satarupa22/MacromolecularLigandDB huggingface dataset:
APE1 exonuclease substrate complex with 8oxoG opposite A (PDB entry 7SUV)
Macromolecule: DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*(8OG))-3')
Type: DNA, polydeoxyribonucleotide
Source organism: synthetic construct
Sequence length: 10 residues
Sequence: GCTGATGCGG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.99
R work: 0.226
R free: 0.2649
Average B factor: 45.81
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5
Crystallization temperature (K): 293.15
Crystal growth procedure: 7 - 14% PEG20000, 100 mM sodium citrate, 15% glycerol, 5 mM calcium chloride
Matthews coefficient: 2.71
Solvent content (%): 54.53
Release date: 2022-09-07
Crystal structure of the FnIII-tandem A84-A86 from the A-band of titin (PDB entry 8BNQ)
Macromolecule: Titin
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 304 residues
Sequence: GAMDRPGPPEGPVVISGVTAEKCTLAWKPPLQDGGSDIINYIVERRETSRLVWTVVDANVQTLSCKVTKLLEGNEYTFRIMAVNKYGVGEPLESEPVVAKNPFVVPDAPKAPEVTTVTKDSMIVVWERPASDGGSEILGYVLEKRDKEGIRWTRCHKRLIGELRLRVTGLIENHDYEFRVSAENAAGLSEPSPPSAYQKACDPIYKPGPPNNPKVIDITRSSVFLSWSKPIYDGGCEIQGYIVEKCDVSVGEWTMCTPPTGINKTNIEVEKLLEKHEYNFRICAINKAGVGEHADVPGPIIVEE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.3
R work: 0.1975
R free: 0.2578
Average B factor: 63.34
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277.15
Crystal growth procedure: 5% [v/v] polyethylene glycol 400 and 40% [v/v] 2-methyl-2,4-pentanediol (MPD)
Matthews coefficient: 2.47
Solvent content (%): 50.28
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: 2023-04-12
Crystal structure of human DNA cross-link repair 1A in complex with hydroxamic acid inhibitor (compound 21). (PDB entry 8C8S)
Macromolecule: DNA cross-link repair 1A protein
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.5.2.6
Sequence length: 343 residues
Sequence: KKTCPFYKKIPGTGFTVDAFQYGVVEGCTAYFLTHFHSDHYAGLSKHFTFPVYCSEITGNLLKNKLHVQEQYIHPLPLDTECIVNGVKVVLLDANHCPGAVMILFYLPNGTVILHTGDFRADPSMERSLLADQKVHMLYLDTTYCSPEYTFPSQQEVIRFAINTAFEAVTLNPHALVVCGTYSIGKEKVFLAIADVLGSKVGMSQEKYKTLQCLNIPEINSLITTDMCSSLVHLLPMMQINFKGLQSHLKKCGGKYNQILAFRPTGWTHSNKFTRIADVIPQTKGNISIYGIPYSEHSSYLEMKRFVQWLKPQKIIPTVNVGTWKSRSTMEKYFREWKLEAGY
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.2121
R free: 0.2463
Average B factor: 33.92
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6
Crystallization temperature (K): 298
