satarupa22/MacromolecularLigandDB huggingface dataset:
THE KINASE DOMAIN OF HUMAN SPLEEN TYROSINE (SYK) IN COMPLEX WITH GTC000250 (PDB entry 4YJV)
Macromolecule: Tyrosine-protein kinase SYK
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 281 residues
Sequence: PEEIRPKEVYLDRKLLTLEDKELGSGNFGTVKKGYYQMKKVVKTVAVKILKNEANDPALKDELLAEANVMQQLDNPYIVRMIGICEAESWMLVMEMAELGPLNKYLQQNRHVKDKNIIELVHQVSMGMKYLEESNFVHRDLAARNVLLVTQHYAKISDFGLSKALRADENYYKAQTHGKWPVKWYAPECINYYKFSSKSDVWSFGVLMWEAFSYGQKPYRGMKGSEVTAMLEKGERMGCPAGCPREMYDLMNLCWTYDVENRPGFAAVELRLRNYYYDVVN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.652
R work: 0.1748
R free: 0.2223
Average B factor: 23.68
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6
Crystallization temperature (K): 293
Crystal growth procedure: 30% Jeffamine ED-2001, 10% Glycerol, 0.1M MES pH6.0, 5mM TCEP
Matthews coefficient: 2.12
Solvent content (%): 42.03
Ligand: 3-[6-({4-[ethyl(1H-indazol-4-yl)amino]-5-fluoropyrimidin-2-yl}amino)-2,4-dihydro-1H-indazol-1-yl]propan-1-ol (4DT)
Ligand formula: C23 H25 F N8 O
Ligand molecular weight: 448.496
Ligand SMILES: CCN(c1cccc2c1cn[nH]2)c3c(cnc(n3)NC4=CCC5=CNN(C5=C4)CCCO)F
Ligand InChI: InChI=1S/C23H25FN8O/c1-2-31(20-6-3-5-19-17(20)13-26-30-19)22-18(24)14-25-23(29-22)28-16-8-7-15-12-27-32(9-4-10-33)21(15)11-16/h3,5-6,8,11-14,27,33H,2,4,7,9-10H2,1H3,(H,26,30)(H,25,28,29)
Release date: 2015-10-14
Human Cytochrome P450 17A1 in complex with inhibitor: abiraterone C6 oxime (PDB entry 6CIR)
Macromolecule: Steroid 17-alpha-hydroxylase/17,20 lyase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.14.19
Sequence length: 494 residues
Sequence: MAKKTGAKYPKSLLSLPLVGSLPFLPRHGHMHNNFFKLQKKYGPIYSVRMGTKTTVIVGHHQLAKEVLIKKGKDFSGRPQMATLDIASNNRKGIAFADSGAHWQLHRRLAMATFALFKDGDQKLEKIICQEISTLCDMLATHNGQSIDISFPVFVAVTNVISLICFNTSYKNGDPELNVIQNYNEGIIDNLSKDSLVDLVPWLKIFPNKTLEKLKSHVKIRNDLLNKILENYKEKFRSDSITNMLDTLMQAKMNSDNGNAGPDQDSELLSDNHILTTIGDIFGAGVETTTSVVKWTLAFLLHNPQVKKKLYEEIDQNVGFSRTPTISDRNRLLLLEATIREVLRLRPVAPMLIPHKANVDSSIGEFAVDKGTEVIINLWALHHNEKEWHQPDQFMPERFLNPAGTQLISPSVSYLPFGAGPRSCIGEILARQELFLIMAWLLQRFDLEVPDDGQLPSLEGIPKVVFLIDSFKVKIKVRQAWREAQAEGSTHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.648
R work: 0.187
R free: 0.2405
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.175 M Tris, pH 8.5 containing 30% PEG 3350, 3% glycerol, and 0.250-0.275 M lithium sulfate
Matthews coefficient: 2.63
Solvent content (%): 53.27
Ligand: PROTOPORPHYRIN IX CONTAINING FE (HEM)
Ligand formula: C34 H32 Fe N4 O4
Ligand molecular weight: 616.487
Ligand SMILES: Cc1c2n3c(c1CCC(=O)O)C=C4C(=C(C5=[N]4[Fe]36[N]7=C(C=C8N6C(=C5)C(=C8C)C=C)C(=C(C7=C2)C)C=C)C)CCC(=O)O
