satarupa22/MacromolecularLigandDB huggingface dataset:
Notum Fragment 634 (PDB entry 7BA1)
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): 1.93
R work: 0.2274
R free: 0.2639
Average B factor: 29.4323
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
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
PanDDA analysis group deposition of models with modelled events (e.g. bound ligands) -- Crystal Structure of NUDT7 in complex with RK4-350 (PDB entry 5QHE)
Macromolecule: Peroxisomal coenzyme A diphosphatase NUDT7
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.1
Sequence length: 196 residues
Sequence: SMLDDAKARLRKYDIGGKYSHLPYNKYSVLLPLVAKEGKLHLLFTVRSEKLRRAPGEVCFPGGKRDPTDMDDAATALREAQEEVGLRPHQVEVVCCLVPCLIDTDTLITPFVGLIDHNFQAQPNPAEVKDVFLVPLAYFLHPQVHDQHYVTRLGHRFINHIFEYTNPEDGVTYQIKGMTANLAVLVAFIILEKKPT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.74
R work: 0.1981
R free: 0.2189
Average B factor: 37.725
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M bis-tris pH 5.5 -- 0.1M ammonium acetate -- 5%(w/v) PEG10K
Matthews coefficient: 4.21
Solvent content (%): 70.77
Ligand: ACETATE ION (ACT)
Ligand formula: C2 H3 O2
Ligand molecular weight: 59.044
Ligand SMILES: CC(=O)[O-]
Ligand InChI: InChI=1S/C2H4O2/c1-2(3)4/h1H3,(H,3,4)/p-1
Release date: 2019-03-27
Renin in complex with (4S)-4-isopropyl-4-methyl-6-oxo-1-(3-(2-oxo-4-phenylpyrrolidin-1-yl)benzyl)tetrahydropyrimidin-2(1H)-iminium (PDB entry 4XX4)
Macromolecule: Renin
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.23.15
Sequence length: 340 residues
Sequence: LTLGNTTSSVILTNYMDTQYYGEIGIGTPPQTFKVVFDTGSSNVWVPSSKCSRLYTACVYHKLFDASDSSSYKHNGTELTLRYSTGTVSGFLSQDIITVGGITVTQMFGEVTEMPALPFMLAEFDGVVGMGFIEQAIGRVTPIFDNIISQGVLKEDVFSFYYNRDSENSQSLGGQIVLGGSDPQHYEGNFHYINLIKTGVWQIQMKGVSVGSSTLLCEDGCLALVDTGASYISGSTSSIEKLMEALGAKKRLFDYVVKCNEGPTLPDISFHLGGKEYTLTSADYVFQESYSSKKLCTLAIHAMDIPPPTGPTWALGATFIRKFYTEFDRRNNRIGFALAR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.4
R work: 0.2098
R free: 0.2293
Average B factor: 46.9442
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 295
Crystal growth procedure: 15% PEG3350, 625 mM NaCl and citrate buffer pH 4.6
Matthews coefficient: 3.25
Solvent content (%): 62.17
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: 2015-02-18
Crystal structure of the bromodomain of human Ep300 bound to the inhibitor XDM3d (PDB entry 5LPM)
Macromolecule: Histone acetyltransferase p300
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1.48
Sequence length: 116 residues
Sequence: SMIFKPEELRQALMPTLEALYRQDPESLPFRQPVDPQLLGIPDYFDIVKSPMDLSTIKRKLDTGQYQEPWQYVDDIWLMFNNAWLYNRKTSRVYKYCSKLSEVFEQEIDPVMQSLG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.5
R work: 0.1579
R free: 0.1871
Average B factor: 25.782
Crystallization method: EVAPORATION
Crystallization pH: 5.5
