satarupa22/MacromolecularLigandDB huggingface dataset:
Structure of Human Neurolysin in complex with bradykinin peptide (PDB entry 8VJX)
Macromolecule: Neurolysin, mitochondrial
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.24.16
Sequence length: 667 residues
Sequence: SSYTVAGRNVLRWDLSPEQIKTRTEELIVQTKQVYDAVGMLGIEEVTYENCLQALADVEVKYIVERTMLDFPQHVSSDKEVRAASTEADKRLSRFDIEMSMRGDIFERIVHLQETCDLGKIKPEARRYLEKSIKMGKRNGLHLPEQVQNEIKSMKKRMSELCIDFNKNLNEDDTFLVFSKAELGALPDDFIDSLEKTDDDKYKITLKYPHYFPVMKKCCIPETRRRMEMAFNTRCKEENTIILQQLLPLRTKVAKLLGYSTHADFVLEMNTAKSTSRVTAFLDDLSQKLKPLGEAEREFILNLKKKECKDRGFEYDGKINAWDLYYYMTQTEELKYSIDQEFLKEYFPIEVVTEGLLNTYQELLGLSFEQMTDAHVWNKSVTLYTVKDKATGEVLGQFYLDLYPREGKYNHAACFGLQPGCLLPDGSRMMAVAALVVNFSQPVAGRPSLLRHDEVRTYFHEFGHVMHQICAQTDFARFSGTNVETDFVEVPSQMLENWVWDVDSLRRLSKHYKDGSPIADDLLEKLVASRLVNTGLLTLRQIVLSKVDQSLHTNTSLDAASEYAKYCSEILGVAATPGTNMPATFGHLAGGYDGQYYGYLWSEVFSMDMFYSCFKKEGIMNPEVGMKYRNLILKPGGSLDGMDMLHNFLKREPNQKAFLMSRGLHAP
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.89
R work: 0.2233
R free: 0.2554
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 295
Crystal growth procedure: 17.5 ~ 30 % polyethylene glycol 3,350 and 50 ~ 125 mM Bis-Tris HCl buffer, pH 6.5
Matthews coefficient: 2.7
Solvent content (%): 54.52
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: 2024-08-21
Crystal structure of the single mutant I16K of Low Molecular Weight Protein Tyrosine Phosphatase (LMW-PTP) (PDB entry 6Y2W)
Macromolecule: Low molecular weight phosphotyrosine protein phosphatase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 157 residues
Sequence: AEQATKSVLFVCLGNKCRSPIAEAVFRKLVTDQNISENWVIDSGAVSDWNVGRSPDPRAVSCLRNHGIHTAHKARQITKEDFATFDYILCMDESNLRDLNRKSNQVKTCKAKIELLGSYDPQKQLIIEDPYYGNDSDFETVYQQCVRCCRAFLEKAH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.77
R work: 0.1634
R free: 0.1965
Average B factor: 33.93
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.2M Sodium acetate trihydrate, 0.1M Bis-Tris, 25% PEG3350, pH 6.5
Matthews coefficient: 2.06
Solvent content (%): 40.28
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: 2020-07-22
Crystal structure of Tdp1 catalytic domain in complex with compound XZ520 (PDB entry 6MYZ)
Macromolecule: Tyrosyl-DNA phosphodiesterase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.4
Sequence length: 461 residues
