satarupa22/MacromolecularLigandDB huggingface dataset:
Crystal structure of SHP2_SH2-CagA EPIYA_D peptide complex (PDB entry 5X94)
Macromolecule: Tyrosine-protein phosphatase non-receptor type 11
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 220 residues
Sequence: MTSRRWFHPNITGVEAENLLLTRGVDGSFLARPSKSNPGDFTLSVRRNGAVTHIKIQNTGDYYDLYGGEKFATLAELVQYYMEHHGQLKEKNGDVIELKYPLNCADPTSERWFHGHLSGKEAEKLLTEKGKHGSFLVRESQSHPGDFVLSVRTGDDKGESNDGKSKVTHVMIRCQELKYDVGGGERFDSLTDLVEHYKKNPMVETLGTVLQLKQPLNTTR
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.6
R work: 0.1569
R free: 0.2459
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 31% PEG 4000, 0.1 M Tris-HCl
Matthews coefficient: 2.17
Solvent content (%): 43.29
Release date: 2017-09-13
Zn-Carbonic Anhydrase II complexed with 3NPA after UV at 120 K (PDB entry 7Y2E)
Macromolecule: Carbonic anhydrase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 260 residues
Sequence: MSHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHAFNVEFDDSQDKAVLKGGPLDGTYRLIQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDFGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTKGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLLECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.2
R work: 0.12465
R free: 0.15466
Average B factor: 13.796
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.8
Crystallization temperature (K): 293
Crystal growth procedure: 1.3 M sodium citrate, 50 mM Tris-HCl
Matthews coefficient: 2.09
Solvent content (%): 41.05
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: 2023-12-20
Crystal structure of uPA_H99Y in complex with 3-azanyl-5-(azepan-1-yl)-N-carbamimidoyl-6-(furan-2-yl)pyrazine-2-carboxamide (PDB entry 6JYQ)
Macromolecule: Urokinase-type plasminogen activator
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.73
Sequence length: 246 residues
Sequence: IIGGEFTTIENQPWFAAIYRRHRGGSVTYVCGGSLISPCWVISATHCFIDYPKKEDYIVYLGRSRLNSNTQGEMKFEVENLILHKDYSADTLAYHNDIALLKIRSKEGRCAQPSRTIQTIALPSMYNDPQFGTSCEITGFGKEQSTDYLYPEQLKMTVVKLISHRECQQPHYYGSEVTTKMLCAADPQWKTDSCQGDSGGPLVCSLQGRMTLTGIVSWGRGCALKDKPGVYTRVSHFLPWIRSHTK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.75
R work: 0.227
R free: 0.263
Average B factor: 36.04
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 298
Crystal growth procedure: 0.05M sodium citrate at pH 4.6, 1.95M (NH4)2SO4, 0.03% NaN3, 5% PEG 400
Matthews coefficient: 2.14
Solvent content (%): 42.55
Ligand: 3-azanyl-5-(azepan-1-yl)-N-carbamimidoyl-6-(furan-2-yl)pyrazine-2-carboxamide (EAU)
Ligand formula: C16 H21 N7 O2
Ligand molecular weight: 343.384
Ligand SMILES: c1cc(oc1)c2c(nc(c(n2)C(=O)NC(=N)N)N)N3CCCCCC3
Ligand InChI: InChI=1S/C16H21N7O2/c17-13-12(15(24)22-16(18)19)20-11(10-6-5-9-25-10)14(21-13)23-7-3-1-2-4-8-23/h5-6,9H,1-4,7-8H2,(H2,17,21)(H4,18,19,22,24)
Release date: 2020-05-13
Specific covalent inhibitor (5) of ERK2 (PDB entry 8AO4)