Crystallization temperature (K): 277
Crystal growth procedure: NaCl, PEG 3350
Matthews coefficient: 2.33
Solvent content (%): 47.14
Ligand: ~{N}-[(1~{S},2~{S})-7-chloranyl-2-oxidanyl-1,2,3,4-tetrahydronaphthalen-1-yl]-4-ethanoyl-3-ethyl-5-methyl-1~{H}-pyrrole
-2-carboxamide (71Y)
Ligand formula: C20 H23 Cl N2 O3
Ligand molecular weight: 374.861
Ligand SMILES: CCc1c(c([nH]c1C(=O)NC2c3cc(ccc3CCC2O)Cl)C)C(=O)C
Ligand InChI: InChI=1S/C20H23ClN2O3/c1-4-14-17(11(3)24)10(2)22-19(14)20(26)23-18-15-9-13(21)7-5-12(15)6-8-16(18)25/h5,7,9,16,18,22,25H,4,6,8H2,1-3H3,(H,23,26)/t16-,18-/m0/s1
Release date: 2017-08-16
LINKED KDM5A JMJ DOMAIN BOUND TO THE INHIBITOR 2-((2-chlorophenyl)(2-(4,4-difluoropiperidin-1-yl)ethoxy)methyl)-1H-pyrrolo[3,2-b]pyridine-7-carboxylic acid(Compound N41) (PDB entry 6BGW)
Macromolecule: Lysine-specific demethylase 5A, linked KDM5A JMJ domain
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11
Sequence length: 330 residues
Sequence: HNMAGVGPGGYAAEFVPPPECPVFEPSWEEFTDPLSFIGRIRPLAEKTGICKIRPPKDWQPPFACEVKSFRFTPRVQRLNELEAMTRVRPREAFGFEQAVREYTLQSFGEMADNFKSDYFNMPVHMVPTELVEKEFWRLVSSIEEDVIVEYGADISSKDFGSGFPVKDGRRKILPEEEEYALSGWNLNNMPVLEQSVLAHINVDISGMKVPWLYVGMCFSSFCWHIEDHWSYSINYLHWGEPKTWYGVPSHAAEQLEEVMRELAPELFESQPDLLHQLVTIMNPNVLMEHGVPVYRTNQCAGEFVVTFPRAYHSGFNQGYNFAEAVNFCT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.644
R work: 0.1884
R free: 0.2131
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 289
Crystal growth procedure: 1.2-1.35 M (NH4)2SO4, 0.1 M Tris-HCl (pH 8.6-9.2), 0-20% glycerol, 25 mM (Na/K) dibasic/monobasic phosphate
Matthews coefficient: 2.22
Solvent content (%): 44.56
Ligand: 2-{(S)-(2-chlorophenyl)[2-(4,4-difluoropiperidin-1-yl)ethoxy]methyl}-1H-pyrrolo[3,2-b]pyridine-7-carboxylic acid (DKS)
Ligand formula: C22 H22 Cl F2 N3 O3
Ligand molecular weight: 449.878
Ligand SMILES: c1ccc(c(c1)C(c2cc3c([nH]2)c(ccn3)C(=O)O)OCCN4CCC(CC4)(F)F)Cl
Ligand InChI: InChI=1S/C22H22ClF2N3O3/c23-16-4-2-1-3-14(16)20(31-12-11-28-9-6-22(24,25)7-10-28)18-13-17-19(27-18)15(21(29)30)5-8-26-17/h1-5,8,13,20,27H,6-7,9-12H2,(H,29,30)/t20-/m0/s1
Release date: 2018-03-28
FKBP12 in complex with PROTAC 6a2 (PDB entry 8PDF)
Macromolecule: Peptidyl-prolyl cis-trans isomerase FKBP1A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 5.2.1.8
Sequence length: 107 residues
Sequence: GVQVETISPGDGRTFPKRGQTVVVHYTGMLEDGKKFDSSRDRNKPFKFMLGKQEVIRGWEEGVAQMSVGQRAKLTISPDYAYGATGHPGIIPPHATLVFDVELLKLE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.2
R work: 0.1516
R free: 0.1756
Average B factor: 17.843
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 1.36 Na/K tartrate, 0.2M ammonium citrate, 0.1M MES pH 6.5
Matthews coefficient: 2.2
Solvent content (%): 44.09
