satarupa22/MacromolecularLigandDB huggingface dataset:
PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with FMSOA001181b (PDB entry 7GT7)
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): 1.84
R work: 0.1998
R free: 0.2309
Average B factor: 43.187
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: 3.39
Solvent content (%): 63.68
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
Structure of Cezanne/OTUD7B OTU domain bound to Lys11-linked diubiquitin (PDB entry 5LRV)
Macromolecule: OTU domain-containing protein 7B
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.19.12
Sequence length: 318 residues
Sequence: MEMPICAFQLPDLTVYNEDFRSFIERDLIEQSMLVALEQAGRLNWWVSVDPTSQRLLPLATTGDGNCLLHAASLGMWGFHDRDLMLRKALYALMEKGVEKEALKRRWRWQQTQQNKESGLVYTEDEWQKEWNELIKLASSEPRMHLGTNGANCGGVESSEEPVYESLEEFHVFVLAHVLRRPIVVVADTMLRDSGGEAFAPIPFGGIYLPLEVPASQCHRSPLVLAYDQAHFSALVSMEQKENTKEQAVIPLTDSEYKLLPLHFAVDPGKGWEWGKDDSDNVRLASVILSLEVKLHLLHSYMNVKWIPLSSKHHHHHH
Oligomeric state: Hetero 3-mer
Stoichiometry: A2, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.8
R work: 0.2072
R free: 0.2442
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 0.1 M phosphate citrate (pH 4.2), 20% (w/v) PEG 8K, 0.2 M sodium chloride
Matthews coefficient: 2.23
Solvent content (%): 44.83
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: 2016-10-19
Human Sirt6 in complex with ADP-ribose and the activator quercetin (PDB entry 6QCD)
Macromolecule: NAD-dependent protein deacetylase sirtuin-6
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.5.1
Sequence length: 302 residues
Sequence: GIDPFTADKGKCGLPEIFDPPEELERKVWELARLVWQSSSVVFHTGAGISTASGIPDFRGPHGVWTMEERGLAPKFDTTFESARPTQTHMALVQLERVGLLRFLVSQNVDGLHVRSGFPRDKLAELHGNMFVEECAKCKTQYVRDTVVGTMGLKATGRLCTVAKARGLRACRGELRDTILDWEDSLPDRDLALADEASRNADLSITLGTSLQIRPSGNLPLATKRRGGRLVIVNLQPTKHDRHADLRIHGYVDEVMTRLMKHLGLEIPAWDGPRVLERALPPLPRPPTPKLEPKEESPTRIN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.84
R work: 0.1682
R free: 0.2023
Average B factor: 37
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.7
Crystallization temperature (K): 293
Crystal growth procedure: 1.6 M (NH4)2SO4, 10% PEG 400, and Bis-Tris buffer pH 5.7
Matthews coefficient: 2.63
Solvent content (%): 53.22
Ligand: [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL
[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE (AR6)
Ligand formula: C15 H23 N5 O14 P2
Ligand molecular weight: 559.316
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)O)O)O)O)O)N
Ligand InChI: InChI=1S/C15H23N5O14P2/c16-12-7-13(18-3-17-12)20(4-19-7)14-10(23)8(21)5(32-14)1-30-35(26,27)34-36(28,29)31-2-6-9(22)11(24)15(25)33-6/h3-6,8-11,14-15,21-25H,1-2H2,(H,26,27)(H,28,29)(H2,16,17,18)/t5-,6-,8-,9-,10-,11-,14-,15+/m1/s1
Release date: 2019-12-25
DDR1 bound to VX-680 (PDB entry 6BRJ)
