%): 42.36
Ligand: Methylenebisphosphonate inositol pentakisphosphate (5A3)
Ligand formula: C7 H21 O26 P7
Ligand molecular weight: 738.042
Ligand SMILES: C(P(=O)(O)O)P(=O)(O)OC1C(C(C(C(C1OP(=O)(O)O)OP(=O)(O)O)OP(=O)(O)O)OP(=O)(O)O)OP(=O)(O)O
Ligand InChI: InChI=1S/C7H21O26P7/c8-34(9,10)1-35(11,12)28-2-3(29-36(13,14)15)5(31-38(19,20)21)7(33-40(25,26)27)6(32-39(22,23)24)4(2)30-37(16,17)18/h2-7H,1H2,(H,11,12)(H2,8,9,10)(H2,13,14,15)(H2,16,17,18)(H2,19,20,21)(H2,22,23,24)(H2,25,26,27)/t2-,3-,4+,5+,6-,7+
Release date: 2021-03-03