Ligand: (2~{S},4~{R})-1-[(2~{S})-2-[2-[2-[2-[4-[(1~{S})-1-[(1~{S},5~{S},6~{R})-10-[3,5-bis(chloranyl)phenyl]sulfonyl-5-ethenyl-2-oxidanylidene-3,10-diazabicyclo[4.3.1]decan-3-yl]ethyl]-1,2,3-triazol-1-yl]ethoxy]ethoxy]ethanoylamino]-3,3-dimethyl-butanoyl]-~{N}-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide (Y5Q)
Ligand formula: C48 H61 Cl2 N9 O9 S2
Ligand molecular weight: 1043.089
Ligand SMILES: Cc1c(scn1)c2ccc(cc2)CNC(=O)C3CC(CN3C(=O)C(C(C)(C)C)NC(=O)COCCOCCn4cc(nn4)C(C)N5CC(C6CCCC(C5=O)N6S(=O)(=O)c7cc(cc(c7)Cl)Cl)C=C)O
Ligand InChI: InChI=1S/C48H61Cl2N9O9S2/c1-7-32-24-57(46(63)40-10-8-9-39(32)59(40)70(65,66)37-20-34(49)19-35(50)21-37)30(3)38-26-56(55-54-38)15-16-67-17-18-68-27-42(61)53-44(48(4,5)6)47(64)58-25-36(60)22-41(58)45(62)51-23-31-11-13-33(14-12-31)43-29(2)52-28-69-43/h7,11-14,19-21,26,28,30,32,36,39-41,44,60H,1,8-10,15-18,22-25,27H2,2-6H3,(H,51,62)(H,53,61)/t30-,32-,36+,39+,40-,41-,44+/m0/s1
Release date: 2023-11-15
Human Carbonic Anhydrase II in complex with fluorinated benzenesulfonamide (PDB entry 6RS5)
Macromolecule: Carbonic anhydrase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 265 residues
Sequence: GSPEFMSHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHAFNVEFDDSQDKAVLKGGPLDGTYRLIQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDFGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTKGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLLECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.07
R work: 0.118
R free: 0.1315
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.8
Crystallization temperature (K): 291
Crystal growth procedure: Ammonium sulfate 2.7 M, TRIS 0.1 M, saturated with para-Chloromercuribenzoic acid
Matthews coefficient: 2.07
Solvent content (%): 40.54
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: 2020-04-15
Ternary complex crystal structure of DNA polymerase Beta with C:A mismatch at the primer terminus (PDB entry 5J2C)
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): 2.1
R work: 0.2119
R free: 0.2655
Average B factor: 29.7909
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 16-18% PEG 3350, 50 mM Imidazole, 350 mM Sodium Acetate
Matthews coefficient: 2.31
Solvent content (%): 46.81
Ligand: 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE (DUP)
Ligand formula: C9 H16 N3 O13 P3
Ligand molecular weight: 467.157
Ligand SMILES: C1C(C(OC1N2C=CC(=O)NC2=O)COP(=O)(NP(=O)(O)OP(=O)(O)O)O)O
Ligand InChI: InChI=1S/C9H16N3O13P3/c13-5-3-8(12-2-1-7(14)10-9(12)15)24-6(5)4-23-26(16,17)11-27(18,19)25-28(20,21)22/h1-2,5-6,8,13H,3-4H2,(H,10,14,15)(H2,20,21,22)(H3,11,16,17,18,19)/t5-,6+,8+/m0/s1
Release date: 2016-10-26
Crystal Structure of CK2alpha with Compound 7 bound (PDB entry 5MMF)
Macromolecule: Casein kinase II subunit alpha
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 352 residues