Macromolecule: Mitogen-activated protein kinase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.24
Sequence length: 368 residues
Sequence: MAHHHHHHMAAAAAAGAGPEMVRGQVFDVGPRYTNLSYIGEGAYGMVCSAYDNVNKVRVAIKKISPFEHQTYCQRTLREIKILLRFRHENIIGINDIIRAPTIEQMKDVYIVQDLMETDLYKLLKTQHLSNDHICYFLYQILRGLKYIHSANVLHRDLKPSNLLLNTTCDLKICDFGLARVADPDHDHTGFLTEYVATRWYRAPEIMLNSKGYTKSIDIWSVGCILAEMLSNRPIFPGKHYLDQLNHILGILGSPSQEDLNCIINLKARNYLLSLPHKNKVPWNRLFPNADSKALDLLDKMLTFNPHKRIEVEQALAHPYLEQYYDPSDEPIAEAPFKFDMELDDLPKEKLKELIFEETARFQPGYRS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.825
R work: 0.1732
R free: 0.2219
Average B factor: 27.831
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.2
Crystallization temperature (K): 293
Crystal growth procedure: 0.25M (NH4)2SO4
33% MPEG 2000
0.02M Mercaptoethanol
0.1M pH=7.2 HEPES/NaOH
Matthews coefficient: 2.3
Solvent content (%): 46.48
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: 2022-09-28
Crystal structure of EGFR kinase domain in complex with compound 78 (PDB entry 6JZ0)
Macromolecule: Epidermal growth factor receptor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 326 residues
Sequence: GEAPNQALLRILKETEFKKIKVLGSGAFGTVYKGLWIPEGEKVKIPVAIKELREATSPKANKEILDEAYVMASVDNPHVCRLLGICLTSTVQLITQLMPFGCLLDYVREHKDNIGSQYLLNWCVQIAKGMNYLEDRRLVHRDLAARNVLVKTPQHVKITDFGLAKLLGAEEKEYHAEGGKVPIKWMALESILHRIYTHQSDVWSYGVTVWELMTFGSKPYDGIPASEISSILEKGERLPQPPICTIDVYMIMVKCWMIDADSRPKFRELIIEFSKMARDPQRYLVIQGDERMHLPSPTDSNFYRALMDEEDMDDVVDADEYLIPQQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.86
R work: 0.1905
R free: 0.2476
Average B factor: 65.3579
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7
Crystallization temperature (K): 291
Crystal growth procedure: 1.0M Ammonium citrate tribase, 0.1M Bis-Tris propane, pH7.0
Matthews coefficient: 3.4
Solvent content (%): 63.8
Ligand: E-4-(dimethylamino)-N-[3-[4-[[(1S)-2-oxidanyl-1-phenyl-ethyl]amino]-6-phenyl-furo[2,3-d]pyrimidin-5-yl]phenyl]but-2-enamide (CKO)
Ligand formula: C32 H31 N5 O3
Ligand molecular weight: 533.62
Ligand SMILES: CN(C)CC=CC(=O)Nc1cccc(c1)c2c3c(ncnc3oc2c4ccccc4)NC(CO)c5ccccc5
Ligand InChI: InChI=1S/C32H31N5O3/c1-37(2)18-10-17-27(39)35-25-16-9-15-24(19-25)28-29-31(36-26(20-38)22-11-5-3-6-12-22)33-21-34-32(29)40-30(28)23-13-7-4-8-14-23/h3-17,19,21,26,38H,18,20H2,1-2H3,(H,35,39)(H,33,34,36)/b17-10+/t26-/m1/s1
Release date: 2019-12-04
Crystal Structure of human ST6GALNAC2 in complex with CMP (PDB entry 6APL)
Macromolecule: Alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.4.99
Sequence length: 374 residues
Sequence: MGLPRGSFFWLLLLLTAACSGLLFALYFSAVQRYPGPAAGARDTTSFEAFFQSKASNSWTGKGQACRHLLHLAIQRHPHFRGLFNLSIPVLLWGDLFTPALWDRLSQHKAPYGWRGLSHQVIASTLSLLNGSESAKLFAPPRDTPPKCIRCAVVGNGGILNGSRQGPNIDAHDYVFRLNGAVIKGFERDVGTKTSFYGFTVNTMKNSLVSYWNLGFTSVPQGQDLQYIFIPSDIRDYVMLRSAILGVPVPEGLDKGDRPHAYFGPEASASKFKLLHPDFISYLTERFLKSKLINTHFGDLYMPSTGALMLLTALHTCDQVSAYGFITSNYWKFSDHYFERKMKPLIFYANHDLSLEAALWRDLHKAGILQLYQR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.35