Macromolecule: Epithelial discoidin domain-containing receptor 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 351 residues
Sequence: QNSVPHYAEADIVTLQGVTGGNTYAVPALPPGAVGDGPPRVDFPRSRLRFKEKLGEGQFGEVHLCEVDSPQDLVSLDFPLNVRKGHPLLVAVKILRPDATKNARNDFLKEVKIMSRLKDPNIIRLLGVCVQDDPLCMITDYMENGDLNQFLSAHQLEDKAAEGAPGDGQAAQGPTISYPMLLHVAAQIASGMRYLATLNFVHRDLATRNCLVGENFTIKIADFGMSRNLYAGDYYRVQGRAVLPIRWMAWECILMGKFTTASDVWAFGVTLWEVLMLCRAQPFGQLTDEQVIENAGEFFRDQGRQVYLSRPPACPQGLYELMLRCWSRESEQRPPFSQLHRFLAEDALNTV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.231
R work: 0.1849
R free: 0.2225
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 298
Crystal growth procedure: 18% PEG 3350 and 0.1 M Bis-Tris pH 5.5
Matthews coefficient: 2.28
Solvent content (%): 46.08
Ligand: CYCLOPROPANECARBOXYLIC ACID {4-[4-(4-METHYL-PIPERAZIN-1-YL)-6-(5-METHYL-2H-PYRAZOL-3-YLAMINO)-PYRIMIDIN-2-YLSULFANYL]-PHENYL}-AMIDE (VX6)
Ligand formula: C23 H28 N8 O S
Ligand molecular weight: 464.586
Ligand SMILES: Cc1cc([nH]n1)Nc2cc(nc(n2)Sc3ccc(cc3)NC(=O)C4CC4)N5CCN(CC5)C
Ligand InChI: InChI=1S/C23H28N8OS/c1-15-13-20(29-28-15)25-19-14-21(31-11-9-30(2)10-12-31)27-23(26-19)33-18-7-5-17(6-8-18)24-22(32)16-3-4-16/h5-8,13-14,16H,3-4,9-12H2,1-2H3,(H,24,32)(H2,25,26,27,28,29)
Release date: 2018-12-05
Crystal structure of human JMJD2C catalytic domain in complex 6-ethyl- 5-methyl-7-oxo-4,7-dihydropyrazolo(1,5-a)pyrimidine-3-carbonitrile (PDB entry 5FJK)
Macromolecule: LYSINE-SPECIFIC DEMETHYLASE 4C
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11
Sequence length: 349 residues
Sequence: GPMNVAEVESPLNPSCKIMTFRPSMEEFREFNKYLAYMESKGAHRAGLAKVIPPKEWKPRQCYDDIDNLLIPAPIQQMVTGQSGLFTQYNIQKKAMTVKEFRQLANSGKYCTPRYLDYEDLERKYWKNLTFVAPIYGADINGSIYDEGVDEWNIARLNTVLDVVEEECGISIEGVNTPYLYFGMWKTTFAWHTEDMDLYSINYLHFGEPKSWYAIPPEHGKRLERLAQGFFPSSSQGCDAFLRHKMTLISPSVLKKYGIPFDKITQEAGEFMITFPYGYHAGFNHGFNCAESTNFATVRWIDYGKVAKLCTCRKDMVKISMDIFVRKFQPDRYQLWKQGKDIYTIDHTK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.66
R work: 0.1592
R free: 0.1974
Crystallization pH: 7.25
Crystal growth procedure: 21% PEG 3350, 5% 1,2 ETHANEDIOL, 0.2 M NANO3, 0.1 M BIS-TRIS PROPANE PH 7.25
Matthews coefficient: 2.51
Solvent content (%): 50.94
Ligand: ZINC ION (ZN)
Ligand formula: Zn
Ligand molecular weight: 65.409
Ligand SMILES: [Zn+2]
Ligand InChI: InChI=1S/Zn/q+2
Release date: 2015-10-21
Crystal structure of the pre-catalytic ternary complex of DNA polymerase lambda with a templating 8-oxo-dG and an incoming dATP (PDB entry 5III)
Macromolecule: DNA polymerase lambda
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 334 residues
Sequence: AQPSSQKATNHNLHITEKLEVLAKAYSVQGDKWRALGYAKAINALKSFHKPVTSYQEACSIPGIGKRMAEKIIEILESGHLRKLDHISESVPVLELFSNIWGAGTKTAQMWYQQGFRSLEDIRSQASLTTQQAIGLKHYSDFLERMPREEATEIEQTVQKAAQAFNSGLLCVACGSYRRGKATCGDVDVLITHPDGRSHRGIFSRLLDSLRQEGFLTDDLVSQEENGQQQKYLGVCRLPGPGRRHRRLDIIVVPYSEFACALLYFTGSAHFNRSMRALAKTKGMSLSEHALSTAVVRNTHGCKVGPGRVLPTPTEKDVFRLLGLPYREPAERDW