Crystal growth procedure: 30% PEG 1000, 0.1M MIB buffer
Matthews coefficient: 2.16
Solvent content (%): 43.16
Ligand: (2~{R})-3-[6-chloranyl-2-(prop-2-enylamino)quinazolin-4-yl]-2-methyl-~{N}-oxidanyl-propanamide (U2O)
Ligand formula: C15 H17 Cl N4 O2
Ligand molecular weight: 320.774
Ligand SMILES: CC(Cc1c2cc(ccc2nc(n1)NCC=C)Cl)C(=O)NO
Ligand InChI: InChI=1S/C15H17ClN4O2/c1-3-6-17-15-18-12-5-4-10(16)8-11(12)13(19-15)7-9(2)14(21)20-22/h3-5,8-9,22H,1,6-7H2,2H3,(H,20,21)(H,17,18,19)/t9-/m1/s1
Release date: 2024-01-31
Crystal Structure of human phosphodiesterase 10 in complex with 7-[(4-methoxy-3,5-dimethylpyridin-2-yl)methylsulfanyl]-6H-imidazo[4,5-g][1,3]benzothiazole (PDB entry 5SHH)
Macromolecule: cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.4.17
Sequence length: 343 residues
Sequence: GSSICTSEEWQGLMQFTLPVRLCKEIELFHFDIGPFENMWPGIFVYMVHRSCGTSCFELEKLCRFIMSVKKNYRRVPYHNWKHAVTVAHCMYAILQNNHTLFTDLERKGLLIACLCHDLDHRGFSNSYLQKFDHPLAALYSTSTMEQHHFSQTVSILQLEGHNIFSTLSSSEYEQVLEIIRKAIIATDLALYFGNRKQLEEMYQTGSLNLNNQSHRDRVIGLMMTACDLCSVTKLWPVTKLTANDIYAEFWAEGDEMKKLGIQPIPMMDRDKKDEVPQGQLGFYNAVAIPCYTTLTQILPPTEPLLKACRDNLSQWEKVIRGEETATWISSPSVAQKAAASED
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.15
R work: 0.1914
R free: 0.2305
Average B factor: 38.098
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 295
Crystal growth procedure: 5-20 mg/mL protein in 25mM HEPES/NaOH pH7.5, 150mM NaCl, 50mM BME mixed 1:1 with reservoir 0.1M HEPES/NaOH pH7.5, 30% PEG550MME, 50mM MgCl2
Matthews coefficient: 2.66
Solvent content (%): 53.77
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: 2022-10-12
Human JAK2 JH1 domain in complex with PROTAC-intermediate linker handle 3 (PDB entry 6WTP)
Macromolecule: Tyrosine-protein kinase JAK2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 309 residues
Sequence: MAFEDRDPTQFEERHLKFLQQLGKGNFGSVEMCRYDPLQDNTGEVVAVKKLQHSTEEHLRDFEREIEILKSLQHDNIVKYKGVCYSAGRRNLKLIMEYLPYGSLRDYLQKHKERIDHIKLLQYTSQICKGMEYLGTKRYIHRDLATRNILVENENRVKIGDFGLTKVLPQDKEYYKVKEPGESPIFWYAPESLTESKFSVASDVWSFGVVLYELFTYIEKSKSPPAEFMRMIGNDKQGQMIVFHLIELLKNNGRLPRPDGCPDEIYMIMTECWNNNVNQRPSFRDLALRVDQIRDNMAGGSGSENLYFQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.5
R work: 0.2377
R free: 0.288
Average B factor: 72.0744
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5
Crystallization temperature (K): 291
Crystal growth procedure: 0.1 M SODIUM CITRATE PH 6.0, 27% PEG 8000 AND 0.2 M AMMONIUM ACETATE.