Ligand InChI: InChI=1S/C34H34N4O4.Fe/c1-7-21-17(3)25-13-26-19(5)23(9-11-33(39)40)31(37-26)16-32-24(10-12-34(41)42)20(6)28(38-32)15-30-22(8-2)18(4)27(36-30)14-29(21)35-25;/h7-8,13-16H,1-2,9-12H2,3-6H3,(H4,35,36,37,38,39,40,41,42);/q;+2/p-2/b25-13-,26-13-,27-14-,28-15-,29-14-,30-15-,31-16-,32-16-;
Release date: 2018-06-06
Crystal structure of human polymerase eta inserting dGMPnPP opposite DNA template containing an abasic site (PDB entry 4RNN)
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): 1.808
R work: 0.1679
R free: 0.2029
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 291
Crystal growth procedure: 0.1 M MES pH 5.5, 5mM magnesium chloride, 25% PEG 2000 MME , VAPOR DIFFUSION, HANGING DROP, temperature 291.0K
Matthews coefficient: 2.1
Solvent content (%): 41.54
Ligand: 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]guanosine (XG4)
Ligand formula: C10 H17 N6 O12 P3
Ligand molecular weight: 506.196
Ligand SMILES: c1nc2c(n1C3CC(C(O3)COP(=O)(NP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
Ligand InChI: InChI=1S/C10H17N6O12P3/c11-10-13-8-7(9(18)14-10)12-3-16(8)6-1-4(17)5(27-6)2-26-29(19,20)15-30(21,22)28-31(23,24)25/h3-6,17H,1-2H2,(H2,23,24,25)(H3,11,13,14,18)(H3,15,19,20,21,22)/t4-,5+,6+/m0/s1
Release date: 2015-02-18
Human protein kinase CK2 alpha in complex with vanillin (PDB entry 6HOU)
Macromolecule: Casein kinase II subunit alpha
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 336 residues
Sequence: MSGPVPSRARVYTDVNTHRPREYWDYESHVVEWGNQDDYQLVRKLGRGKYSEVFEAINITNNEKVVVKILKPVKKKKIKREIKILENLRGGPNIITLADIVKDPVSRTPALVFEHVNNTDFKQLYQTLTDYDIRFYMYEILKALDYCHSMGIMHRDVKPHNVMIDHEHRKLRLIDWGLAEFYHPGQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRKEPFFHGHDNYDQLVRIAKVLGTEDLYDYIDKYNIELDPRFNDILGRHSRKRWERFVHSENQHLVSPEALDFLDKLLRYDHQSRLTAREAMEHPYFYTVVKDQARMGS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.1723
R free: 0.2081
Average B factor: 27.4001
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 293
Crystal growth procedure: 32% PEG4000, 0.2 M Lithium Sulfate
Matthews coefficient: 1.99
Solvent content (%): 38.12
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: 2019-10-02
Crystal Structure of human phosphodiesterase 10 in complex with 4-pyrrolidin-1-yl-7H-pyrrolo[2,3-d]pyrimidine (PDB entry 5SHQ)
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): 2.08
R work: 0.1821
R free: 0.2215
Average B factor: 42.18
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: 2.61
Solvent content (%): 52.86
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: 2022-10-12
Carbonic Anhydrase IX-mimic in complex with the alkyl urea compound 3j (PDB entry 8FR4)
Macromolecule: Carbonic anhydrase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 257 residues
