satarupa22/MacromolecularLigandDB huggingface dataset:
The crystal structure of 2-(4-Benzhydrylpiperazin-1-yl)-N-(4-sulfamoylphenyl)acetamide in complex with human carbonic anhydrase II (PDB entry 6ZR8)
Macromolecule: Carbonic anhydrase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 262 residues
Sequence: MGMSHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHAFNVEFDDSQDKAVLKGGPLDGTYRLIQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDFGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTKGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLLECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.79
R work: 0.1637
R free: 0.1991
Average B factor: 13.5192
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 1.2 M Sodium Citrate, 0.1 M Tris-HCl pH 8.5
Matthews coefficient: 2.06
Solvent content (%): 40.21
Ligand: 2-[4-(diphenylmethyl)piperazin-1-yl]-~{N}-(4-sulfamoylphenyl)ethanamide (QOZ)
Ligand formula: C25 H28 N4 O3 S
Ligand molecular weight: 464.58
Ligand SMILES: c1ccc(cc1)C(c2ccccc2)N3CCN(CC3)CC(=O)Nc4ccc(cc4)S(=O)(=O)N
Ligand InChI: InChI=1S/C25H28N4O3S/c26-33(31,32)23-13-11-22(12-14-23)27-24(30)19-28-15-17-29(18-16-28)25(20-7-3-1-4-8-20)21-9-5-2-6-10-21/h1-14,25H,15-19H2,(H,27,30)(H2,26,31,32)
Release date: 2021-06-16
Selectivity switch between FAK and Pyk2: Macrocyclization of FAK inhibitors improves Pyk2 potency (PDB entry 5TOB)
Macromolecule: Protein-tyrosine kinase 2-beta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 282 residues
Sequence: GSMGGPQYGIAREDVVLNRILGEGFFGEVYEGVYTNHKGEKINVAVKTCKKDCTLDNKEKFMSEAVIMKNLDHPHIVKLIGIIEEEPTWIIMELYPYGELGHYLERNKNSLKVLTLVLYSLQICKAMAYLESINCVHRDIAVRNILVASPECVKLGDFGLSRYIEDEDYYKASVTRLPIKWMSPESINFRRFTTASDVWMFAVCMWEILSFGKQPFFWLENKDVIGVLEKGDRLPKPDLCPPVLYTLMTRCWDYDPSDRPRFTELVCSLSDVYQMEKDIAME
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.117
R work: 0.2061
R free: 0.2615
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 298
Crystal growth procedure: 25% PEG3350, 100 mM Bis-Tris pH 5.5, 100 mM MgCl2
Matthews coefficient: 2.3
Solvent content (%): 46.48
Ligand: N-methyl-N-{3-[({2-[(2-oxo-2,3-dihydro-1H-indol-5-yl)amino]-5-(trifluoromethyl)pyrimidin-4-yl}amino)methyl]pyridin-2-yl}methanesulfonamide (YAM)
Ligand formula: C21 H20 F3 N7 O3 S
Ligand molecular weight: 507.489
Ligand SMILES: CN(c1c(cccn1)CNc2c(cnc(n2)Nc3ccc4c(c3)CC(=O)N4)C(F)(F)F)S(=O)(=O)C
Ligand InChI: InChI=1S/C21H20F3N7O3S/c1-31(35(2,33)34)19-12(4-3-7-25-19)10-26-18-15(21(22,23)24)11-27-20(30-18)28-14-5-6-16-13(8-14)9-17(32)29-16/h3-8,11H,9-10H2,1-2H3,(H,29,32)(H2,26,27,28,30)
Release date: 2017-11-29
Crystal structure of the human METTL3-METTL14 complex bound to Compound 19 (ADO_AE_009) (PDB entry 7O28)
Macromolecule: N6-adenosine-methyltransferase catalytic subunit
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1.348
Sequence length: 246 residues
Sequence: MGHHHHHHSSGRENLYFQGALTQSVGGDSSADRLFPPQWICCDIRYLDVSILGKFAVVMADPPWDIHMELPYGTLTDDEMRRLNIPVLQDDGFLFLWVTGRAMELGRECLNLWGYERVDEIIWVKTNQLQRIIRTGRTGHWLNHGKEHCLVGVKGNPQGFNQGLDCDVIVAEVRSTSHKPDEIYGMIERLSPGTRKIELFGRPHNVQPNWITLGNQLDGIHLLDPDVVARFKQRYPDGIISKPKNL