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.2007
R free: 0.2251
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Matthews coefficient: 2.86
Solvent content (%): 57.02
Ligand: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE (DTP)
Ligand formula: C10 H16 N5 O12 P3
Ligand molecular weight: 491.182
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3CC(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)N
Ligand InChI: InChI=1S/C10H16N5O12P3/c11-9-8-10(13-3-12-9)15(4-14-8)7-1-5(16)6(25-7)2-24-29(20,21)27-30(22,23)26-28(17,18)19/h3-7,16H,1-2H2,(H,20,21)(H,22,23)(H2,11,12,13)(H2,17,18,19)/t5-,6+,7+/m0/s1
Release date: 2016-08-17
CDK2/CyclinA in complex with Flavopiridol (PDB entry 6GUB)
Macromolecule: Cyclin-dependent kinase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.22
Sequence length: 302 residues
Sequence: GPGSMENFQKVEKIGEGTYGVVYKARNKLTGEVVALKKIRLDTETEGVPSTAIREISLLKELNHPNIVKLLDVIHTENKLYLVFEFLHQDLKKFMDASALTGIPLPLIKSYLFQLLQGLAFCHSHRVLHRDLKPQNLLINTEGAIKLADFGLARAFGVPVRTYTHEVVTLWYRAPEILLGCKYYSTAVDIWSLGCIFAEMVTRRALFPGDSEIDQLFRIFRTLGTPDEVVWPGVTSMPDYKPSFPKWARQDFSKVVPPLDEDGRSLLSQMLHYDPNKRISAKAALAHPFFQDVTKPVPHLRL
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.52
R work: 0.19543
R free: 0.23822
Average B factor: 46.819
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277
Crystal growth procedure: PROTEIN AT 5MG PER ML. 0.6 TO 0.8M KCL, 0.9 TO 1.2M (NH402SO4, AND 100MM HEPES (PH 7.0), 0.5mM Inhibitor
Matthews coefficient: 2.95
Solvent content (%): 58.25
Ligand: 2-(2-chlorophenyl)-8-[(3~{R},4~{R})-1-methyl-3-oxidanyl-piperidin-4-yl]-5,7-bis(oxidanyl)chromen-4-one (F9Z)
Ligand formula: C21 H20 Cl N O5
Ligand molecular weight: 401.84
Ligand SMILES: CN1CCC(C(C1)O)c2c(cc(c3c2OC(=CC3=O)c4ccccc4Cl)O)O
Ligand InChI: InChI=1S/C21H20ClNO5/c1-23-7-6-12(17(27)10-23)19-14(24)8-15(25)20-16(26)9-18(28-21(19)20)11-4-2-3-5-13(11)22/h2-5,8-9,12,17,24-25,27H,6-7,10H2,1H3/t12-,17-/m0/s1
Release date: 2018-12-05
Structural insights into the interaction of p97 N-terminal domain and SHP motif in Derlin-1 rhomboid pseudoprotease (PDB entry 5GLF)
Macromolecule: Transitional endoplasmic reticulum ATPase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.4.6
Sequence length: 184 residues
Sequence: GAMGSNRPNRLIVDEAINEDNSVVSLSQPKMDELQLFRGDTVLLKGKKRREAVCIVLSDDTCSDEKIRMNRVVRNNLRVRLGDVISIQPCPDVKYGKRIHVLPIDDTVEGITGNLFEVYLKPYFLEAYRPIRKGDIFLVRGGMRAVEFKVVETDPSPYCIVAPDTVIHCEGEPIKREDEEESLN
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.25
R work: 0.189
R free: 0.23
Average B factor: 37.36
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 25% PEG 3350, BIS-TRIS PH 6.5, 0.2M