Sequence: HWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHSFQVTFDDSQDKAVLKGGPLDGTYRLLQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDVGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTEGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLAECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.123
R work: 0.1686
R free: 0.1731
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.8
Crystallization temperature (K): 293
Crystal growth procedure: 1.6 M sodium citrate, 50 mM Tris base
Matthews coefficient: 2.13
Solvent content (%): 42.27
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: 2023-02-01
CRYSTAL STRUCTURE OF RIP1 KINASE BOUND TO INHIBITOR (PDB entry 6C3E)
Macromolecule: Receptor-interacting serine/threonine-protein kinase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 297 residues
Sequence: GGSGQPDMSLNVIKMKSSDFLESAELDSGGFGKVSLAFHRTQGLMIMKTVYKGPNCIEHNEALLEEAKMMNRLRHSRVVKLLGVIIEEGKYSLVMEYMEKGNLMHVLKAEMSTPLSVKGRIILEIIEGMAYLHGKGVIHKDLKPENILVDNDFHIKIADLGLASFKMWSKLNNEEHNELREVDGTAKKNGGTLYYMAPEHLNDVNAKPTEKSDVYSFAVVLWAIFANKEPYENAIAEQQLIMAIKSGNRPDVDDLTEYCPREIISLMKLCWEANPEARPTFPGIEEKFRPFYLSQLE
Oligomeric state: Homo 2-mer
Stoichiometry: A2
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.6
R work: 0.259
R free: 0.30665
Average B factor: 44.744
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 7
Crystallization temperature (K): 277
Crystal growth procedure: 0.25 M ammonium iodide, 0.03 M glycyl-glycyl-glycine and polyethylene glycol (PEG) 3350
Matthews coefficient: 2.01
Solvent content (%): 38.82
Ligand: 2-benzyl-5-nitro-1H-benzimidazole (EJY)
Ligand formula: C14 H11 N3 O2
Ligand molecular weight: 253.256
Ligand SMILES: c1ccc(cc1)Cc2[nH]c3ccc(cc3n2)[N+](=O)[O-]
Ligand InChI: InChI=1S/C14H11N3O2/c18-17(19)11-6-7-12-13(9-11)16-14(15-12)8-10-4-2-1-3-5-10/h1-7,9H,8H2,(H,15,16)
Release date: 2018-03-21
Human DNA polymerase eta-DNA-araC-ended primer ternary complex:reaction with 20 mM Mg2+ for 600s (PDB entry 8V7J)
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): 1.66
R work: 0.2008
R free: 0.2235
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7
Crystallization temperature (K): 298
Crystal growth procedure: PEG 2000MME, 0.1 M MES
Matthews coefficient: 2.11
Solvent content (%): 41.74
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: 2024-05-15
INPP5D PanDDA analysis group deposition -- Crystal Structure of the phosphatase and C2 domains of SHIP1 in complex with Z2443429438 (PDB entry 5RX5)
Macromolecule: Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.86
Sequence length: 463 residues