Sequence: SGEGQDIWDMLDKGNPFQFYLTRVSGVKPKYNSGALHIKDILSPLFGTLVSSAQFNYCFDVDWLVKQYPPEFRKKPILLVHGDKREAKAHLHAQAKPYENISLCQAKLDIAFGTHHTKMMLLLYEEGLRVVIHTSNLIHADWHQKTQGIWLSPLYPRIADGTHKSGESPTHFKADLISYLMAYNAPSLKEWIDVIHKHDLSETNVYLIGSTPGRFQGSQKDNWGHFRLKKLLKDHASSMPNAESWPVVGQFSSVGSLGADESKWLCSEFKESMLTLGKESKTPGKSSVPLYLIYPSVENVRTSLEGYPAGGSLPYSIQTAEKQNWLHSYFHKWSAETSGRSNAMPHIKTYMRPSPDFSKIAWFLVTSANLSKAAWGALEKNGTQLMIRSYELGVLFLPSAFGLDSFKVKQKFFAGSQEPMATFPVPYDLPPELYGSKDRPWIWNIPYVKAPDTHGNMWVPS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.661
R work: 0.1919
R free: 0.2272
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 291
Crystal growth procedure: 0.1M MOPS/HEPES-Na pH 7.5, 10% (w/v) PEG 8000, 20% (v/v) ethylene glycol, 0.03 M sodium fluoride, 0.03 M sodium bromide, 0.03 M sodium iodide
Matthews coefficient: 2.47
Solvent content (%): 50.16
Ligand: 4-oxo-8-phenyl-1,4-dihydroquinoline-3-carboxylic acid (K7D)
Ligand formula: C16 H11 N O3
Ligand molecular weight: 265.263
Ligand SMILES: c1ccc(cc1)c2cccc3c2NC=C(C3=O)C(=O)O
Ligand InChI: InChI=1S/C16H11NO3/c18-15-12-8-4-7-11(10-5-2-1-3-6-10)14(12)17-9-13(15)16(19)20/h1-9H,(H,17,18)(H,19,20)
Release date: 2019-11-06
Crystal structure of Low Molecular Weight Protein Tyrosine Phosphatase isoform A complexed with benzylphosphonic acid (PDB entry 4Z9B)
Macromolecule: Low molecular weight phosphotyrosine protein phosphatase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 164 residues
Sequence: GSHMEFMAEQATKSVLFVCLGNICRSPIAEAVFRKLVTDQNISENWRVDSAATSGYEIGNPPDYRGQSCMKRHGIPMSHVARQITKEDFATFDYILCMDESNLRDLNRKSNQVKTCKAKIELLGSYDPQKQLIIEDPYYGNDSDFETVYQQCVRCCRAFLEKAH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.41
R work: 0.21479
R free: 0.30148
Average B factor: 35.003
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7
Crystallization temperature (K): 291
Crystal growth procedure: 32% (w/v) PEG 5000, 0.1 M malic acid:Tris, molar ratio 1:2, pH 7.0
Matthews coefficient: 2.36
Solvent content (%): 47.87
Ligand: benzylphosphonic acid (B85)
Ligand formula: C7 H9 O3 P
Ligand molecular weight: 172.118
Ligand SMILES: c1ccc(cc1)CP(=O)(O)O
Ligand InChI: InChI=1S/C7H9O3P/c8-11(9,10)6-7-4-2-1-3-5-7/h1-5H,6H2,(H2,8,9,10)
Release date: 2015-07-15
Crystal Structure of Ephrin A2 (EphA2) Receptor Protein Kinase with Compound 2a (PDB entry 5NK7)
Macromolecule: Ephrin type-A receptor 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 306 residues
Sequence: GDPNQAVLKFTTEIHPSCVTRQKVIGAGEFGEVYKGMLKTSSGKKEVPVAIKTLKAGYTEKQRVDFLGEAGIMGQFSHHNIIRLEGVISKYKPMMIITEYMENGALDKFLREKDGEFSVLQLVGMLRGIAAGMKYLANMNYVHRDLAARNILVNSNLVCKVSDFGLSRVLEDDPEATYTTSGGKIPIRWTAPEAISYRKFTSASDVWSFGIVMWEVMTYGERPYWELSNHEVMKAINDGFRLPTPMDCPSAIYQLMMQCWQQERARRPKFADIVSILDKLIRAPDSLKTLADFDPRVSIRLPSTSG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.889