R work: 0.1961
R free: 0.2357
Crystallization method: MICROBATCH
Crystallization pH: 4.2
Crystallization temperature (K): 277
Crystal growth procedure: 0.1M Sodium Citrate (pH 4.2), 0.1M Ammonium Sulfate, and 24% (w/v) PEG 20000
Matthews coefficient: 2.5
Solvent content (%): 52.47
Ligand: CYTIDINE-5'-MONOPHOSPHATE (C5P)
Ligand formula: C9 H14 N3 O8 P
Ligand molecular weight: 323.197
Ligand SMILES: C1=CN(C(=O)N=C1N)C2C(C(C(O2)COP(=O)(O)O)O)O
Ligand InChI: InChI=1S/C9H14N3O8P/c10-5-1-2-12(9(15)11-5)8-7(14)6(13)4(20-8)3-19-21(16,17)18/h1-2,4,6-8,13-14H,3H2,(H2,10,11,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1
Release date: 2017-12-20
Human p70s6k1 with ruthenium-based inhibitor FL772 (PDB entry 4RLP)
Macromolecule: p70S6K1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 288 residues
Sequence: KIRPECFELLRVLGKGGYGKVFQVRKVTGANTGKIFAMKVLKKAMIVRNAKDTAHTKAERNILEEVKHPFIVDLIYAFQTGGKLYLILEYLSGGELFMQLEREGIFMEDTACFYLAEISMALGHLHQKGIIYRDLKPENIMLNHQGHVKLTDFGLCKESIHDGTVTHTFCGTIEYMAPEILMRSGHNRAVDWWSLGALMYDMLTGAPPFTGENRKKTIDKILKCKLNLPPYLTQEARDLLKKLLKRNAASRLGAGPGDAGEVQAHPFFRHINWEELLARKVEPPFKPL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.79
R work: 0.2063
R free: 0.2301
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 288
Crystal growth procedure: 0.1M Tris, 3.5M Sodium Formate, with staurosporine, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Matthews coefficient: 3.32
Solvent content (%): 62.95
Ligand: [(amino-kappaN)methanethiolato](3-fluoro-9-methoxypyrido[2,3-a]pyrrolo[3,4-c]carbazole-5,7(6H,12H)-dionato-kappa~2~N,N')(N-methyl-1,4,7-trithiecan-9-amine-kappa~3~S~1~,S~4~,S~7~)ruthenium (72B)
Ligand formula: C27 H29 F N5 O3 Ru S4
Ligand molecular weight: 719.879
Ligand SMILES: CNC1C[S]2CC[S]3[Ru]24(n5c6ccc(cc6c7c5c8c(c9c7C(=O)NC9=O)C=C(C=[N]48)F)OC)([S](C1)CC3)[N]CS
Ligand InChI: InChI=1S/C18H10FN3O3.C8H17NS3.CH4NS.Ru/c1-25-8-2-3-11-9(5-8)12-14-13(17(23)22-18(14)24)10-4-7(19)6-20-15(10)16(12)21-11;1-9-8-6-11-4-2-10-3-5-12-7-8;2-1-3;/h2-6H,1H3,(H2,20,21,22,23,24);8-9H,2-7H2,1H3;2-3H,1H2;/q;;-1;+2/p-1
Release date: 2015-01-21
Crystal structure of TYK2 kinase with compound 13 (PDB entry 6VNS)
Macromolecule: Non-receptor tyrosine-protein kinase TYK2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 318 residues
Sequence: MAHHHHHHHHHHGALEVLFQGPGDPTVFHKRYLKKIRDLGEGHFGKVSLYCYDPTNDGTGEMVAVKALKADAGPQHRSGWKQEIDILRTLYHEHIIKYKGCCEDAGAASLQLVMEYVPLGSLRDYLPRHSIGLAQLLLFAQQICEGMAYLHSQHYIHRDLAARNVLLDNDRLVKIGDFGLAKAVPEGHEYYRVREDGDSPVFWYAPECLKEYKFYYASDVWSFGVTLYELLTHCDSSQSPPTKFLELIGIAQGQMTVLRLTELLERGERLPRPDKCPAEVYHLMKNCWETEASFRPTFENLIPILKTVHEKYQGQAPS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.09
R work: 0.1853
R free: 0.2313
Average B factor: 38.88
Crystallization method: EVAPORATION
Crystallization pH: 8
Crystallization temperature (K): 298