Sequence: GSMDIEFDDDADDDGSGSGSGSGSSGPVPSRARVYTDVNTHRPSEYWDYESHVVEWGNQDDYQLVRKLGRGKYSEVFEAINITNNEKVVVKILKPVKKKKIKREIKILENLRGGPNIITLADIVKDPVSRTPALVFEHVNNTDFKQLYQTLTDYDIRFYMYEILKALDYCHSMGIMHRDVKPHNVMIDHEHRKLRLIDWGLAEFYHPGQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRKEPFFHGHDNYDQLVRIAKVLGTEDLYDYIDKYNIELDPRFNDILGRHSRKRWERFVHSENQHLVSPEALDFLDKLLRYDHQSRLTAREAMEHPYFYTVVK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.99
R work: 0.2021
R free: 0.2185
Average B factor: 51.09
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 298
Crystal growth procedure: 112.5mM Mes pH 6.5, 35% glycerol ethoxylate, 180 mM ammonium acetate
Matthews coefficient: 2.23
Solvent content (%): 44.82
Ligand: (3-chloranyl-4-phenyl-phenyl)methyl-propyl-azanium (JMB)
Ligand formula: C16 H19 Cl N
Ligand molecular weight: 260.782
Ligand SMILES: CCC[NH2+]Cc1ccc(c(c1)Cl)c2ccccc2
Ligand InChI: InChI=1S/C16H18ClN/c1-2-10-18-12-13-8-9-15(16(17)11-13)14-6-4-3-5-7-14/h3-9,11,18H,2,10,12H2,1H3/p+1
Release date: 2017-05-24
Structure based optimization of JAK1-ATP binding pocket Inhibitors in the aminopyrazole class (PDB entry 6RSD)
Macromolecule: Tyrosine-protein kinase JAK1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 302 residues
Sequence: GDIVSEKKPATEVDPTHFEKRFLKRIRDLGEGHFGKVELCRYDPEGDNTGEQVAVKSLKPESGGNHIADLKKEIEILRNLYHENIVKYKGICTEDGGNGIKLIMEFLPSGSLKEYLPKNKNKINLKQQLKYAVQICKGMDYLGSRQYVHRDLAARNVLVESEHQVKIGDFGLTKAIETDKEYYTVKDDRDSPVFWYAPECLMQSKFYIASDVWSFGVTLHELLTYCDSDSSPMALFLKMIGPTHGQMTVTRLVNTLKEGKRLPCPPNCPDEVYQLMRKCWEFQPSNRTSFQNLIEGFEALLK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.76
R work: 0.1998
R free: 0.238
Average B factor: 25.615
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 5.6
Crystallization temperature (K): 277
Crystal growth procedure: 0.1M MES, 25-35% PEG6000
Matthews coefficient: 2.53
Solvent content (%): 51.46
Ligand: 1-[4-(cyanomethyl)-1-[(3-oxidanyl-4-phenyl-phenyl)methyl]piperidin-4-yl]-3-(cyclopropylcarbonylamino)pyrazole-4-carboxamide (KH8)
Ligand formula: C28 H30 N6 O3
Ligand molecular weight: 498.576
Ligand SMILES: c1ccc(cc1)c2ccc(cc2O)CN3CCC(CC3)(CC#N)n4cc(c(n4)NC(=O)C5CC5)C(=O)N
Ligand InChI: InChI=1S/C28H30N6O3/c29-13-10-28(34-18-23(25(30)36)26(32-34)31-27(37)21-7-8-21)11-14-33(15-12-28)17-19-6-9-22(24(35)16-19)20-4-2-1-3-5-20/h1-6,9,16,18,21,35H,7-8,10-12,14-15,17H2,(H2,30,36)(H,31,32,37)
Release date: 2020-07-08
Irak4 kinase - compound 1 co-structure (PDB entry 5T1S)
Macromolecule: Interleukin-1 receptor-associated kinase 4
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 301 residues
Sequence: VSDTRFHSFSFYELKNVTNNFDERPISVGGNKMGEGGFGVVYKGYVNNTTVAVKKLAAMVDITTEELKQQFDQEIKVMAKCQHENLVELLGFSSDGDDLCLVYVYMPNGSLLDRLSCLDGTPPLSWHMRCKIAQGAANGINFLHENHHIHRDIKSANILLDEAFTAKISDFGLARASEKFAQTVMTSRIVGTTAYMAPEALRGEITPKSDIYSFGVVLLEIITGLPAVDEHREPQLLLDIKEEIEDEEKTIEDYIDKKMNDADSTSVEAMYSVASQCLHEKKNKRPDIKKVQQLLQEMTAS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.3