REMARK 280  6.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K
Matthews coefficient: 2.19
Solvent content (%): 43.8
Ligand: tert-butyl 4-[(4-{1-[3-(cyanomethyl)-1-(ethylsulfonyl)azetidin-3-yl]-1H-pyrazol-4-yl}-7H-pyrrolo[2,3-d]pyrimidin-2-yl)amino]benzoate (U8P)
Ligand formula: C27 H30 N8 O4 S
Ligand molecular weight: 562.643
Ligand SMILES: CCS(=O)(=O)N1CC(C1)(CC#N)n2cc(cn2)c3c4cc[nH]c4nc(n3)Nc5ccc(cc5)C(=O)OC(C)(C)C
Ligand InChI: InChI=1S/C27H30N8O4S/c1-5-40(37,38)34-16-27(17-34,11-12-28)35-15-19(14-30-35)22-21-10-13-29-23(21)33-25(32-22)31-20-8-6-18(7-9-20)24(36)39-26(2,3)4/h6-10,13-15H,5,11,16-17H2,1-4H3,(H2,29,31,32,33)
Release date: 2021-05-05
Crystal structure of haspin (GSG2) in complex with macrocycle ODS2004070 (PDB entry 6Z5C)
Macromolecule: Serine/threonine-protein kinase haspin
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 357 residues
Sequence: MHHHHHHSSGVDLGTENLYFQSMGECSQKGPVPFSHCLPTEKLQRCEKIGEGVFGEVFQTIADHTPVAIKIIAIEGPDLVNGSHQKTFEEILPEIIISKELSLLSGEVCNRTEGFIGLNSVHCVQGSYPPLLLKAWDHYNSTKGSANDRPDFFKDDQLFIVLEFEFGGIDLEQMRTKLSSLATAKSILHQLTASLAVAEASLRFEHRDLHWGNVLLKKTSLKKLHYTLNGKSSTIPSCGLQVSIIDYTLSRLERDGIVVFCDVSMDEDLFTGDGDYQFDIYRLMKKENNNRWGEYHPYSNVLWLHYLTDKMLKQMTFKTKCNTPAMKQIKRKIQEFHRTMLNFSSATDLLCQHSLFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.75
R work: 0.158
R free: 0.1881
Average B factor: 17.664
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6
Crystallization temperature (K): 277.15
Crystal growth procedure: 60.0% MPD, 0.1M SPG pH 6.0
Matthews coefficient: 3.08
Solvent content (%): 60.08
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: 2020-06-03
Kinase domain of human EphB1, G703C mutant, covalently bound to a quinazoline-based inhibitor (PDB entry 5MJB)
Macromolecule: Ephrin type-B receptor 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 305 residues
Sequence: MGHHHHHHGSDPNEAVREFAKEIDVSFVKIEEVIGAGEFGEVYKGRLKLPGKREIYVAIKTLKAGYSEKQRRDFLSEASIMGQFDHRNIIRLEGVVTKSRPVMIITEFMENCALDSFLRQNDGQFTVIQLVGMLRGIAAGMKYLSEMNYVHRDLAARNILVNSNLVCKVSDFGLSRYLQDDTSDPTYTSSLGGKIPVRWTAPEAIAYRKFTSASDVWSYGIVMWEVMSFGERPYWDMSNQDVINAIEQDYRLPPPMDCPAALHQLMLDCWQKDRNSRPRFAEIVNTLDKMIRNPASLKTVATITA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.23
R work: 0.198
R free: 0.214
Average B factor: 59.29
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 18 % PEG3350, 0.1-0.2 M ammonium sulfate and 0.1 M PCTP (Sodium propionate, Sodium cacodylate trihydrate, Bis-Tris propane) buffer pH 6-9
Matthews coefficient: 3.42
Solvent content (%): 64.08
Ligand: 2-chloranyl-~{N}-[4-[(2-chloranyl-5-oxidanyl-phenyl)amino]quinazolin-7-yl]ethanamide (7O3)
Ligand formula: C16 H12 Cl2 N4 O2
Ligand molecular weight: 363.198
Ligand SMILES: c1cc2c(cc1NC(=O)CCl)ncnc2Nc3cc(ccc3Cl)O
Ligand InChI: InChI=1S/C16H12Cl2N4O2/c17-7-15(24)21-9-1-3-11-13(5-9)19-8-20-16(11)22-14-6-10(23)2-4-12(14)18/h1-6,8,23H,7H2,(H,21,24)(H,19,20,22)
Release date: 2017-05-17
PCSK9 in complex with compound 2 (PDB entry 6U3X)