 MGCL2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K
Matthews coefficient: 2.03
Solvent content (%): 39.36
Release date: 2016-11-09
PanDDA analysis group deposition -- Crystal structure of PTP1B in complex with compound_FMOMB000149a (PDB entry 5QEU)
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): 1.735
R work: 0.1893
R free: 0.2169
Average B factor: 43.4163
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: 3.35
Solvent content (%): 63.32
Ligand: N-[(4-chlorophenyl)methyl]methanesulfonamide (JKY)
Ligand formula: C8 H10 Cl N O2 S
Ligand molecular weight: 219.688
Ligand SMILES: CS(=O)(=O)NCc1ccc(cc1)Cl
Ligand InChI: InChI=1S/C8H10ClNO2S/c1-13(11,12)10-6-7-2-4-8(9)5-3-7/h2-5,10H,6H2,1H3
Release date: 2018-10-10
Tankyrase 2 in complex with an inhibitor (OM-2700) (PDB entry 6TKQ)
Macromolecule: Tankyrase-2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.4.2.30
Sequence length: 240 residues
Sequence: MHHHHHHSSGVDLGTENLYFQSMLNTSGSGTILIDLSPDDKEFQSVEEEMQSTVREHRDGGHAGGIFNRYNILKIQKVCNKKLWERYTHRRKEVSEENHNHANERMLFHGSPFVNAIIHKGFDERHAYIGGMFGAGIYFAENSSKSNQYVYGIGGGTGCPVHKDRSCYICHRQLLFCRVTLGKSFLQFSAMKMAHSPPGHHSVTGRPSVNGLALAEYVIYRGEQAYPEYLITYQIMRPEG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.5
R work: 0.1991
R free: 0.2516
Average B factor: 32.103
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 295.15
Crystal growth procedure: 7.5-25% PEG 6000, Bicine pH=9.0
Matthews coefficient: 2.21
Solvent content (%): 44.22
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: 2020-07-08
Src Kinase Domain in complex with ponatinib (PDB entry 7OTE)
Macromolecule: Proto-oncogene tyrosine-protein kinase Src
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 293 residues
Sequence: HHHHHHGSDIQTQGLAKDAWEIPRESLRLEVKLGQGCFGEVWMGTWNGTTRVAIKTLKPGTMSPEAFLQEAQVMKKLRHEKLVQLYAVVSEEPIYIVTEYMSKGSLLDFLKGETGKYLRLPQLVDMAAQIASGMAYVERMNYVHRDLRAANILVGENLVCKVADFGLARLIEDNEYTARQGAKFPIKWTAPEAALYGRFTIKSDVWSFGILLTELTTKGRVPYPGMVNREVLDQVERGYRMPCPPECPESLHDLMCQCWRKEPEERPTFEYLQAFLEDYFTSTEPQYQPGENL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.49
R work: 0.1751
R free: 0.2521
Average B factor: 43.689
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8
Crystallization temperature (K): 293
Crystal growth procedure: Tris 20 mM pH 8, 150 mM Sodium chloride, 1 mM DTT, 2-propanol and PEG 4.000
Matthews coefficient: 2.51
Solvent content (%): 51.08
Ligand: 3-(imidazo[1,2-b]pyridazin-3-ylethynyl)-4-methyl-N-{4-[(4-methylpiperazin-1-yl)methyl]-3-(trifluoromethyl)phenyl}benzam
ide (0LI)
Ligand formula: C29 H27 F3 N6 O
Ligand molecular weight: 532.559
Ligand SMILES: Cc1ccc(cc1C#Cc2cnc3n2nccc3)C(=O)Nc4ccc(c(c4)C(F)(F)F)CN5CCN(CC5)C
Ligand InChI: InChI=1S/C29H27F3N6O/c1-20-5-6-22(16-21(20)8-10-25-18-33-27-4-3-11-34-38(25)27)28(39)35-24-9-7-23(26(17-24)29(30,31)32)19-37-14-12-36(2)13-15-37/h3-7,9,11,16-18H,12-15,19H2,1-2H3,(H,35,39)