R work: 0.2067
R free: 0.2226
Average B factor: 65.42
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.4
Crystallization temperature (K): 289
Crystal growth procedure: .80 to 2.0 M Sodium Malonate 0.2 M Sodium Acetate 25 mM Hexamminecobalt(III)chloride 0.05%w/v Pluronic-F-68
Matthews coefficient: 2.81
Solvent content (%): 56.22
Ligand: 5-[3-(3,5-dimethylphenyl)-4-[4-(methylamino)butyl]quinolin-6-yl]pyridin-3-ol (76Q)
Ligand formula: C27 H29 N3 O
Ligand molecular weight: 411.539
Ligand SMILES: Cc1cc(cc(c1)c2cnc3ccc(cc3c2CCCCNC)c4cc(cnc4)O)C
Ligand InChI: InChI=1S/C27H29N3O/c1-18-10-19(2)12-21(11-18)26-17-30-27-8-7-20(22-13-23(31)16-29-15-22)14-25(27)24(26)6-4-5-9-28-3/h7-8,10-17,28,31H,4-6,9H2,1-3H3
Release date: 2017-05-03
The crystal structure of Lp-PLA2 in complex with a novel inhibitor (PDB entry 5YEA)
Macromolecule: Platelet-activating factor acetylhydrolase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.1.47
Sequence length: 388 residues
Sequence: GPLGSAAASFGQTKIPRGNGPYSVGCTDLMFDHTNKGTFLRLYYPSQDNDRLDTLWIPNKEYFWGLSKFLGTHWLMGNILRLLFGSMTTPANWNSPLRPGEKYPLVVFSHGLGAFRTLYSAIGIDLASHGFIVAAVEHRDRSASATYYFKDQSAAEIGDKSWLYLRTLKQEEETHIRNEQVRQRAKECSQALSLILDIDHGKPVKNALDLKFDMEQLKDSIDREKIAVIGHSFGGATVIQTLSEDQRFRCGIALDAWMFPLGDEVYSRIPQPLFFINSEYFQYPANIIKMKKCYSPDKERKMITIRGSVHQNFADFTFATGKIIGHMLKLKGDIDSNVAIDLSNKASLAFLQKHLGLHKDFDQWDCLIEGDDENLIPGTNINTTNQHI
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.805
R work: 0.1769
R free: 0.2111
Average B factor: 21.0212
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M MOPS pH 6.6, 0.4M Li2SO4, 27% (w/v) (NH4)2SO4, 1M Na-Ac, 1.4% 1,4-butanediol
Matthews coefficient: 2.42
Solvent content (%): 49.23
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: 2018-07-25
CRYSTAL STRUCTURE OF HUMAN FKBP51 FK1 DOMAIN A19T MUTANT IN COMPLEX WITH SAFit2 (PDB entry 6TXX)
Macromolecule: Peptidyl-prolyl cis-trans isomerase FKBP5
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 5.2.1.8
Sequence length: 128 residues
Sequence: GAPATVTEQGEDITSKKDRGVLKIVKRVGNGEETPMIGDKVYVHYKGKLSNGKKFDSSHDRNEPFVFSLGKGQVIKAWDIGVATMKKGEICHLLCKPEYAYGSAGSLPKIPSNATLFFEIELLDFKGE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.1
R work: 0.1897
R free: 0.2479
Average B factor: 29.62
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293.15
Crystal growth procedure: 28-43% PEG3350, 0.2M NH4OAc, 0.1M HEPES
Matthews coefficient: 2.24
Solvent content (%): 45.16
Ligand: (1R)-3-(3,4-dimethoxyphenyl)-1-{3-[2-(morpholin-4-yl)ethoxy]phenyl}propyl (2S)-1-[(2S)-2-[(1S)-cyclohex-2-en-1-yl]-2-(3,4,5-trimethoxyphenyl)acetyl]piperidine-2-carboxylate (37K)
Ligand formula: C46 H60 N2 O10
Ligand molecular weight: 800.976
Ligand SMILES: COc1ccc(cc1OC)CCC(c2cccc(c2)OCCN3CCOCC3)OC(=O)C4CCCCN4C(=O)C(c5cc(c(c(c5)OC)OC)OC)C6CCCC=C6