Crystal growth procedure: 0.1 M bis-tris pH 5.5, 0.25 M NaCl, 10 mM TCEP, 27-33% PEG-3350
Matthews coefficient: 1.87
Solvent content (%): 34.26
Ligand: (1R,2R)-2-cyano-N-[(1S,5R)-3-(5-fluoro-2-{[1-(2-hydroxyethyl)-1H-pyrazol-4-yl]amino}pyrimidin-4-yl)-3-azabicyclo[3.1.0]hexan-1-yl]cyclopropane-1-carboxamide (R5D)
Ligand formula: C19 H21 F N8 O2
Ligand molecular weight: 412.421
Ligand SMILES: c1c(cn(n1)CCO)Nc2ncc(c(n2)N3CC4CC4(C3)NC(=O)C5CC5C#N)F
Ligand InChI: InChI=1S/C19H21FN8O2/c20-15-7-22-18(24-13-6-23-28(9-13)1-2-29)25-16(15)27-8-12-4-19(12,10-27)26-17(30)14-3-11(14)5-21/h6-7,9,11-12,14,29H,1-4,8,10H2,(H,26,30)(H,22,24,25)/t11-,12+,14+,19+/m0/s1
Release date: 2020-04-08
Structure of Human alpha-Phosphomannomutase 1 containing mutations R180T and R183I (PDB entry 6CFT)
Macromolecule: Phosphomannomutase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 5.4.2.8
Sequence length: 262 residues
Sequence: MAVTAQAARRKERVLCLFDVDGTLTPARQKIDPEVAAFLQKLRSRVQIGVVGGSDYCKIAEQLGDGDEVIEKFDYVFAENGTVQYKHGRLLSKQTIQNHLGEELLQDLINFCLSYMALLRLPKKRGTFIEFRNGMLNISPIGRSCTLEERIEFSELDKKEKIREKFVEALKTEFAGKGLTFSIGGMISFDVFPEGWDKRYCLDSLDQDSFDTIHFFGNETSPGGNDFEIFADPRTVGHSVVSPQDTVQRCREIFFPETAHEA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.43
R work: 0.2085
R free: 0.2757
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 290
Crystal growth procedure: 20% polyethylene glycol 3350, 0.15 M DL-malate, pH 7.0, 50 mM MgCl2, 0.05 M L-lysine and 8 mM  beta-mercaptoethanol
Matthews coefficient: 2.38
Solvent content (%): 48.34
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
Pre-catalytic ternary complex of DNA Polymerase Lambda with bound 1-nt gapped SSB substrate and incoming dUMPNPP (PDB entry 7M07)
Macromolecule: DNA polymerase lambda
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 346 residues
Sequence: GSAAAVLDKWVCAQPSSQKATNHNLHITEKLEVLAKAYSVQGDKWRALGYAKAINALKSFHKPVTSYQEACSIPGIGKRMAEKIIEILESGHLRKLDHISESVPVLELFSNIWGAGTKTAQMWYQQGFRSLEDIRSQASLTTQQAIGLKHYSDFLERMPREEATEIEQTVQKAAQAFNSGLLCVACGSYRRGKATCGDVDVLITHPDGRSHRGIFSRLLDSLRQEGFLTDDLVSQEENGQQQKYLGVCRLPGPGRRHRRLDIIVVPYSEFACALLYFTGSAHFNRSMRALAKTKGMSLSEHALSTAVVRNTHGCKVGPGRVLPTPTEKDVFRLLGLPYREPAERDW
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.57
R work: 0.1705
R free: 0.1877
Average B factor: 26.72
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 37.5mM Na cacodylate pH 6.5, 150mM KCl, 75mM magnesium acetate, 7.5% (w/v) PEG 8000
Matthews coefficient: 3
Solvent content (%): 59
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: 2022-03-16
Crystal structure of BACE with amino thiazine inhibitor LY2811376 (PDB entry 4YBI)
Macromolecule: Beta-secretase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.23.46
Sequence length: 442 residues