Release date: 2022-06-22
X-ray crystal structure of perdeuterated (D) small monoclinic unit cell CA IX SV. (PDB entry 6RQW)
Macromolecule: Carbonic anhydrase 9
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 256 residues
Sequence: HWRYGGDPPWPRVSPACAGRFQSPVDIRPQLAAFSPALRPLELSGFQLPPLPELRLRNNGHSVQLTLPPGLEMKLGPGREYRALQLHLHWGAAGRPGSEHTVEGHRFPAEIHVVHLSTKYARVDEALGRPGGLAVLAAFLEEGPEENSAYEQLLSRLEEIAEEGSETQVPGLDISALLPSDFSRYFQYEGSLTTPPCAQGVIWTVFNQTVSLSAKQLHTLSDTLWGPGDSRLQLNFRATQPLNGRVIEASFPAGVD
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.488
R work: 0.1725
R free: 0.2033
Average B factor: 30.2325
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 298
Crystal growth procedure: 30% (w/v) PEG 4000, 0.2 M ammonium formate, 0.1 M Tris-HCl pH 8.5
Matthews coefficient: 2.18
Solvent content (%): 43.5
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: 2019-09-11
Crystal structure of a constitutively active mutant of the alpha beta heterodimer of human IDH3 in complex with ADP and Mg (PDB entry 8GRD)
Macromolecule: Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.1.1.41
Sequence length: 339 residues
Sequence: TGGVQTVTLIPGDGIGPEISAAVMKIFDAAKAPIQWEERNVTAIQGPGGKWMIPSEAKESMDKNKMGLKGPLKTPIAAGHPSMNLLLRKTFDLYANVRPCVSIEGYKTPYTDVNIVTIRENTEGEYSGIEHVIVDGVVASIKLITEGASKRIAEFAFEYARNNHRSNVTAVHKANIMRMSDGLFLQKCREVAESCKDIKFNEMYLDTVCLNMVQDPSQFDVLVMPNLYGDILSDLCAGLIGGLGVTPSGNIGANGVAIFESVHGTAPDIAGKDMANPTALLLSAVMMLRHMGLFDHAARIEAACFATIKDGKSLTKDLGGNAKCSDFTEEICRRVKDLD
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.699
R work: 0.194
R free: 0.2418
Average B factor: 50.1481
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.1
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M sodium cacodylate (pH 5.1), 0.1 M calcium acetate, 10% (w/v) PEG 8000, 4 mM ADP, 4 mM CIT and 0.4 mM MgCl2
Matthews coefficient: 2.94
Solvent content (%): 58.18
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: 2022-11-30
TorsinAdeltaE-LULL1 complex, H. sapiens, bound to VHH-BS2 (PDB entry 5J1T)
Macromolecule: Torsin-1A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.4
Sequence length: 283 residues
Sequence: GPGQKRSLSREALQKDLDDNLFGQHLAKKIILNAVFGFINNPKPKKPLTLSLHGWTGTGKNFVSKIIAENIYEGGLNSDYVHLFVATLHFPHASNITLYKDQLQLWIRGNVSACARSIFIFDQMDKMHAGLIDAIKPFLDYYDLVDGVSYQKAMFIFLSNAGAERITDVALDFWRSGKQREDIKLKDIEHALSVSVFNNKNSGFWHSSLIDRNLIDYFVPFLPLEYKHLKMCIRVEMQSRGYEIDEDIVSRVAEMTFFPKEERVFSDKGCKTVFTKLDYYYDD
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.402
R work: 0.148
R free: 0.1768
Average B factor: 25.3491
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 291
Crystal growth procedure: 19 % PEG3350
200 mM ammonium sulfate
100 mM Bis-Tris/HCl pH 6.5
Matthews coefficient: 2.42
Solvent content (%): 49.14