Macromolecule: Proprotein convertase subtilisin/kexin type 9
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21
Sequence length: 707 residues
Sequence: QEDEDGDYEELVLALRSEEDGLAEAPEHGTTATFHRCAKDPWRLPGTYVVVLKEETHLSQSERTARRLQAQAARRGYLTKILHVFHGLLPGFLVKMSGDLLELALKLPHVDYIEEDSSVFAQSIPWNLERITPPRYRADEYQPPDGGSLVEVYLLDTSIQSDHREIEGRVMVTDFENVPEEDGTRFHRQASKCDSHGTHLAGVVSGRDAGVAKGASMRSLRVLNCQGKGTVSGTLIGLEFIRKSQLVQPVGPLVVLLPLAGGYSRVLNAACQRLARAGVVLVTAAGNFRDDACLYSPASAPEVITVGATNAQDQPVTLGTLGTNFGRCVDLFAPGEDIIGASSDCSTCFVSQSGTSQAAAHVAGIAAMMLSAEPELTLAELRQRLIHFSAKDVINEAWFPEDQRVLTPNLVAALPPSTHGAGWQLFCRTVWSAHSGPTRMATAIARCAPDEELLSCSSFSRSGKRRGERMEAQGGKLVCRAHNAFGGEGVYAIARCCLLPQANCSVHTAPPAEASMGTRVHCHQQGHVLTGCSSHWEVEDLGTHKPPVLRPRGQPNQCVGHREASIHASCCHAPGLECKVKEHGIPAPQEQVTVACEEGWTLTGCSALPGTSHVLGAYAVDNTCVVRSRDVSTTGSTSEEAVTAVAICCRSRHLAQASQELQKGNSADIQHSGGRSSLEGPRFEGKPIPNPLLGLDSTRTGHHHHHH
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.64
R work: 0.248
R free: 0.284
Average B factor: 47.5
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 303
Crystal growth procedure: 10-22% PEG 10K, 0.1M Tris, pH 8.5, 10% ethylene glycol, 1% BAM
Matthews coefficient: 2.88
Solvent content (%): 57.22
Ligand: 2-[(1R)-6,7-dimethoxy-1-methyl-1,2,3,4-tetrahydroisoquinolin-1-yl]-N-(1,3-thiazol-2-yl)acetamide (PVV)
Ligand formula: C17 H21 N3 O3 S
Ligand molecular weight: 347.432
Ligand SMILES: CC1(c2cc(c(cc2CCN1)OC)OC)CC(=O)Nc3nccs3
Ligand InChI: InChI=1S/C17H21N3O3S/c1-17(10-15(21)20-16-18-6-7-24-16)12-9-14(23-3)13(22-2)8-11(12)4-5-19-17/h6-9,19H,4-5,10H2,1-3H3,(H,18,20,21)/t17-/m1/s1
Release date: 2019-11-06
Cryogenic Human Hsp90a-NTD bound to EC144 (PDB entry 7S9H)
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): 1.45
R work: 0.1571
R free: 0.1841
Average B factor: 28.85
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 1.8 M Malic acid, pH 7
Matthews coefficient: 2.74
Solvent content (%): 55.03
Ligand: 5-{2-amino-4-chloro-7-[(4-methoxy-3,5-dimethylpyridin-2-yl)methyl]-7H-pyrrolo[2,3-d]pyrimidin-5-yl}-2-methylpent-4-yn-2
-ol (7PP)
Ligand formula: C21 H24 Cl N5 O2
Ligand molecular weight: 413.901
Ligand SMILES: Cc1cnc(c(c1OC)C)Cn2cc(c3c2nc(nc3Cl)N)C#CCC(C)(C)O
Ligand InChI: InChI=1S/C21H24ClN5O2/c1-12-9-24-15(13(2)17(12)29-5)11-27-10-14(7-6-8-21(3,4)28)16-18(22)25-20(23)26-19(16)27/h9-10,28H,8,11H2,1-5H3,(H2,23,25,26)
Release date: 2022-08-03
Structural basis for thymine glycosylase activity on T:O6-methylG mismatch by methyl-CpG binding domain protein 4: Implications for roles of Arg468 in mismatch recognition and catalysis (PDB entry 4OFE)
Macromolecule: Methyl-CpG-binding domain protein 4
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.2.2
Sequence length: 192 residues
Sequence: MGSSHHHHHHSSGLVPRGSHMASMTGGQQMGRGSEFMALSPPRRKAFKKWTPPRSPFNLVQETLFHDPWKLLIATIFLNKTSGKMAIPVLWKFLEKYPSAEVARTADWRDVSELLKPLGLYDLRAKTIVKFSDEYLTKQWKYPIELHGIGKYGNDSYRIFCVNEWKQVHPENHKLNKYHDWLWENHEKLSLS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.15