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.47
R work: 0.2045
R free: 0.2535
Average B factor: 68.11
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 295
Crystal growth procedure: 20% PEG 3350, 400mM Mg acetate
Matthews coefficient: 2.14
Solvent content (%): 42.53
Ligand: 9-(2-chloranyl-7~{H}-pyrrolo[2,3-d]pyrimidin-4-yl)-4-[4-[(4,4-dimethylpiperidin-1-yl)methyl]phenyl]-1,4,9-triazaspiro[5.5]undecan-2-one (UZB)
Ligand formula: C28 H36 Cl N7 O
Ligand molecular weight: 522.085
Ligand SMILES: CC1(CCN(CC1)Cc2ccc(cc2)N3CC(=O)NC4(C3)CCN(CC4)c5c6cc[nH]c6nc(n5)Cl)C
Ligand InChI: InChI=1S/C28H36ClN7O/c1-27(2)8-13-34(14-9-27)17-20-3-5-21(6-4-20)36-18-23(37)33-28(19-36)10-15-35(16-11-28)25-22-7-12-30-24(22)31-26(29)32-25/h3-7,12H,8-11,13-19H2,1-2H3,(H,33,37)(H,30,31,32)
Release date: 2021-09-15
Human DNA polymerase beta crosslinked complex, 20 s Ca to Mg exchange (PDB entry 7RBI)
Macromolecule: DNA polymerase beta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 341 residues
Sequence: MSKRKAPQETLNGGITDMLTELANFEKNVSQAIHKYNAYRKAASVIAKYPHKIKSGAEAKKLPGVGTKIAEKIDEFLATGKLRKLEKIRQDDTSSSINFLTRVSGIGPSAARKFVDEGIKTLEDLRKNEDKLNHHQRIGLKYFGDFEKRIPREEMLQMQDIVLNEVKKVDSEYIATVCGSFRRGAESSGDMDVLLTHPSFTSESTKQPKLLHQVVEQLQKVHFITDTLSKGETKFMGVCQLPSKNDEKEYPHRRIDIRLIPKDQYYCGVLYFTGSDIFNKNMRAHALEKGFTINEYTIRPLGVTGVAGEPLPVDSEKDIFDYIQWKYREPKDRSEHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.93
R work: 0.1857
R free: 0.2204
Average B factor: 30.486
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 298
Crystal growth procedure: 0.1 M Citrate pH 5.5, 18% PEG6000
Matthews coefficient: 2.12
Solvent content (%): 41.88
Ligand: 2-deoxy-3,5-di-O-phosphono-D-erythro-pentitol (QPJ)
Ligand formula: C5 H14 O10 P2
Ligand molecular weight: 296.106
Ligand SMILES: C(CO)C(C(COP(=O)(O)O)O)OP(=O)(O)O
Ligand InChI: InChI=1S/C5H14O10P2/c6-2-1-5(15-17(11,12)13)4(7)3-14-16(8,9)10/h4-7H,1-3H2,(H2,8,9,10)(H2,11,12,13)/t4-,5+/m1/s1
Release date: 2022-03-09
Human sterol 14a-demethylase (CYP51) in complex with the substrate lanosterol (PDB entry 6UEZ)
Macromolecule: Lanosterol 14-alpha demethylase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.14.154
Sequence length: 454 residues
Sequence: MAKKTSSKGKLPPYIFSPIPFLGHAIAFGKSPIEFLENAYEKYGPVFSFTMVGKTFTYLLGSDAAALLFNSKNEDLNAEDVYSRLTTPVFGKGVAYDVPNPVFLEQKKMLKSGLNIAHFKQHVSIIEKETKEYFESWGESGEKNVFEALSELIILTASHCLHGKEIRSQLNEKVAQLYADLAGGFSHAAWLLPGWLPLPSFRRRDRAHREIKDIFYKAIQKRRQSQEKIDDILQTLLDATYKDGRPLTDDEVAGMLIGLLLAGQATSSTTSAWMGFFLARDKTLQKKCYLEQKTVCGENLPPLTYDQLKDLNLLDRCIKETLRLRPPIMIMMRMARTPQTVAGYTIPPGHQVCVSPTVNQRLKDSWVERLDFNPDRYLQDNPASGEKFAYVPFGAGRHRCIGENFAYVQIKTIWSTMLRLYEFDLIDGYFPTVNYTTMIHTPENPVIRYKRRSK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.98
R work: 0.191
R free: 0.2221
Average B factor: 53.135
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 7.4
Crystallization temperature (K): 293
Crystal growth procedure: PEG3350, HEGA-11, potassium phosphate, lanosterol
Matthews coefficient: 2.85
Solvent content (%): 56.81
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: 2020-06-10