Sequence: SMEQPEPDMITIFIGTWNMGNAPPPKKITSWFLSKGQGKTRDDSADYIPHDIYVIGTQEDPLSEKEWLEILKHSLQEITSVTFKTVAIHTLWNIRIVVLAKPEHENRISHICTDNVKTGIANTLGNKGAVGVSFMFNGTSLGFVNSHLTSGSEKKLRRNQNYMNILRFLALGDKKLSPFNITHRFTHLFWFGDLNYRVDLPTWEAETIIQKIKQQQYADLLSHDQLLTERREQKVFLHFEEEEITFAPTYRFERLTRDKYAYTKQKATGMKYNLPSWCDRVLWKSYPLVHVVCQSYGSTSDIMTSDHSPVFATFEAGVTSQFVSKNGPGTVDSQGQIEFLRCYATLKTKSQTKFYLEFHSSCLESFVKSQEGENEEGSEGELVVKFGETLPKLKPIISDPEYLLDQHILISIKSSDSDESYGEGCIALRLEATETQLPIYTPLTHHGELTGHFQGEIKLQTSQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.28
R work: 0.1959
R free: 0.2228
Average B factor: 22.16
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 30 mM sodium nitrate, 30 mM dibasic sodium phosphate, 30 mM ammonium sulfate, 100 mM MES/imidazole, pH 6.5, 20% PEG500 MME, 10% PEG20000
Matthews coefficient: 2.11
Solvent content (%): 41.71
Ligand: (3S)-1-(phenylsulfonyl)pyrrolidin-3-amine (WNM)
Ligand formula: C10 H14 N2 O2 S
Ligand molecular weight: 226.295
Ligand SMILES: c1ccc(cc1)S(=O)(=O)N2CCC(C2)N
Ligand InChI: InChI=1S/C10H14N2O2S/c11-9-6-7-12(8-9)15(13,14)10-4-2-1-3-5-10/h1-5,9H,6-8,11H2/t9-/m0/s1
Release date: 2020-11-11
Crystal Structure of AKR1C1 complexed with glibenclamide (PDB entry 4YVP)
Macromolecule: Aldo-keto reductase family 1 member C1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.1.1
Sequence length: 323 residues
Sequence: MDSKYQCVKLNDGHFMPVLGFGTYAPAEVPKSKALEATKLAIEAGFRHIDSAHLYNNEEQVGLAIRSKIADGSVKREDIFYTSKLWCNSHRPELVRPALERSLKNLQLDYVDLYLIHFPVSVKPGEEVIPKDENGKILFDTVDLCATWEAVEKCKDAGLAKSIGVSNFNRRQLEMILNKPGLKYKPVCNQVECHPYFNQRKLLDFCKSKDIVLVAYSALGSHREEPWVDPNSPVLLEDPVLCALAKKHKRTPALIALRYQLQRGVVVLAKSYNEQRIRQNVQVFEFQLTSEEMKAIDGLNRNVRYLTLDIFAGPPNYPFSDEY
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.6
R work: 0.21159
R free: 0.24724
Average B factor: 19.05
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.3
Crystallization temperature (K): 289
Crystal growth procedure: 23-27% (w/v) PEG 4000, 100 mM Hepes, 10mM CaCl2, 0.4M NaCl
Matthews coefficient: 2.3
Solvent content (%): 46.58
Ligand: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE (NAP)
Ligand formula: C21 H28 N7 O17 P3
Ligand molecular weight: 743.405
Ligand SMILES: c1cc(c[n+](c1)C2C(C(C(O2)COP(=O)([O-])OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)OP(=O)(O)O)O)O)O)C(=O)N
Ligand InChI: InChI=1S/C21H28N7O17P3/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(44-46(33,34)35)14(30)11(43-21)6-41-48(38,39)45-47(36,37)40-5-10-13(29)15(31)20(42-10)27-3-1-2-9(4-27)18(23)32/h1-4,7-8,10-11,13-16,20-21,29-31H,5-6H2,(H7-,22,23,24,25,32,33,34,35,36,37,38,39)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
Release date: 2015-11-25
EGFR(T790M/V948R) in complex with AZD9291 and DDC4002 (PDB entry 6XL4)