R work: 0.14223
R free: 0.20153
Average B factor: 28.328
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8
Crystallization temperature (K): 295
Crystal growth procedure: 15% PEG1500, 0.1M MES at pH of 6.5, 0.2M Na Acetate., VAPOR DIFFUSION, HANGING DROP, temperature 295K
Matthews coefficient: 2.03
Solvent content (%): 39.37
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: 2015-04-22
Carbonic Anhydrase IX like mutant in Complex with Steriod_Sulphamoyl inhibitor VK4 (PDB entry 8OLA)
Macromolecule: Carbonic anhydrase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 260 residues
Sequence: MSHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHSFQVTFDDSQDKAVLKGGPLDGTYRLLQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDVGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTEGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLAECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.4
R work: 0.14633
R free: 0.17014
Average B factor: 13.209
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.8
Crystallization temperature (K): 291
Crystal growth procedure: 1.6 M sodium citrate, 50 mM Tris-H2SO4
Matthews coefficient: 2.06
Solvent content (%): 40.41
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: 2024-04-10
Structure of the PGK1 from Biortus. (PDB entry 8YHP)
Macromolecule: Phosphoglycerate kinase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.2.3
Sequence length: 416 residues
Sequence: SLSNKLTLDKLDVKGKRVVMRVDFNVPMKNNQITNNQRIKAAVPSIKFCLDNGAKSVVLMSHLGRPDGVPMPDKYSLEPVAVELKSLLGKDVLFLKDCVGPEVEKACANPAAGSVILLENLRFHVEEEGKGKDASGNKVKAEPAKIEAFRASLSKLGDVYVNDAFGTAHRAHSSMVGVNLPQKAGGFLMKKELNYFAKALESPERPFLAILGGAKVADKIQLINNMLDKVNEMIIGGGMAFTFLKVLNNMEIGTSLFDEEGAKIVKDLMSKAEKNGVKITLPVDFVTADKFDENAKTGQATVASGIPAGWMGLDCGPESSKKYAEAVTRAKQIVWNGPVGVFEWEAFARGTKALMDEVVKATSRGCITIIGGGDTATCCAKWNTEDKVSHVSTGGGASLELLEGKVLPGVDALSNI
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.95
R work: 0.2337
R free: 0.2864
Average B factor: 37.359
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.2M Na/K PO4, 20% PEG 3,350
Matthews coefficient: 2.32
Solvent content (%): 46.92
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: 2024-03-13
Crystal structure of death effector domain of Caspase8 in Homo Sapiens (PDB entry 4ZBW)
Macromolecule: Caspase-8
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.22.61
Sequence length: 190 residues
Sequence: GSMDFSRNLYDIGEQLDSEDLASLKFLSLDYIPQRKQEPIKDALMLFQRLQEKRMLEESNLSFLKELLFRINRLDLLITYLNTRKEEMERELQTPGRAQISAYRVMLYQISEEVSRSELRSFKALLQEEDSKCKLDDDMNLLDIFIEMEKRVILGEGKLDILKRVCAQINKSLLKIINDYEEFSKERSSS
Oligomeric state: Homo 2-mer
Stoichiometry: A2
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.2
R work: 0.2041
R free: 0.251
Average B factor: 41.3
Crystallization method: EVAPORATION
Crystallization pH: 8.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.2M sodium chloride,  25% PEG3350