Human Aprataxin (Aptx) L248M bound to DNA, AMP and Zn product (PDB entry 6CVS)
Macromolecule: Aprataxin
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.11.7
Sequence length: 182 residues
Sequence: GSHMGHWSQGLKISMQDPKMQVYKDEQVVVIKDKYPKARYHWLVLPWTSISSLKAVAREHLELLKHMHTVGEKVIVDFAGSSKLRFRMGYHAIPSMSHVHLHVISQDFDSPCLKNKKHWNSFNTEYFLESQAVIEMVQEAGRVTVRDGMPELLKLPLRCHECQQLLPSIPQLKEHLRKHWTQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.11
R work: 0.1738
R free: 0.1964
Average B factor: 39.2242
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 277
Crystal growth procedure: 100 mM MES, 25% w/v polyethylene glycol 4000
Matthews coefficient: 2.54
Solvent content (%): 51.64
Ligand: ADENOSINE MONOPHOSPHATE (AMP)
Ligand formula: C10 H14 N5 O7 P
Ligand molecular weight: 347.221
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)O)O)O)N
Ligand InChI: InChI=1S/C10H14N5O7P/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(22-10)1-21-23(18,19)20/h2-4,6-7,10,16-17H,1H2,(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
Release date: 2018-07-04
human PDE10A in complex with 3-(2-phenylpyrazol-3-yl)-1-[3-(trifluoromethoxy)phenyl]pyridazin-4-one (PDB entry 5I2R)
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: 318 residues
Sequence: AQGLMQFTLPVRLCKEIELFHFDIGPFENMWPGIFVYMVHRSCGTSCFELEKLCRFIMSVKKNYRRVPYHNWKHAVTVAHCMYAILQNNHTLFTDLERKGLLIACLCHDLDHRGFSNSYLQKFDHPLAALYSTSTMEQHHFSQTVSILQLEGHNIFSTLSSSEYEQVLEIIRKAIIATDLALYFGNRKQLEEMYQTGSLNLNNQSHRDRVIGLMMTACDLCSVTKLWPVTKLTANDIYAEFWAEGDEMKKLGIQPIPMMDRDKKDEVPQGQLGFYNAVAIPCYTTLTQILPPTEPLLKACRDNLSQWEKVIRGEETAT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.5
R work: 0.191
R free: 0.25
Average B factor: 37.91
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 295
Crystal growth procedure: none
Matthews coefficient: 2.87
Solvent content (%): 57.15
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: 2016-03-09
Crystal structure of the D263G missense variant of human PGM1 (PDB entry 5TR2)
Macromolecule: Phosphoglucomutase-1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 5.4.2.2
Sequence length: 585 residues
Sequence: MHHHHHHSSGVDLGTENLYFQSNMVKIVTVKTQAYQDQKPGTSGLRKRVKVFQSSANYAENFIQSIISTVEPAQRQEATLVVGGDGRFYMKEAIQLIARIAAANGIGRLVIGQNGILSTPAVSCIIRKIKAIGGIILTASHNPGGPNGDFGIKFNISNGGPAPEAITDKIFQISKTIEEYAVCPDLKVDLGVLGKQQFDLENKFKPFTVEIVDSVEAYATMLRSIFDFSALKELLSGPNRLKIRIDAMHGVVGPYVKKILCEELGAPANSAVNCVPLEDFGGHHPGPNLTYAADLVETMKSGEHDFGAAFDGDGDRNMILGKHGFFVNPSDSVAVIAANIFSIPYFQQTGVRGFARSMPTSGALDRVASATKIALYETPTGWKFFGNLMDASKLSLCGEESFGTGSDHIREKDGLWAVLAWLSILATRKQSVEDILKDHWQKYGRNFFTRYDYEEVEAEGANKMMKDLEALMFDRSFVGKQFSANDKVYTVEKADNFEYSDPVDGSISRNQGLRLIFTDGSRIVFRLSGTGSAGATIRLYIDSYEKDVAKINQDPQVMLAPLISIALKVSQLQERTGRTAPTVIT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.5
R work: 0.22
R free: 0.2919
Average B factor: 56.38
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 292
Crystal growth procedure: 1.6 M Ammonium Sulfate, 0.1 M NaCl, and 0.1 M HEPES pH 7.5
Matthews coefficient: 2.85
Solvent content (%): 60
Ligand: SULFATE ION (SO4)
Ligand formula: O4 S
Ligand molecular weight: 96.063
Ligand SMILES: [O-]S(=O)(=O)[O-]