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: 2016-08-17
FACTOR XIA IN COMPLEX WITH THE INHIBITOR ethyl (2R,7S)-7-({(2E)-3-[5-chloro-2-(1H-tetrazol-1-yl)phenyl]prop-2-enoyl}amino)-15-[(methoxycarbonyl)amino]-2,3,4,5,6,7-hexahydro-1H-12,8-(metheno)-1,9-benzodiazacyclotetradecine-2-carboxylate (PDB entry 5QTY)
Macromolecule: Coagulation factor XI
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.27
Sequence length: 244 residues
Sequence: IVGGTASVRGEWPWQVTLHTTSPTQRHLCGGSIIGNQWILTAAHCFYGVESPKILRVYSGILNQSEIKEDTSFFGVQEIIIHDQYKMAESGYDIALLKLETTVGYGDSQRPICLPSKGDRNVIYTDCWVTGWGYRKLRDKIQNTLQKAKIPLVTNEECQKRYRGHKITHKMICAGYREGGKDACKGDSGGPLSCKHNEVWHLVGITSWGEGCAQRERPGVYTNVVEYVDWILEKTQAVHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.89
R work: 0.1546
R free: 0.1712
Average B factor: 29.4
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7
Crystallization temperature (K): 277
Crystal growth procedure: 100 mM sodium acetate, pH 4.6, 25% (w/v) MePEG2000, 200 mM ammonium sulfate, then transferred to 100 mM Tris-HCl, pH 7.0, 25% (w/v) MePEG2000, 200 MM ammonium sulfate
Matthews coefficient: 3.42
Solvent content (%): 64
Ligand: ethyl (2R,7S)-7-({(2E)-3-[5-chloro-2-(1H-tetrazol-1-yl)phenyl]prop-2-enoyl}amino)-15-[(methoxycarbonyl)amino]-2,3,4,5,6,7-hexahydro-1H-12,8-(metheno)-1,9-benzodiazacyclotetradecine-2-carboxylate (QLJ)
Ligand formula: C32 H33 Cl N8 O5
Ligand molecular weight: 645.108
Ligand SMILES: CCOC(=O)C1CCCCC(c2cc(ccn2)-c3ccc(cc3N1)NC(=O)OC)NC(=O)C=Cc4cc(ccc4n5cnnn5)Cl
Ligand InChI: InChI=1S/C32H33ClN8O5/c1-3-46-31(43)26-7-5-4-6-25(38-30(42)13-8-21-16-22(33)9-12-29(21)41-19-35-39-40-41)28-17-20(14-15-34-28)24-11-10-23(18-27(24)37-26)36-32(44)45-2/h8-19,25-26,37H,3-7H2,1-2H3,(H,36,44)(H,38,42)/b13-8+/t25-,26+/m0/s1
Release date: 2020-01-29
Crystal structure of human chitotriosidase-1 catalytic domain in complex with chitobiose (2.5mM) at 1.10 A resolution (PDB entry 4WKF)
Macromolecule: Chitotriosidase-1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.2.1.14
Sequence length: 377 residues
Sequence: AKLVCYFTNWAQYRQGEARFLPKDLDPSLCTHLIYAFAGMTNHQLSTTEWNDETLYQEFNGLKKMNPKLKTLLAIGGWNFGTQKFTDMVATANNRQTFVNSAIRFLRKYSFDGLDLDWEYPGSQGSPAVDKERFTTLVQDLANAFQQEAQTSGKERLLLSAAVPAGQTYVDAGYEVDKIAQNLDFVNLMAYDFHGSWEKVTGHNSPLYKRQEESGAAASLNVDAAVQQWLQKGTPASKLILGMPTYGRSFTLASSSDTRVGAPATGSGTPGPFTKEGGMLAYYEVCSWKGATKQRIQDQKVPYIFRDNQWVGFDDVESFKTKVSYLKQKGLGGAMVWALDLDDFAGFSCNQGRYPLIQTLRQELSLVPRGSHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.101
R work: 0.1433
R free: 0.1622
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 290
Crystal growth procedure: 25 % (w/v) polyethylene glycol (PEG) 3350, 0.2 M potassium sodium tartrate at pH 7.2
2.5mM 4-methylumbelliferyl triacetylchitotrioside
Matthews coefficient: 2.18
Solvent content (%): 43.51