Macromolecule: Epidermal growth factor receptor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 328 residues
Sequence: SGEAPNQALLRILKETEFKKIKVLGSGAFGTVYKGLWIPEGEKVKIPVAIKELREATSPKANKEILDEAYVMASVDNPHVCRLLGICLTSTVQLIMQLMPFGCLLDYVREHKDNIGSQYLLNWCVQIAKGMNYLEDRRLVHRDLAARNVLVKTPQHVKITDFGLAKLLGAEEKEYHAEGGKVPIKWMALESILHRIYTHQSDVWSYGVTVWELMTFGSKPYDGIPASEISSILEKGERLPQPPICTIDVYMIMRKCWMIDADSRPKFRELIIEFSKMARDPQRYLVIQGDERMHLPSPTDSNFYRALMDEEDMDDVVDADEYLIPQQG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.06
R work: 0.2145
R free: 0.252
Average B factor: 40.7071
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 298
Crystal growth procedure: 25% PEG 3350, 0.1 M Bis-Tris
Matthews coefficient: 2.06
Solvent content (%): 40.26
Ligand: 10-benzyl-8-fluoro-5,10-dihydro-11H-dibenzo[b,e][1,4]diazepin-11-one (NQ1)
Ligand formula: C20 H15 F N2 O
Ligand molecular weight: 318.344
Ligand SMILES: c1ccc(cc1)CN2c3cc(ccc3Nc4ccccc4C2=O)F
Ligand InChI: InChI=1S/C20H15FN2O/c21-15-10-11-18-19(12-15)23(13-14-6-2-1-3-7-14)20(24)16-8-4-5-9-17(16)22-18/h1-12,22H,13H2
Release date: 2021-06-30
Crystal structure of SAH-bound METTL3-METTL14 complex (PDB entry 5IL2)
Macromolecule: METTL3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1.62
Sequence length: 212 residues
Sequence: FPPQWICCDIRYLDVSILGKFAVVMADPPWDIHMELPYGTLTDDEMRRLNIPVLQDDGFLFLWVTGRAMELGRECLNLWGYERVDEIIWVKTNQLQRIIRTGRTGHWLNHGKEHCLVGVKGNPQGFNQGLDCDVIVAEVRSTSHKPDEIYGMIERLSPGTRKIELFGRPHNVQPNWITLGNQLDGIHLLDPDVVARFKQRYPDGIISKPKNL
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.606
R work: 0.1848
R free: 0.1992
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.7
Crystallization temperature (K): 291
Crystal growth procedure: PEG 8000, sodium citrate
Matthews coefficient: 2.66
Solvent content (%): 53.7
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: 2016-05-25
Crystal structure of indoleamine 2,3-dioxygenagse 1 (IDO1) in complex with compound 47 (PDB entry 6KOF)
Macromolecule: Indoleamine 2,3-dioxygenase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.13.11.52
Sequence length: 403 residues
Sequence: MAHAMENSWTISKEYHIDEEVGFALPNPQENLPDFYNDWMFIAKHLPDLIESGQLRERVEKLNMLSIDHLTDHKSQRLARLVLGCITMAYVWGKGHGDVRKVLPRNIAVPYCQLSKKLELPPILVYADCVLANWKKKDPNKPLTYENMDVLFSFRDGDCSKGFFLVSLLVEIAAASAIKVIPTVFKAMQMQERDTLLKALLEIASCLEKALQVFHQIHDHVNPKAFFSVLRIYLSGWKGNPQLSDGLVYEGFWEDPKEFAGGSAGQSSVFQCFDVLLGIQQTAGGGHAAQFLQDMRRYMPPAHRNFLCSLESNPSVREFVLSKGDAGLREAYDACVKALVSLRSYHLQIVTKYILIPASQQPKENKTSEDPSKLEAKGTGGTDLMNFLKTVRSTTEKSLLKEG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.263
R work: 0.1946
R free: 0.2273
Average B factor: 54.3475
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6
Crystallization temperature (K): 291