R work: 0.169
R free: 0.1995
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 291
Crystal growth procedure: 37.5% MPD/PEG1000/PEG3350 (MD), 0.25 M Amino Acids Mix (MD), 0.1 M Buffer System 3 (MD) pH8.5
Matthews coefficient: 1.97
Solvent content (%): 37.49
Ligand: ~{N}-(2-chloranyl-6-methyl-phenyl)-2-[[3-[[(3~{R},4~{R})-3-fluoranylpiperidin-4-yl]carbamoyl]phenyl]amino]-1,3-thiazole-5-carboxamide (8ZZ)
Ligand formula: C23 H23 Cl F N5 O2 S
Ligand molecular weight: 487.977
Ligand SMILES: Cc1cccc(c1NC(=O)c2cnc(s2)Nc3cccc(c3)C(=O)NC4CCNCC4F)Cl
Ligand InChI: InChI=1S/C23H23ClFN5O2S/c1-13-4-2-7-16(24)20(13)30-22(32)19-12-27-23(33-19)28-15-6-3-5-14(10-15)21(31)29-18-8-9-26-11-17(18)25/h2-7,10,12,17-18,26H,8-9,11H2,1H3,(H,27,28)(H,29,31)(H,30,32)/t17-,18-/m1/s1
Release date: 2017-06-07
Binary structure of DNA polymerase eta in complex with templating hypoxanthine (PDB entry 6MP3)
Macromolecule: DNA polymerase eta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 435 residues
Sequence: GPHMATGQDRVVALVDMDCFFVQVEQRQNPHLRNKPCAVVQYKSWKGGGIIAVSYEARAFGVTRSMWADDAKKLCPDLLLAQVRESRGKANLTKYREASVEVMEIMSRFAVIERASIDEAYVDLTSAVQERLQKLQGQPISADLLPSTYIEGLPQGPTTAEETVQKEGMRKQGLFQWLDSLQIDNLTSPDLQLTVGAVIVEEMRAAIERETGFQCSAGISHNKVLAKLACGLNKPNRQTLVSHGSVPQLFSQMPIRKIRSLGGKLGASVIEILGIEYMGELTQFTESQLQSHFGEKNGSWLYAMCRGIEHDPVKPRQLPKTIGCSKNFPGKTALATREQVQWWLLQLAQELEERLTKDRNDNDRVATQLVVSIRVQGDKRLSSLRRCCALTRYDAHKMSHDAFTVIKNCNTSGIQTEWSPPLTMLFLCATKFSAS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.907
R work: 0.1679
R free: 0.209
Average B factor: 38.5663
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 291.15
Crystal growth procedure: 100mM MES 5.5, PEG 2K MME, 10mM MgSo4
Matthews coefficient: 2.11
Solvent content (%): 41.69
Ligand: SODIUM ION ()
Ligand formula: Na
Ligand molecular weight: 22.99
Ligand SMILES: [Na+]
Ligand InChI: InChI=1S/Na/q+1
Release date: 2019-10-16
MerTK kinase domain in complex with NPS-1034 (PDB entry 7AVX)
Macromolecule: Tyrosine-protein kinase Mer
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 313 residues
Sequence: MGSSHHHHHHSSGLVPRGSEELQNKLEDVVIDRNLLILGKILGEGEFGSVMEGNLKQEDGTSLKVAVKTMKLDNSSQREIEEFLSEAACMKDFSHPNVIRLLGVCIEMSSQGIPKPMVILPFMKYGDLHTYLLYSRLETGPKHIPLQTLLKFMVDIALGMEYLSNRNFLHRDLAARNCMLRDDMTVCVADFGLSKKIYSGDYYRQGRIAKMPVKWIAIESLADRVYTSKSDVWAFGVTMWEIATRGMTPYPGVQNHEMYDYLLHGHRLKQPEDCLDELYEIMYSCWRTDPLDRPTFSVLRLQLEKLLESLPDV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.44
R work: 0.2138
R free: 0.2586
Average B factor: 45.9
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 8.5