Ligand InChI: InChI=1S/H2O4S/c1-5(2,3)4/h(H2,1,2,3,4)/p-2
Release date: 2017-02-08
Crystal structure of human carbonic anhydrase isozyme II with 2-(Benzylamino)-3,5,6-trifluoro-4-[(2-phenylethyl)thio]benzene- sulfonamide (PDB entry 5DOG)
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): 1.7
R work: 0.162
R free: 0.214
Average B factor: 16.753
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 made from 1M sodium BICINE and 3.4M sodium malonate
Matthews coefficient: 2.04
Solvent content (%): 39.2
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: 2016-09-28
APO MAP4K4 T181E Phosphomimetic Mutant (PDB entry 4U3Z)
Macromolecule: Mitogen-activated protein kinase kinase kinase kinase 4
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 332 residues
Sequence: GSANDSPAKSLVDIDLSSLRDPAGIFELVEVVGNGTYGQVYKGRHVKTGQLAAIKVMDVTEDEEEEIKLEINMLKKYSHHRNIATYYGAFIKKSPPGHDDQLWLVMEFCGAGSITDLVKNTKGNTLKEDWIAYISREILRGLAHLHIHHVIHRDIKGQNVLLTENAEVKLVDFGVSAQLDREVGRRNTFIGTPYWMAPEVIACDENPDATYDYRSDLWSCGITAIEMAEGAPPLCDMHPMRALFLIPRNPPPRLKSKKWSKKFFSFIEGCLVKNYMQRPSTEQLLKHPFIRDQPNERQVRIQLKDHIDRTRKKRGEKDETEYEYSGSEEGNS
Oligomeric state: Homo 2-mer
Stoichiometry: A2
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.09
R work: 0.1826
R free: 0.249
Average B factor: 36.1921
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.3
Crystallization temperature (K): 292
Crystal growth procedure: 0.2 M potassium citrate, pH 8.3, 20% PEG 3350
Matthews coefficient: 1.97
Solvent content (%): 37.54
Ligand: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID (MES)
Ligand formula: C6 H13 N O4 S
Ligand molecular weight: 195.237
Ligand SMILES: C1COCC[NH+]1CCS(=O)(=O)[O-]
Ligand InChI: InChI=1S/C6H13NO4S/c8-12(9,10)6-3-7-1-4-11-5-2-7/h1-6H2,(H,8,9,10)
Release date: 2016-01-06
PanDDA analysis group deposition of models with modelled events (e.g. bound ligands) -- Crystal Structure of NUDT7 in complex with FMOPL000710a (PDB entry 5QGI)
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): 1.95
R work: 0.1917
R free: 0.2236
Average B factor: 39.686
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: 4.34
Solvent content (%): 71.66
Ligand: 2-methoxy-~{N}-(2,4,6-trimethylphenyl)ethanamide (B0V)
Ligand formula: C12 H17 N O2
Ligand molecular weight: 207.269
Ligand SMILES: Cc1cc(c(c(c1)C)NC(=O)COC)C
Ligand InChI: InChI=1S/C12H17NO2/c1-8-5-9(2)12(10(3)6-8)13-11(14)7-15-4/h5-6H,7H2,1-4H3,(H,13,14)
Release date: 2019-03-27
Crystal Structure of CK2alpha with Compound 5 bound (PDB entry 5CVF)
Macromolecule: Casein kinase II subunit alpha
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 328 residues
Sequence: SGPVPSRARVYTDVNTHRPSEYWDYESHVVEWGNQDDYQLVRKLGRGKYSEVFEAINITNNEKVVVKILKPVAAAKIKREIKILENLRGGPNIITLADIVKDPVSRTPALVFEHVNNTDFKQLYQTLTDYDIRFYMYEILKALDYCHSMGIMHRDVKPHNVMIDHEHRKLRLIDWGLAEFYHPGQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRKEPFFHGHDNYDQLVRIAKVLGTEDLYDYIDKYNIELDPRFNDILGRHSRKRWERFVHSENQHLVSPEALDFLDKLLRYDHQSRLTAREAMEHPYFYTVVK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.63
R work: 0.2009
R free: 0.209
Average B factor: 22.37