Crystal growth procedure: PEG3350, Ammonium fluoride,MES
Matthews coefficient: 2.83
Solvent content (%): 56.6
Ligand: 1-(4-cyanophenyl)-3-[[3-(2-cyclopropylethynyl)imidazo[2,1-b][1,3]thiazol-5-yl]methyl]thiourea (DO9)
Ligand formula: C19 H15 N5 S2
Ligand molecular weight: 377.486
Ligand SMILES: c1cc(ccc1C#N)NC(=S)NCc2cnc3n2c(cs3)C#CC4CC4
Ligand InChI: InChI=1S/C19H15N5S2/c20-9-14-3-6-15(7-4-14)23-18(25)21-10-17-11-22-19-24(17)16(12-26-19)8-5-13-1-2-13/h3-4,6-7,11-13H,1-2,10H2,(H2,21,23,25)
Release date: 2020-03-25
Structure of E3 ligase SopA bound to ubiquitin (PDB entry 8ST8)
Macromolecule: E3 ubiquitin-protein ligase SopA
Type: Protein, polypeptide(L)
Source organism: Salmonella enterica subsp. enterica serovar Typhimurium
EC number: 2.3.2.26
Sequence length: 197 residues
Sequence: HHHHHHSSGLEVLFQGPRRFGELIDIILSTEEHGELNQQFLAATNQKHSTVKLIDDASVSRLATIFDPLLPEGKLSPAHYQHILSAYHLTDATPQKQAETLFCLSTAFARYSSSAIFGTEHDSPPALRGYAEALMQKAWELSPAIFPSSEQFTEWSDRFHGLHGAFTCTSVVADSMQRHARKYFPSVLSSILPLAWA
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.75
R work: 0.1765
R free: 0.1963
Average B factor: 29.61
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 295
Crystal growth procedure: 22.5% PEG 8000, 0.2 M ammonium sulfate, 0.1 M sodium cacodylate pH 7.0, and 20% glycerol
Matthews coefficient: 2.2
Solvent content (%): 44.12
Ligand: prop-2-en-1-amine (AYE)
Ligand formula: C3 H7 N
Ligand molecular weight: 57.094
Ligand SMILES: C=CCN
Ligand InChI: InChI=1S/C3H7N/c1-2-3-4/h2H,1,3-4H2
Release date: 2023-07-12
CRYSTAL STRUCTURE OF CDK8-CycC IN COMPLEX WITH COMPOUND 1 (PDB entry 6R3S)
Macromolecule: Cyclin-dependent kinase 8
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.22
Sequence length: 406 residues
Sequence: DDKMDYDFKVKLSSERERVEDLFEYEGCKVGRGTYGHVYKAKRKDGKDDKDYALKQIEGTGISMSACREIALLRELKHPNVISLQKVFLSHADRKVWLLFDYAEHDLWHIIKFHRASKANKKPVQLPRGMVKSLLYQILDGIHYLHANWVLHRDLKPANILVMGEGPERGRVKIADMGFARLFNSPLKPLADLDPVVVTFWYRAPELLLGARHYTKAIDIWAIGCIFAELLTSEPIFHCRQEDIKTSNPYHHDQLDRIFNVMGFPADKDWEDIKKMPEHSTLMKDFRRNTYTNCSLIKYMEKHKVKPDSKAFHLLQKLLTMDPIKRITSEQAMQDPYFLEDPLPTSDVFAGCQIPYPKREFLTEEEPDDKGDKKNQQQQQGNNHTNGTGHPGNQDSSHTQGPPLKK
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.19
R work: 0.20071
R free: 0.22679
Average B factor: 40.457
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 293.15
Crystal growth procedure: 20% PEG3350, 0.2 M sodium formate, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K
Matthews coefficient: 3
Solvent content (%): 58.99
Ligand: 6-[5-chloranyl-4-[(1~{S})-1-oxidanylethyl]pyridin-3-yl]-3,4-dihydro-2~{H}-1,8-naphthyridine-1-carboxamide (JRE)
Ligand formula: C16 H17 Cl N4 O2
Ligand molecular weight: 332.785