Matthews coefficient: 2.6
Solvent content (%): 54.26
Release date: 2015-07-01
The Crystal Structure of Human IL-18 in Complex With Human IL-18 Binding Protein (PDB entry 7AL7)
Macromolecule: Interleukin-18-binding protein
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 172 residues
Sequence: TGQCPALEVTWPEVEVPLNGTLSLSCVACSRFPNFSILYWLGNGSFIEHLPGRLWEGSTSRERGSTGTQLCKALVLEQLTPALHSTNFSCVLVDPEQVVQRHVVLAQLWAGLRATLPPTQEALPSSHSSPQQQGGTSDEVDGGSGGSGLNDIFEAQKIEWHEGRTKHHHHHH
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.801
R work: 0.2088
R free: 0.2315
Average B factor: 38.4789
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.2 M Calcium acetate hydrate, 0.1 M Sodium cacodylate trihydrate pH 6.5, 18% w/v Polyethylene glycol 8000
Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose (NAG)
Ligand formula: C8 H15 N O6
Ligand molecular weight: 221.208
Ligand SMILES: CC(=O)NC1C(C(C(OC1O)CO)O)O
Ligand InChI: InChI=1S/C8H15NO6/c1-3(11)9-5-7(13)6(12)4(2-10)15-8(5)14/h4-8,10,12-14H,2H2,1H3,(H,9,11)/t4-,5-,6-,7-,8-/m1/s1
Release date: 2022-04-20
The crystal structure of human carbonic anhydrase II in complex with 4-(4-phenylpiperidine-1-carbonyl)benzenesulfonamide. (PDB entry 6H2Z)
Macromolecule: Carbonic anhydrase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 262 residues
Sequence: MGMSHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHAFNVEFDDSQDKAVLKGGPLDGTYRLIQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDFGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTKGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLLECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.94
R work: 0.179
R free: 0.214
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 293
Crystal growth procedure: sodium citrate 1.3M, Tris-HCl 0.1 M, pH 8.5
Matthews coefficient: 2.05
Solvent content (%): 40.05
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: 2018-12-19
Discovery of VX-509 (Decernotinib): A Potent and Selective Janus kinase (JAK) 3 Inhibitor for the Treatment of Autoimmune Disease (PDB entry 4YTC)
Macromolecule: Tyrosine-protein kinase JAK2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 296 residues
Sequence: GSHNMTQFEERHLKFLQQLGKGNFGSVEMCRYDPLQDNTGEVVAVKKLQHSTEEHLRDFEREIEILKSLQHDNIVKYKGVCYSAGRRNLKLIMEYLPYGSLRDYLQKHKERIDHIKLLQYTSQICKGMEYLGTKRYIHRDLATRNILVENENRVKIGDFGLTKVLPQDKEYYKVKEPGESPIFWYAPESLTESKFSVASDVWSFGVVLYELFTYIEKSKSPPAEFMRMIGNDKQGQMIVFHLIELLKNNGRLPRPDGCPDEIYMIMTECWNNNVNQRPSFRDLALRVDQIRDNMAG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.16
R work: 0.1898
R free: 0.2128
Average B factor: 36.24
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 1.7-2.1M dl-malic acid, pH 7.0, 2mM DTT
Matthews coefficient: 2.35
Solvent content (%): 47.69
Ligand: N~3~-phenyl-1-[6-(phenylamino)pyrimidin-4-yl]-1H-1,2,4-triazole-3,5-diamine (4HW)
Ligand formula: C18 H16 N8
Ligand molecular weight: 344.373
Ligand SMILES: c1ccc(cc1)Nc2cc(ncn2)n3c(nc(n3)Nc4ccccc4)N