Crystallization temperature (K): 293
Crystal growth procedure: co-crystallisation of 0.3 mM protein with 0.5 mM compound (1 % DMSO) in 4.0 M sodium chloride, 0.1 M Tris pH 8.5
Matthews coefficient: 2.42
Solvent content (%): 49.23
Ligand: 1-(4-fluorophenyl)-N-[3-fluoro-4-[(3-phenyl-1H-pyrrolo[2,3-b]pyridin-4-yl)oxy]phenyl]-2,3-dimethyl-5-oxopyrazole-4-carboxamide (S4K)
Ligand formula: C31 H23 F2 N5 O3
Ligand molecular weight: 551.543
Ligand SMILES: CC1=C(C(=O)N(N1C)c2ccc(cc2)F)C(=O)Nc3ccc(c(c3)F)Oc4ccnc5c4c(c[nH]5)c6ccccc6
Ligand InChI: InChI=1S/C31H23F2N5O3/c1-18-27(31(40)38(37(18)2)22-11-8-20(32)9-12-22)30(39)36-21-10-13-25(24(33)16-21)41-26-14-15-34-29-28(26)23(17-35-29)19-6-4-3-5-7-19/h3-17H,1-2H3,(H,34,35)(H,36,39)
Release date: 2021-03-03
X-ray structure of human PPAR gamma ligand binding domain-pemafibrate co-crystals obtained by co-crystallization (PDB entry 7WGQ)
Macromolecule: Isoform 1 of Peroxisome proliferator-activated receptor gamma
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 279 residues
Sequence: GSHMQLNPESADLRALAKHLYDSYIKSFPLTKAKARAILTGKTTDKSPFVIYDMNSLMMGEDKIKFKHITPLQEQSKEVAIRIFQGCQFRSVEAVQEITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQGFMTREFLKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQDNLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLLQVIKKTETDMSLHPLLQEIYKDLY
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.43
R work: 0.2067
R free: 0.2518
Average B factor: 60.6654
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M HEPES (pH 7.5), 1.1 M trisodium citrate
Matthews coefficient: 2.87
Solvent content (%): 57.09
Ligand: (2~{R})-2-[3-[[1,3-benzoxazol-2-yl-[3-(4-methoxyphenoxy)propyl]amino]methyl]phenoxy]butanoic acid (P7F)
Ligand formula: C28 H30 N2 O6
Ligand molecular weight: 490.548
Ligand SMILES: CCC(C(=O)O)Oc1cccc(c1)CN(CCCOc2ccc(cc2)OC)c3nc4ccccc4o3
Ligand InChI: InChI=1S/C28H30N2O6/c1-3-25(27(31)32)35-23-9-6-8-20(18-23)19-30(28-29-24-10-4-5-11-26(24)36-28)16-7-17-34-22-14-12-21(33-2)13-15-22/h4-6,8-15,18,25H,3,7,16-17,19H2,1-2H3,(H,31,32)/t25-/m1/s1
Release date: 2022-05-25
Crystal structure of RIP1 kinase with a benzo[b][1,4]oxazepin-4-one (PDB entry 5HX6)
Macromolecule: Receptor-interacting serine/threonine-protein kinase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 303 residues
Sequence: MDYKDDDDKMQPDMSLNVIKMKSSDFLESAELDSGGFGKVSLAFHRTQGLMIMKTVYKGPNCIEHNEALLEEAKMMNRLRHSRVVKLLGVIIEEGKYSLVMEYMEKGNLMHVLKAEMSTPLSVKGRIILEIIEGMAYLHGKGVIHKDLKPENILVDNDFHIKIADLGLASFKMWSKLNNEEHNELREVDGTAKKNGGTLYYMAPEHLNDVNAKPTEKSDVYSFAVVLWAIFANKEPYENAIAEQQLIMAIKSGNRPDVDDITEYCPREIISLMKLCWEANPEARPTFPGIEEKFRPFYLSQLE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.23