Ligand SMILES: CC(c1c(cncc1Cl)c2cc3c(nc2)N(CCC3)C(=O)N)O
Ligand InChI: InChI=1S/C16H17ClN4O2/c1-9(22)14-12(7-19-8-13(14)17)11-5-10-3-2-4-21(16(18)23)15(10)20-6-11/h5-9,22H,2-4H2,1H3,(H2,18,23)/t9-/m0/s1
Release date: 2020-04-08
CRYSTAL STRUCTURE OF JANUS KINASE 2 IN COMPLEX WITH N,N-DICYCLOPROPYL-10-ETHYL-7-[(3-METHOXYPROPYL)AMINO] -3-METHYL-3,5,8,10-TETRAAZATRICYCLO[7.3.0.0,6] DODECA-1(9),2(6),4,7,11-PENTAENE-11-CARBOXAMIDE (PDB entry 5CF4)
Macromolecule: Tyrosine-protein kinase JAK2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 321 residues
Sequence: MGSSHHHHHHSSGLVPRGSHMRDPTQFEERHLKFLQQLGKGNFGSVEMCRYDPLQDNTGEVVAVKKLQHSTEEHLRDFEREIEILKSLQHDNIVKYKGVCYSAGRRNLKLIMEYLPYGSLRDYLQKHKERIDHIKLLQYTSQICKGMEYLGTKRYIHRDLATRNILVENENRVKIGDFGLTKVLPQDKEYYKVKEPGESPIFWYAPESLTESKFSVASDVWSFGVVLYELFTYIEKSKSPPAEFMRMIGNDKQGQMIVFHLIELLKNNGRLPRPDGCPDEIYMIMTECWNNNVNQRPSFRDLALRVDQIRDNMAGHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.38
R work: 0.2522
R free: 0.2527
Average B factor: 34.51
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 295
Crystal growth procedure: 100MM MES BUFFER, 100MM NACL, 28% (w/v) PEG3350, 2MM DTT AND 200MM TRI-SODIUM CITRATE
Matthews coefficient: 2.94
Solvent content (%): 52.39
Ligand: N,N-dicyclopropyl-6-ethyl-4-[(3-methoxypropyl)amino]-1-methyl-1,6-dihydroimidazo[4,5-d]pyrrolo[2,3-b]pyridine-7-carboxamide (50Y)
Ligand formula: C22 H30 N6 O2
Ligand molecular weight: 410.513
Ligand SMILES: CCn1c(cc2c1nc(c3c2n(cn3)C)NCCCOC)C(=O)N(C4CC4)C5CC5
Ligand InChI: InChI=1S/C22H30N6O2/c1-4-27-17(22(29)28(14-6-7-14)15-8-9-15)12-16-19-18(24-13-26(19)2)20(25-21(16)27)23-10-5-11-30-3/h12-15H,4-11H2,1-3H3,(H,23,25)
Release date: 2015-08-26
Crystal structure of KDM4B in complex with QC6352 (PDB entry 7JM5)
Macromolecule: Lysine-specific demethylase 4B
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11.66
Sequence length: 367 residues
Sequence: SMGSEDHGAQNPSCKIMTFRPTMEEFKDFNKYVAYIESQGAHRAGLAKIIPPKEWKPRQTYDDIDDVVIPAPIQQVVTGQSGLFTQYNIQKKAMTVGEYRRLANSEKYCTPRHQDFDDLERKYWKNLTFVSPIYGADISGSLYDDDVAQWNIGSLRTILDMVERECGTIIEGVNTPYLYFGMWKTTFAWHTEDMDLYSINYLHFGEPKSWYAIPPEHGKRLERLAIGFFPGSSQGCDAFLRHKMTLISPIILKKYGIPFSRITQEAGEFMITFPYGYHAGFNHGFNCAESTNFATLRWIDYGKVATQCTCRKDMVKISMDVFVRILQPERYELWKQGKDLTVLDHTRPTALTSPELSSWSASRASLK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.7
R work: 0.1956
R free: 0.2437
Average B factor: 78.42
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: tri-sodium citrate, PEG 3350
Matthews coefficient: 2.64
Solvent content (%): 53.43
Ligand: NICKEL (II) ION (NI)
Ligand formula: Ni
Ligand molecular weight: 58.693
Ligand SMILES: [Ni+2]
Ligand InChI: InChI=1S/Ni/q+2
Release date: 2022-02-02