Ligand InChI: InChI=1S/C18H16N8/c19-17-24-18(23-14-9-5-2-6-10-14)25-26(17)16-11-15(20-12-21-16)22-13-7-3-1-4-8-13/h1-12H,(H,20,21,22)(H3,19,23,24,25)
Release date: 2015-08-12
5-methyl-6-(3'-trifluromethoxyphenylthio)[2,3-d]pyrimidine 2,4-diamine (PDB entry 5HVE)
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: 0.19886
R free: 0.22806
Average B factor: 24.047
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.9
Crystallization temperature (K): 283
Crystal growth procedure: 100 mM KPO4, ph 6.9, 60% sat AmSO4, 3% ETOH
Matthews coefficient: 2.53
Solvent content (%): 51.38
Ligand: 5-methyl-6-{[3-(trifluoromethoxy)phenyl]sulfanyl}thieno[2,3-d]pyrimidine-2,4-diamine (65Q)
Ligand formula: C14 H11 F3 N4 O S2
Ligand molecular weight: 372.389
Ligand SMILES: Cc1c2c(nc(nc2sc1Sc3cccc(c3)OC(F)(F)F)N)N
Ligand InChI: InChI=1S/C14H11F3N4OS2/c1-6-9-10(18)20-13(19)21-11(9)24-12(6)23-8-4-2-3-7(5-8)22-14(15,16)17/h2-5H,1H3,(H4,18,19,20,21)
Release date: 2017-02-01
Crystal Structure of Factor VIIa in complex with (2S)-2-hydroxy-N-[[3-[5-hydroxy-4-(1H-pyrrolo[3,2-c]pyridin-2-yl)pyrazol-1-yl]phenyl]methyl]propanamide (PDB entry 5PAE)
Macromolecule: Coagulation factor VII light chain
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.21
Sequence length: 64 residues
Sequence: LICVNENGGCEQYCSDHTGTKRSCRCHEGYSLLADGVSCTPTVEYPCGKIPILEKRNASKPQGR
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.45
R work: 0.1786
R free: 0.1875
Average B factor: 19.383
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 277
Crystal growth procedure: 16 mg/ml protein in 20mM Tris/HCl pH 8.4, 5 mM benzamidine, 0.1 M NaCl, 50 mM CaCl2 mixed 1+1 with 32-35% AMMONIUM SULPHATE, 2% PEG 4000, 0.1 M Bicine-NaOH pH 8.5, 15% glycerol
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: 2017-06-21
Crystal structure of human MTH1(G2K mutant) in complex with 8-oxo-dGTP at pH 7.7 (PDB entry 8I18)
Macromolecule: 7,8-dihydro-8-oxoguanine triphosphatase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.1.55
Sequence length: 156 residues
Sequence: MKASRLYTLVLVLQPQRVLLGMKKRGFGAGRWNGFGGKVQEGETIEDGARRELQEESGLTVDALHKVGQIVFEFVGEPELMDVHVFCTDSIQGTPVESDEMRPCWFQLDQIPFKDMWPDDSYWFPLLLQKKKFHGYFKFQGQDTILDYTLREVDTV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.1
R work: 0.1448
R free: 0.1693
Average B factor: 17.31
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: sodium citrate, tris, NaCl
Matthews coefficient: 1.91
Solvent content (%): 35.52
Ligand: 8-OXO-2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE (8DG)
Ligand formula: C10 H16 N5 O14 P3
Ligand molecular weight: 523.18
Ligand SMILES: C1C(C(OC1N2C3=C(C(=O)NC(=N3)N)NC2=O)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O
Ligand InChI: InChI=1S/C10H16N5O14P3/c11-9-13-7-6(8(17)14-9)12-10(18)15(7)5-1-3(16)4(27-5)2-26-31(22,23)29-32(24,25)28-30(19,20)21/h3-5,16H,1-2H2,(H,12,18)(H,22,23)(H,24,25)(H2,19,20,21)(H3,11,13,14,17)/t3-,4+,5+/m0/s1
Release date: 2023-03-22