Ligand InChI: InChI=1S/C46H60N2O10/c1-51-39-20-18-32(28-40(39)52-2)17-19-38(34-14-11-15-36(29-34)57-27-24-47-22-25-56-26-23-47)58-46(50)37-16-9-10-21-48(37)45(49)43(33-12-7-6-8-13-33)35-30-41(53-3)44(55-5)42(31-35)54-4/h7,11-12,14-15,18,20,28-31,33,37-38,43H,6,8-10,13,16-17,19,21-27H2,1-5H3/t33-,37+,38-,43+/m1/s1
Release date: 2020-05-27
PanDDA analysis group deposition -- Crystal Structure of JMJD1B in complex with FM001677a (PDB entry 5RB4)
Macromolecule: Lysine-specific demethylase 3B
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11
Sequence length: 372 residues
Sequence: MHHHHHHSSGVDLGTENLYFQSMTSHSWLCDGRLLCLHDPSNKNNWKIFRECWKQGQPVLVSGVHKKLKSELWKPEAFSQEFGDQDVDLVNCRNCAIISDVKVRDFWDGFEIICKRLRSEDGQPMVLKLKDWPPGEDFRDMMPTRFEDLMENLPLPEYTKRDGRLNLASRLPSYFVRPDLGPKMYNAYGLITAEDRRVGTTNLHLDVSDAVNVMVYVGIPIGEGAHDEEVLKTIDEGDADEVTKERIHDHKEKPGALWHIYAAKDAEKIRELLRKVGEEQGQENPPDHDPIHDQSWYLDQTLRKRLYEEYGVQGWAIVQFLGDAVFIPAGAPHQVHNLYSCIKVAEDFVSPEHVKHCFRLTQEFRHLSNTHT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.55
R work: 0.1854
R free: 0.2092
Average B factor: 32.391
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.1M bis-tris pH 5.5 21% PEG3350  0.3M magnesium chloride
Matthews coefficient: 2.8
Solvent content (%): 56.15
Ligand: 2-[4-(3-chlorophenyl)piperazin-1-ium-1-yl]ethanenitrile (A6Z)
Ligand formula: C12 H15 Cl N3
Ligand molecular weight: 236.721
Ligand SMILES: c1cc(cc(c1)Cl)N2CC[NH+](CC2)CC#N
Ligand InChI: InChI=1S/C12H14ClN3/c13-11-2-1-3-12(10-11)16-8-6-15(5-4-14)7-9-16/h1-3,10H,5-9H2/p+1
Release date: 2020-04-22
Post-catalytic complex of human Polymerase Mu (W434H) mutant with incoming UTP (PDB entry 5VZH)
Macromolecule: DNA-directed DNA/RNA polymerase mu
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 354 residues
Sequence: GSAAASPAWMPAYACQRPTPLTHHNTGLSEALEILAEAAGFEGSEGRLLTFCRAASVLKALPSPVTTLSQLQGLPHFGEHSSRVVQELLEHGVCEEVERVRRSERYQTMKLFTQIFGVGVKTADRWYREGLRTLDDLREQPQKLTQQQKAGLQHHQDLSTPVLRSDVDALQQVVEEAVGQALPGATVTLTGGFRRGKLQGHDVDFLITHPKEGQEAGLLPRVMCRLQDQGLILYHQHQHSCCESPTRLAQQSHMDAFERSFCIFRLPQPGSWKAVRVDLVVAPVSQFPFALLGHTGSKLFQRELRRFSRKEKGLWLNSHGLFDPEQKTFFQAASEEDIFRHLGLEYLPPEQRNA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.95
R work: 0.1789
R free: 0.2108
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: 90mM HEPES pH 7.5, 18% PEG4K
Matthews coefficient: 2.81
Solvent content (%): 56.3
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: 2017-07-05
Crystal structure of human CD38 in complex with hydrolysed compound JMS713 (PDB entry 4TMF)
Macromolecule: ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.2.2.6
Sequence length: 257 residues
Sequence: EFWRQTWSGPGTTKRFPETVLARCVKYTEIHPEMRHVDCQSVWDAFKGAFISKHPCDITEEDYQPLMKLGTQTVPCNKILLWSRIKDLAHQFTQVQRDMFTLEDTLLGYLADDLTWCGEFDTSKINYQSCPDWRKDCSNNPVSVFWKTVSRRFAEAACDVVHVMLDGSRSKIFDKDSTFGSVEVHNLQPEKVQTLEAWVIHGGREDSRDLCQDPTIKELESIISKRNIQFSCKNIYRPDKFLQCVKNPEDSSCTSEI