R work: 0.199
R free: 0.2476
Average B factor: 53.63
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 7.5
Crystallization temperature (K): 310
Crystal growth procedure: Well solution 26 % PEG 4K, 0.1 M HEPES pH 7.5; co-crystallized with NEC-4 and cmpd 8 back soaked into crystals at 5mM concentration
Cryo was transfer 6 % to 25 % glycerol added to well solution
Matthews coefficient: 2.04
Solvent content (%): 39.84
Ligand: 5-benzyl-N-[(3S)-5-methyl-4-oxo-2,3,4,5-tetrahydro-1,5-benzoxazepin-3-yl]-1,2-oxazole-3-carboxamide (65U)
Ligand formula: C21 H19 N3 O4
Ligand molecular weight: 377.393
Ligand SMILES: CN1c2ccccc2OCC(C1=O)NC(=O)c3cc(on3)Cc4ccccc4
Ligand InChI: InChI=1S/C21H19N3O4/c1-24-18-9-5-6-10-19(18)27-13-17(21(24)26)22-20(25)16-12-15(28-23-16)11-14-7-3-2-4-8-14/h2-10,12,17H,11,13H2,1H3,(H,22,25)/t17-/m0/s1
Release date: 2016-03-02
Crystal structure of human carbonic anhydrase isozyme II with 3-(Methylamino)-2,5,6-trifluoro-4-[(2-phenylethyl)sulfonyl]benzenesulfonamide (PDB entry 5LLC)
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): 1.1
R work: 0.1377
R free: 0.1611
Average B factor: 17.652
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 291
Crystal growth procedure: Crystallization buffer: 0.1M sodium bicine (pH 9), 0.2 M ammonium sulfate and 2M sodium malonate (pH 7)
Matthews coefficient: 2.02
Solvent content (%): 38.6
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: 2017-08-16
Structure of PI3K gamma in complex with an inhibitor (PDB entry 4XZ4)
Macromolecule: Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.1.153
Sequence length: 966 residues
Sequence: MSEESQAFQRQLTALIGYDVTDVSNVHDDELEFTRRGLVTPRMAEVASRDPKLYAMHPWVTSKPLPEYLWKKIANNCIFIVIHRSTTSQTIKVSPDDTPGAILQSFFTKMAKKKSLMDIPESQSEQDFVLRVCGRDEYLVGETPIKNFQWVRHCLKNGEEIHVVLDTPPDPALDEVRKEEWPLVDDCTGVTGYHEQLTIHGKDHESVFTVSLWDCDRKFRVKIRGIDIPVLPRNTDLTVFVEANIQHGQQVLCQRRTSPKPFTEEVLWNVWLEFSIKIKDLPKGALLNLQIYCGKAPALSSKASAESPSSESKGKVRLLYYVNLLLIDHRFLLRRGEYVLHMWQISGKGEDQGSFNADKLTSATNPDKENSMSISILLDNYCHPIALPKHQPTPDPEGDRVRAEMPNQLRKQLEAIIATDPLNPLTAEDKELLWHFRYESLKHPKAYPKLFSSVKWGQQEIVAKTYQLLARREVWDQSALDVGLTMQLLDCNFSDENVRAIAVQKLESLEDDDVLHYLLQLVQAVKFEPYHDSALARFLLKRGLRNKRIGHFLFWFLRSEIAQSRHYQQRFAVILEAYLRGCGTAMLHDFTQQVQVIEMLQKVTLDIKSLSAEKYDVSSQVISQLKQKLENLQNSQLPESFRVPYDPGLKAGALAIEKCKVMASKKKPLWLEFKCADPTALSNETIGIIFKHGDDLRQDMLILQILRIMESIWETESLDLCLLPYGCISTGDKIGMIEIVKDATTIAKIQQSTVGNTGAFKDEVLNHWLKEKSPTEEKFQAAVERFVYSCAGYCVATFVLGIGDRHNDNIMITETGNLFHIDFGHILGNYKSFLGINKERVPFVLTPDFLFVMGTSGKKTSPHFQKFQDICVKAYLALRHHTNLLIILFSMMLMTGMPQLTSKEDIEYIRDALTVGKNEEDAKKYFLDQIEVCRDKGWTVQFNWFLHLVLGIKQGEKHSAHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.6