Sequence: MAGVLPAHGTQHGIRLPLRSGLGGAPLGLRLPRETDEEPEEPGRRGSFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHPFLHRYYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTVRANIAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTHVPNLFSLQLCGAGFPLNQSEVLASVGGSMIIGGIDHSLYTGSLWYTPIRREWYYEVIIVRVEINGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVKSIKAASSTEKFPDGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRITILPQQYLRPVEDVATSQDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSACHVHDEFRTAAVEGPFVTLDMEDCGYNIPQTDEST
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.84
R work: 0.1794
R free: 0.22253
Average B factor: 25.894
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.4
Crystallization temperature (K): 277
Crystal growth procedure: PEG8000, sodium cacodylate, ammonium sulfate
Matthews coefficient: 2.65
Solvent content (%): 53.57
Ligand: (4S)-4-[2,4-difluoro-5-(pyrimidin-5-yl)phenyl]-4-methyl-5,6-dihydro-4H-1,3-thiazin-2-amine (4B2)
Ligand formula: C15 H14 F2 N4 S
Ligand molecular weight: 320.36
Ligand SMILES: CC1(CCSC(=N1)N)c2cc(c(cc2F)F)c3cncnc3
Ligand InChI: InChI=1S/C15H14F2N4S/c1-15(2-3-22-14(18)21-15)11-4-10(12(16)5-13(11)17)9-6-19-8-20-7-9/h4-8H,2-3H2,1H3,(H2,18,21)/t15-/m0/s1
Release date: 2015-04-01
Crystal structure of human KDM4A in complex with compound 16m (PDB entry 6H4S)
Macromolecule: Lysine-specific demethylase 4A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11
Sequence length: 360 residues
Sequence: SMASESETLNPSARIMTFYPTMEEFRNFSRYIAYIESQGAHRAGLAKVVPPKEWKPRASYDDIDDLVIPAPIQQLVTGQSGLFTQYNIQKKAMTVREFRKIANSDKYCTPRYSEFEELERKYWKNLTFNPPIYGADVNGTLYEKHVDEWNIGRLRTILDLVEKESGITIEGVNTPYLYFGMWKTSFAWHTEDMDLYSINYLHFGEPKSWYSVPPEHGKRLERLAKGFFPGSAQSCEAFLRHKMTLISPLMLKKYGIPFDKVTQEAGEFMITFPYGYHAGFNHGFNCAESTNFATRRWIEYGKQAVLCSCRKDMVKISMDVFVRKFQPERYKLWKAGKDNTVIDHTLPTPEAAEFLKESEL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.45
R work: 0.173
R free: 0.218
Average B factor: 47.65
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: Crystallisation solution is 0.1M Bis-Tris-Propane pH7.5, 12-16% PEG-4000. Inhibitor is soaked in crystals by addition directly to the drops of DMSO dissolved compound
Matthews coefficient: 2.46
Solvent content (%): 50.08
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: 2019-06-12
S100B-RSK1 crystal structure A (PDB entry 5CSF)
Macromolecule: Ribosomal protein S6 kinase alpha-1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 55 residues
Sequence: GSQSQLSHQDLQLVKGAMAATYSALNSSKPTPQLKPIESSILAQRRVRKLPSTTL
Oligomeric state: Hetero 3-mer
Stoichiometry: A2, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.4
R work: 0.2432
R free: 0.2907
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 296
Crystal growth procedure: 0.1 M Hepes 7, 150 mM NaCl, 20% PEG6000
Matthews coefficient: 2.32
Solvent content (%): 47.04
Ligand: CALCIUM ION (CA)
Ligand formula: Ca
Ligand molecular weight: 40.078
Ligand SMILES: [Ca+2]
Ligand InChI: InChI=1S/Ca/q+2
Release date: 2015-11-11
Bat influenza A/H17N10 polymerase bound to four heptad repeats of serine 5 phosphorylated Pol II CTD (PDB entry 5M3H)