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.05
R work: 0.198
R free: 0.227
Average B factor: 67.282
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 4
Crystallization temperature (K): 298
Crystal growth procedure: 0.1M sodium acetate pH4.0, 0.2M ammonium acetate, 3% isopropanol, 15% PEG10000
Matthews coefficient: 2.26
Solvent content (%): 45.67
Ligand: 5-O-[(R)-{[(S)-[4-(8-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)butoxy](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-alpha-D-
 ribofuranose (JS2)
Ligand formula: C14 H23 N5 O12 P2
Ligand molecular weight: 515.306
Ligand SMILES: C1=Nc2c(nc(n2CCCCOP(=O)(O)OP(=O)(O)OCC3C(C(C(O3)O)O)O)N)C(=O)N1
Ligand InChI: InChI=1S/C14H23N5O12P2/c15-14-18-8-11(16-6-17-12(8)22)19(14)3-1-2-4-28-32(24,25)31-33(26,27)29-5-7-9(20)10(21)13(23)30-7/h6-7,9-10,13,20-21,23H,1-5H2,(H2,15,18)(H,24,25)(H,26,27)(H,16,17,22)/t7-,9-,10-,13+/m1/s1
Release date: 2015-05-13
Crystal structure of death-associated protein kinase 1 with a crucial phosphomimicking mutation (PDB entry 4TL0)
Macromolecule: Death-associated protein kinase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 336 residues
Sequence: GPMTVFRQENVDDYYDTGEELGSGQFAVVKKCREKSTGLQYAAKFIKKRRTKSSRRGVSREDIEREVSILKEIQHPNVITLHEVYENKTDVILILELVAGGELFDFLAEKESLTEEEATEFLKQILNGVYYLHSLQIAHFDLKPENIMLLDRNVPKPRIKIIDFGLAHKIDFGNEFKNIFGTPEFVAPEIVNYEPLGLEADMWSIGVITYILLSGASPFLGDTKQETLANVSAVNYEFEDEYFSNTSALAKDFIRRLLVKDPKKRMTIQDSLQHPWIKPKDTQQALSRKAEAVNMEKFKKFAARKKWKQSVRLISLCQRLSRSFLSRSNMSVARSD
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.7
R work: 0.1678
R free: 0.2178
Average B factor: 45.71
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8
Crystallization temperature (K): 292
Crystal growth procedure: 0.15 ammonium sulfate, 0.1M TRIS, pH 8.0, 15%(w/v) PEG 4000
Matthews coefficient: 2.79
Solvent content (%): 55.91
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: 2015-06-10
Crystal structure of hMTH1 D120N in the presence of acetate (PDB entry 6GLT)
Macromolecule: 7,8-dihydro-8-oxoguanine triphosphatase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.1.55
Sequence length: 182 residues
Sequence: MKHHHHHHPMSDYDIPTTENLYFQGAMGASRLYTLVLVLQPQRVLLGMKKRGFGAGRWNGFGGKVQEGETIEDGARRELQEESGLTVDALHKVGQIVFEFVGEPELMDVHVFCTDSIQGTPVESDEMRPCWFQLDQIPFKDMWPDNSYWFPLLLQKKKFHGYFKFQGQDTILDYTLREVDTV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.596
R work: 0.1817
R free: 0.213
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 4.5
Crystallization temperature (K): 293
Crystal growth procedure: 23-27% PEG3350, 0.2 M LiSO4, 0.1 M sodium acetate pH 4.5
Matthews coefficient: 1.71
Solvent content (%): 28.18
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: 2019-02-20