R work: 0.19891
R free: 0.26197
Average B factor: 46.165
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 298
Crystal growth procedure: 25% PEG3350, 200MM Lithium Sulfate, 10 MM DTT, 10 MM EDTA, 100 MM Tris
Matthews coefficient: 2.33
Solvent content (%): 47.3
Ligand: N-[5-(6-methoxypyrazin-2-yl)-4,5,6,7-tetrahydro[1,3]thiazolo[5,4-c]pyridin-2-yl]acetamide (456)
Ligand formula: C13 H15 N5 O2 S
Ligand molecular weight: 305.356
Ligand SMILES: CC(=O)Nc1nc2c(s1)CN(CC2)c3cncc(n3)OC
Ligand InChI: InChI=1S/C13H15N5O2S/c1-8(19)15-13-16-9-3-4-18(7-10(9)21-13)11-5-14-6-12(17-11)20-2/h5-6H,3-4,7H2,1-2H3,(H,15,16,19)
Release date: 2016-02-03
Human cationic trypsin K97D mutant in complex with bovine pancreatic trypsin inhibitor (BPTI) (PDB entry 4WXV)
Macromolecule: Trypsin-1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.4
Sequence length: 224 residues
Sequence: IVGGYNCEENSVPYQVSLNSGYHFCGGSLINEQWVVSAGHCYKSRIQVRLGEHNIEVLEGNEQFINAAKIIRHPQYDRDTLNNDIMLIKLSSRAVINAHVSTISLPTAPPATGTKCLISGWGNTASSGADYPDELQCLDAPVLSQAKCEASYPGKITSNMFCVGFLEGGKDSCQGDAGGPVVCNGQLQGVVSWGDGCAQKNKPGVYTKVYNYVKWIKNTIAANS
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.1
R work: 0.2157
R free: 0.2809
Average B factor: 25.878
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 298
Crystal growth procedure: 0.2M ammonium sulfate, 0.1 sodium cacodylate trihydrate, 30% PEG-8000
Matthews coefficient: 2.28
Solvent content (%): 45.97
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: 2015-07-22
Crystal structure of the Angiotensin-1 converting enzyme N-domain in complex with amyloid-beta fluorogenic fragment 4-10 (PDB entry 5AMC)
Macromolecule: ANGIOTENSIN-CONVERTING ENZYME
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.15.1
Sequence length: 629 residues
Sequence: LDPGLQPGQFSAEDAGAQLFAQSYQSSAEQVLFQSVAASWAHDTNITAENARRQEEAALLSQEFAEAWGQKAKELYEPIWQQFTDPQLRRIIGAVRTLGSANLPLAKRQQYNALLSQMSRIYSTAKVCLPQKTATCWSLDPDLTNILASSRSYAMLLFAWEGWHNAAGIPLKPLYEDFTALSNEAYKQDGFTDTGAYWRSWYNSPTFEDDLEHLYQQLEPLYLNLHAFVRRALHRRYGDRYINLRGPIPAHLLGDMWAQSWENIYDMVVPFPDKPNLDVTSTMLQQGWQATHMFRVAEEFFTSLELSPMPPEFWEGSMLEKPADGREVVCHASAWDFYNRKDFRIKQCTRVTMDQLSTVHHEMGHIQYYLQYKDLPVSLRRGANPGFHEAIGDVLALSVSTPEHLHKIGLLDRVTNDTESDINYLLKMALEKIAFLPFGYLVDQWRWGVFSGRTPPSRYNFDWWYLRTKYQGICPPVTRNETHFDAGAKFHVPNVTPYIRYFVSFVLQFQFHEALCKEAGYEGPLHQCDIYRSTKAGAKLRKVLRAGSSRPWQEVLKDMVGLDALDAQPLLKYFQLVTQWLQEQNQQNGEVLGWPEYQWHPPLPDNYPEGIDLVTDEAEASKFVEEYDL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.65