Macromolecule: Polymerase acidic protein
Type: Protein, polypeptide(L)
Source organism: Influenza A virus
Sequence length: 728 residues
Sequence: GSGSMENFVRTNFNPMILERAEKTMKEYGENPQNEGNKFAAISTHMEVCFMYSDFHFIDLEGNTIVKENDDDNAMLKHRFEIIEGQERNIAWTIVNSICNMTENSKPRFLPDLYDYKTNKFIEIGVTRRKVEDYYYEKASKLKGENVYIHIFSFDGEEMATDDEYILDEESRARIKTRLFVLRQELATAGLWDSFRQSEKGEETLEEEFSYPPTFQRLANQSLPPSFKDYHQFKAYVSSFKANGNIEAKLGAMSEKVNAQIESFDPRTIRELELPEGKFCTQRSKFLLMDAMKLSVLNPAHEGEGIPMKDAKACLDTFWGWKKATIIKKHEKGVNTNYLMIWEQLLESIKEMEGKFLNLKKTNHLKWGLGEGQAPEKMDFEDCKEVPDLFQYKSEPPEKRKLASWIQSEFNKASELTNSNWIEFDELGNDVAPIEHIASRRRNFFTAEVSQCRASEYIMKAVYINTALLNSSCTAMEEYQVIPIITKCRDTSGQRRTNLYGFIIKGRSHLRNDTDVVNFISLEFSLTDPRNEIHKWEKYCVLEIGDMEIRTSISTIMKPVYLYVRTNGTSKIKMKWGMEMRRCLLQSLQQVESMIEAESAVKEKDMTEPFFRNRENDWPIGESPQGIEKGTIGKVCRVLLAKSVFNSIYASAQLEGFSAESRKLLLLIQAFRDNLDPGTFDLKGLYEAIEECIINDPWVLLNASWFNSFLKAVQLSMGSGSGENLYFQ
Oligomeric state: Hetero 5-mer
Stoichiometry: A1, B1, C1, D1, E1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.5
R work: 0.21
R free: 0.2449
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5
Crystallization temperature (K): 278
Crystal growth procedure: Bat influenza polymerase at 10 mgs per ml in 50 mM HEPES NaOH, 500 mM NaCl, 5% (v/v) glycerol, 2 mM TCEP at pH 7.5 with 1:1 ratio of vRNA promoter and CTD peptide mixed with 0.7-1.5 M sodium/potassium phosphate at pH 5.0
Matthews coefficient: 3.12
Solvent content (%): 60.58
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: 2016-12-21
Crystal structure of (R,S)-S-{4-[(5-Bromo-4-{[(2R,3R)-2-hydroxy-1-methylpropyl]oxy}- pyrimidin-2-yl)amino]phenyl}-S-cyclopropylsulfoximide bound to CDK2 (PDB entry 5IEX)
Macromolecule: Cyclin-dependent kinase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.22
Sequence length: 298 residues
Sequence: MENFQKVEKIGEGTYGVVYKARNKLTGEVVALKKIRLDTETEGVPSTAIREISLLKELNHPNIVKLLDVIHTENKLYLVFEFLHQDLKKFMDASALTGIPLPLIKSYLFQLLQGLAFCHSHRVLHRDLKPQNLLINTEGAIKLADFGLARAFGVPVRTYTHEVVTLWYRAPEILLGCKYYSTAVDIWSLGCIFAEMVTRRALFPGDSEIDQLFRIFRTLGTPDEVVWPGVTSMPDYKPSFPKWARQDFSKVVPPLDEDGRSLLSQMLHYDPNKRISAKAALAHPFFQDVTKPVPHLRL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.03
R work: 0.20316
R free: 0.25396
Average B factor: 31.553
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.8
Crystallization temperature (K): 293.15
Crystal growth procedure: 10% PEG 3350, 0.2M ammonium acetate, 100mM HEPES pH 7.8
Matthews coefficient: 2.04
Solvent content (%): 39.67
Ligand: (2R,3R)-3-[(5-bromo-2-{[4-(S-cyclopropylsulfonimidoyl)phenyl]amino}pyrimidin-4-yl)oxy]butan-2-ol (6AF)
Ligand formula: C17 H21 Br N4 O3 S
Ligand molecular weight: 441.343
Ligand SMILES: CC(C(C)Oc1c(cnc(n1)Nc2ccc(cc2)S(=N)(=O)C3CC3)Br)O
Ligand InChI: InChI=1S/C17H21BrN4O3S/c1-10(23)11(2)25-16-15(18)9-20-17(22-16)21-12-3-5-13(6-4-12)26(19,24)14-7-8-14/h3-6,9-11,14,19,23H,7-8H2,1-2H3,(H,20,21,22)/t10-,11-,26+/m1/s1
Release date: 2016-04-27