Release date: 2015-07-08
The structure of human CamKII with bound inhibitor (PDB entry 6AYW)
Macromolecule: Calcium/calmodulin-dependent protein kinase type II subunit delta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.17
Sequence length: 302 residues
Sequence: GHMSTTTCTRFTDEYQLFEELGKGAFSVVRRCMKIPTGQEYAAKIINTKKLSARDHQKLEREARICRLLKHPNIVRLHDSISEEGFHYLVFDLVTGGELFEDIVAREYYSEADASHCIQQILESVNHCHLNGIVHRDLKPENLLLASKSKGAAVKLADFGLAIEVQGDQQAWFGFAGTPGYLSPEVLRKDPYGKPVDMWACGVILYILLVGYPPFWDEDQHRLYQQIKAGAYDFPSPEWDTVTPEAKDLINKMLTINPAKRITASEALKHPWICQRSTVASMMHRQETVDCLKKFNARRKLK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.05
R work: 0.1985
R free: 0.2669
Average B factor: 38.2
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: CamKII S3-K301, in 20mM imidazole pH 8.5, 0.3M sodium chloride, 5mM TCEP, was concentrated to 36 mg/ml and flash frozen in liquid nitrogen for long term storage at -80 C in 10 microL aliquots. The protein was thawed and diluted down to 12 mg/mL in the same buffer just prior to crystallization experiments. Sitting drop vapor diffusion droplets were assembled with 250 nL of 12 mg/mL CamKII, 0.6 mM inhibitor and 250 nL of reservoir solution 24% peg 3350, 0.2 M ammonium tartrate, 0.1 M arginine. Flat crystal plates (typically 0.03 mm x 0.2 mm x 0.4 mm in size) grew in 4-7 days at 20 C. A crystal seed suspension was prepared with ten crushed crystals combined into 100 uL of reservoir solution and stored at -80 C. A thirty fold seed dilution was prepared in the same solution for addition to protein droplets in a 1 to 1 volume ratio to enhance crystallization of difficult to crystallize inhibitors.
Matthews coefficient: 2.33
Solvent content (%): 47.14
Ligand: N-[2-(dimethylamino)ethyl]-3-[6-(thiophen-2-yl)imidazo[1,2-b]pyridazin-3-yl]benzamide (C2V)
Ligand formula: C21 H21 N5 O S
Ligand molecular weight: 391.489
Ligand SMILES: CN(C)CCNC(=O)c1cccc(c1)c2cnc3n2nc(cc3)c4cccs4
Ligand InChI: InChI=1S/C21H21N5OS/c1-25(2)11-10-22-21(27)16-6-3-5-15(13-16)18-14-23-20-9-8-17(24-26(18)20)19-7-4-12-28-19/h3-9,12-14H,10-11H2,1-2H3,(H,22,27)
Release date: 2017-11-15
Crystal structure of human angiogenin and RNA duplex (PDB entry 8AF0)
Macromolecule: RNA (5'-R(*GP*CP*CP*CP*GP*CP*CP*UP*GP*UP*CP*AP*CP*GP*CP*GP*GP*GP*C)-3')
Type: RNA, polyribonucleotide
Source organism: Homo sapiens
Sequence length: 19 residues
Sequence: GCCCGCCUGUCACGCGGGC
Oligomeric state: Homo 2-mer
Stoichiometry: A2
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.43
R work: 0.2051
R free: 0.2681
Average B factor: 61.85
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277.15
Crystal growth procedure: 200 mM NaCl, 20 % (w/v) PEG6000, 100 mM Hepes pH 7.0
Matthews coefficient: 2.11
Solvent content (%): 41.74
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: 2022-09-14