R work: 0.20772
R free: 0.24169
Average B factor: 30.142
Crystallization pH: 8.5
Crystal growth procedure: 0.06 M DIVALENT CATIONS, 0.1 M TRIS/BICINE PH 8.5, 30 % PEG550MME/PEG20000
Matthews coefficient: 2.85
Solvent content (%): 57
Ligand: GLYCINE (GLY)
Ligand formula: C2 H5 N O2
Ligand molecular weight: 75.067
Ligand SMILES: C(C(=O)O)N
Ligand InChI: InChI=1S/C2H5NO2/c3-1-2(4)5/h1,3H2,(H,4,5)
Release date: 2016-01-13
PanDDA analysis group deposition -- Crystal Structure of human PARP14 Macrodomain 3 in complex with FMOPL000466a (PDB entry 5QI4)
Macromolecule: Poly [ADP-ribose] polymerase 14
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.4.2.30
Sequence length: 183 residues
Sequence: SMFYGTVSSPDSGVYEMKIGSIIFQVASGDITKEEADVIVNSTSNSFNLKAGVSKAILECAGQNVERECSQQAQQRKNDYIITGGGFLRCKNIIHVIGGNDVKSSVSSVLQECEKKNYSSICLPAIGTGNAKQHPDKVAEAIIDAIEDFVQKGSAQSVKKVKVVIFLPQVLDVFYANMKKREG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.2
R work: 0.1901
R free: 0.2198
Average B factor: 18.019
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.4
Crystallization temperature (K): 277
Crystal growth procedure: 80 mM KBr, 30 % PEG2kMME
Matthews coefficient: 1.98
Solvent content (%): 37.91
Ligand: CHLORIDE ION (CL)
Ligand formula: Cl
Ligand molecular weight: 35.453
Ligand SMILES: [Cl-]
Ligand InChI: InChI=1S/ClH/h1H/p-1
Release date: 2019-04-10
PCSK9 in complex with compound 5 (PDB entry 6U2P)
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): 2.04
R work: 0.183
R free: 0.216
Average B factor: 37.76
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 303
Crystal growth procedure: (10-22)% PEG 10000, 0.1M Tris, pH 8.5, 10% Ethylene Glycol, 1% BAM
Matthews coefficient: 2.69
Solvent content (%): 54.21
Ligand: 2-fluoro-4-{[(1R)-6-methoxy-1-methyl-1-{2-oxo-2-[(1,3-thiazol-2-yl)amino]ethyl}-1,2,3,4-tetrahydroisoquinolin-7-yl]oxy}benzoic acid (PUV)
Ligand formula: C23 H22 F N3 O5 S
Ligand molecular weight: 471.501
Ligand SMILES: CC1(c2cc(c(cc2CCN1)OC)Oc3ccc(c(c3)F)C(=O)O)CC(=O)Nc4nccs4
Ligand InChI: InChI=1S/C23H22FN3O5S/c1-23(12-20(28)27-22-25-7-8-33-22)16-11-19(18(31-2)9-13(16)5-6-26-23)32-14-3-4-15(21(29)30)17(24)10-14/h3-4,7-11,26H,5-6,12H2,1-2H3,(H,29,30)(H,25,27,28)/t23-/m1/s1
Release date: 2019-11-06
Crystal Structure of TrkA kinase with ligand (PDB entry 5H3Q)
Macromolecule: High affinity nerve growth factor receptor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 324 residues