human plasmakallikrein protease domain in complex with active site directed inhibitor (PDB entry 6T7P)
Macromolecule: Plasma kallikrein
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.34
Sequence length: 242 residues
Sequence: IVGGTNSSWGEWPWQVSLQVKLTAQRHLCGGSLIGHQWVLTAAHCFDGLPLQDVWRIYSGILNLSDITKDTPFSQIKEIIIHQNYKVSEGNHDIALIKLQAPLNYTEFQKPICLPSKGDTSTIYTNCWVTGWGFSKEKGEIQNILQKVNIPLVTNEECQKRYQDYKITQRMVCAGYKEGGKDACKGDSGGPLVCKHNGMWRLVGITSWGEGCARREQPGVYTKVAEYMDWILEKTQSSDGKA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.416
R work: 0.1524
R free: 0.1878
Average B factor: 24.8591
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 20% PEG10000, 200 mM Sodium phosphate (monobasic), corresponds to Nextal condition #87 from PEG series
Matthews coefficient: 2.69
Solvent content (%): 54.33
Ligand: GLUTATHIONE (GSH)
Ligand formula: C10 H17 N3 O6 S
Ligand molecular weight: 307.323
Ligand SMILES: C(CC(=O)NC(CS)C(=O)NCC(=O)O)C(C(=O)O)N
Ligand InChI: InChI=1S/C10H17N3O6S/c11-5(10(18)19)1-2-7(14)13-6(4-20)9(17)12-3-8(15)16/h5-6,20H,1-4,11H2,(H,12,17)(H,13,14)(H,15,16)(H,18,19)/t5-,6-/m0/s1
Release date: 2020-07-08
Crystal structure of DUSP22 mutant_C88S (PDB entry 6L1S)
Macromolecule: Dual specificity protein phosphatase 22
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.16
Sequence length: 157 residues
Sequence: GPMGNGMNKILPGLYIGNFKDARDAEQLSKNKVTHILSVHDSARPMLEGVKYLCIPAADSPSQNLTRHFKESIKFIHECRLRGESCLVHSLAGVSRSVTLVIAYIMTVTDFGWEDALHTVRAGRSCANPNVGFQRQLQEFEKHEVHQYRQWLKEEYG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.3611
R work: 0.1797
R free: 0.1954
Average B factor: 19.1077
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 8
Crystallization temperature (K): 293
Crystal growth procedure: 0.2M Imidazole, 0.4M NaH2PO4/1.6M K2HPO4, 0.2M NaCl
Matthews coefficient: 2.48
Solvent content (%): 50.48
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: 2020-10-28
Structure of human DNA polymerase beta complexed with a nicked DNA containing a GT at N-1 position and GC at N position (PDB entry 4PGY)
Macromolecule: DNA polymerase beta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 329 residues
Sequence: PQETLNGGITDMLTELANFEKNVSQAIHKYNAYRKAASVIAKYPHKIKSGAEAKKLPGVGTKIAEKIDEFLATGKLRKLEKIRQDDTSSSINFLTRVSGIGPSAARKFVDEGIKTLEDLRKNEDKLNHHQRIGLKYFGDFEKRIPREEMLQMQDIVLNEVKKVDSEYIATVCGSFRRGAESSGDMDVLLTHPSFTSESTKQPKLLHQVVEQLQKVHFITDTLSKGETKFMGVCQLPSKNDEKEYPHRRIDIRLIPKDQYYCGVLYFTGSDIFNKNMRAHALEKGFTINEYTIRPLGVTGVAGEPLPVDSEKDIFDYIQWKYREPKDRSE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.26
R work: 0.21
R free: 0.2646
Average B factor: 40.66
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 298
Crystal growth procedure: 14%?23% PEG3400, and 350 mM sodium acetate in 50 mM imidazole (pH 7.5)
Matthews coefficient: 2.36
Solvent content (%): 47.92
Ligand: SODIUM ION ()
Ligand formula: Na
Ligand molecular weight: 22.99
Ligand SMILES: [Na+]
Ligand InChI: InChI=1S/Na/q+1
Release date: 2015-05-06