Sequence: GSSLSPTEGKGSGLQGHIIENPQYFSDACVHHIKRRDIVLKWELGEGAFGKVFLAECHNLLPEQDKMLVAVKALKEASESARQDFQREAELLTMLQHQHIVRFFGVCTEGRPLLMVFEYMRHGDLNRFLRSHGPDAKLLAGGEDVAPGPLGLGQLLAVASQVAAGMVYLAGLHFVHRDLATRNCLVGQGLVVKIGDFGMSRDIYSTDYYRVGGRTMLPIRWMPPESILYRKFTTESDVWSFGVVLWEIFTYGKQPWYQLSNTEAIDCITQGRELERPRACPPEVYAIMRGCWQREPQQRHSIKDVHARLQALAQAPPVYLDVLG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.1
R work: 0.1884
R free: 0.2151
Average B factor: 45.184
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 293
Crystal growth procedure: 1.2M Sodium Tartrate, 100mM Tris-HCl pH 8.5, 5 mM DTT
Matthews coefficient: 3.97
Solvent content (%): 68.99
Ligand: 1-[(3S,4R)-4-[3,4-bis(fluoranyl)phenyl]-1-(2-methoxyethyl)pyrrolidin-3-yl]-3-(5-ethoxy-4-methyl-2-phenyl-pyrazol-3-yl)urea (7HF)
Ligand formula: C26 H31 F2 N5 O3
Ligand molecular weight: 499.553
Ligand SMILES: CCOc1c(c(n(n1)c2ccccc2)NC(=O)NC3CN(CC3c4ccc(c(c4)F)F)CCOC)C
Ligand InChI: InChI=1S/C26H31F2N5O3/c1-4-36-25-17(2)24(33(31-25)19-8-6-5-7-9-19)30-26(34)29-23-16-32(12-13-35-3)15-20(23)18-10-11-21(27)22(28)14-18/h5-11,14,20,23H,4,12-13,15-16H2,1-3H3,(H2,29,30,34)/t20-,23+/m0/s1
Release date: 2017-02-22
HUMAN ARTD1 (PARP1) - CATALYTIC DOMAIN IN COMPLEX WITH INHIBITOR TALAZOPARIB (PDB entry 4UND)
Macromolecule: POLY [ADP-RIBOSE] POLYMERASE 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.4.2.30
Sequence length: 373 residues
Sequence: MHHHHHHSSGVDLGTENLYFQSMKSKLPKPVQDLIKMIFDVESMKKAMVEYEIDLQKMPLGKLSKRQIQAAYSILSEVQQAVSQGSSDSQILDLSNRFYTLIPHDFGMKKPPLLNNADSVQAKAEMLDNLLDIEVAYSLLRGGSDDSSKDPIDVNYEKLKTDIKVVDRDSEEAEIIRKYVKNTHATTHNAYDLEVIDIFKIEREGECQRYKPFKQLHNRRLLWHGSRTTNFAGILSQGLRIAPPEAPVTGYMFGKGIYFADMVSKSANYCHTSQGDPIGLILLGEVALGNMYELKHASHISKLPKGKHSVKGLGKTTPDPSANISLDGVDVPLGTGISSGVNDTSLLYNEYIVYDIAQVNLKYLLKLKFNFKT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.2
R work: 0.22644
R free: 0.2464
Average B factor: 60.941
Crystallization pH: 6.6
Crystal growth procedure: 39% PEGMME2000, 0.2M KSCN, 0.1M HEPES, pH 6.6
Matthews coefficient: 2.69
Solvent content (%): 54
Ligand: (8S,9R)-5-fluoro-8-(4-fluorophenyl)-9-(1-methyl-1H-1,2,4-triazol-5-yl)-2,7,8,9-tetrahydro-3H-pyrido[4,3,2-de]phthalazin-3-one (2YQ)
Ligand formula: C19 H14 F2 N6 O
Ligand molecular weight: 380.351
Ligand SMILES: Cn1c(ncn1)C2C(Nc3cc(cc4c3C2=NNC4=O)F)c5ccc(cc5)F
Ligand InChI: InChI=1S/C19H14F2N6O/c1-27-18(22-8-23-27)15-16(9-2-4-10(20)5-3-9)24-13-7-11(21)6-12-14(13)17(15)25-26-19(12)28/h2-8,15-16,24H,1H3,(H,26,28)/t15-,16-/m1/s1
Release date: 2015-06-17