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: 2.01
Solvent content (%): 38.93
Ligand: ADENOSINE-5'-TRIPHOSPHATE (ATP)
Ligand formula: C10 H16 N5 O13 P3
Ligand molecular weight: 507.181
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N
Ligand InChI: InChI=1S/C10H16N5O13P3/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(26-10)1-25-30(21,22)28-31(23,24)27-29(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H,23,24)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
Release date: 2016-07-27
Crystal Structure of wild-type human formylglycine generating enzyme bound to Cu(I) (PDB entry 5SSZ)
Macromolecule: Formylglycine-generating enzyme
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.8.3.7
Sequence length: 323 residues
Sequence: ADLGSSMEFEANAPGPVPGERQLAHSKMVPIPAGVFTMGTDDPQIKQDGEAPARRVTIDAFYMDAYEVSNTEFEKFVNSTGYLTEAEKFGDSFVFEGMLSEQVKTNIQQAVAAAPWWLPVKGANWRHPEGPDSTILHRPDHPVLHVSWNDAVAYCTWAGKRLPTEAEWEYSCRGGLHNRLFPWGNKLQPKGQHYANIWQGEFPVTNTGEDGFQGTAPVDAFPPNGYGLYNIVGNAWEWTSDWWTVHHSVEETLNPKGPPSGKDRVKKGGSYMCHRSYCYRYRCAARSQNTPDSSASNLGFRCAADRLPTMDSGRGSHHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.02
R work: 0.1307
R free: 0.1417
Average B factor: 12.4298
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 293
Crystal growth procedure: 9.6 mg/mL protein in 20mM Tris/HCl pH8.0 mixed 1:1 with reservoir 0.1M Tris/HCl pH 8.5, 20-25% PEG4000, 0.2-0.3M CaCl2
Matthews coefficient: 2.05
Solvent content (%): 40.14
Ligand: COPPER (I) ION (CU1)
Ligand formula: Cu
Ligand molecular weight: 63.546
Ligand SMILES: [Cu+]
Ligand InChI: InChI=1S/Cu/q+1
Release date: 2023-08-23
Structure of the PR domain from human PRDM5 (PDB entry 6XAZ)
Macromolecule: PR domain zinc finger protein 5
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1
Sequence length: 130 residues
Sequence: GSGMLGMYVPDRFSLKSSRVQDGMGLYTARRVRKGEKFGPFAGEKRMPEDLDENMDYRLMWEVRGSKGEVLYILDATNPRHSNWLRFVHEAPSQEQKNLAAIQEGENIFYLAVEDIETDTELLIGYLDSD
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.7
R work: 0.2114
R free: 0.2593
Average B factor: 38.36
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 0.1 M sodium cacodylate pH 6.5, 2.0 M ammonium sulfate, 0.2 M NaCl
Matthews coefficient: 2.35
Solvent content (%): 47.67
Ligand: DI(HYDROXYETHYL)ETHER (PEG)
Ligand formula: C4 H10 O3
Ligand molecular weight: 106.12
Ligand SMILES: C(COCCO)O
Ligand InChI: InChI=1S/C4H10O3/c5-1-3-7-4-2-6/h5-6H,1-4H2
Release date: 2021-06-09
DNA Polymerase Mu, dGTP:Ct Reaction State Ternary Complex, 10 mM Mg2+ (10min) (PDB entry 7KSW)
Macromolecule: DNA-directed DNA/RNA polymerase mu
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 356 residues
Sequence: GSAAAPLSPAWMPAYACQRPTPLTHHNTGLSEALEILAEAAGFEGSEGRLLTFCRAASVLKALPSPVTTLSQLQGLPHFGEHSSRVVQELLEHGVCEEVERVRRSERYQTMKLFTQIFGVGVKTADRWYREGLRTLDDLREQPQKLTQQQKAGLQHHQDLSTPVLRSDVDALQQVVEEAVGQALPGATVTLTGGFRRGKLQGHDVDFLITHPKEGQEAGLLPRVMCRLQDQGLILYHQHQHSCCESPTRLAQQSHMDAFERSFCIFRLPQPGSWKAVRVDLVVAPVSQFPFALLGWTGSKLFQRELRRFSRKEKGLWLNSHGLFDPEQKTFFQAASEEDIFRHLGLEYLPPEQRNA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.49
R work: 0.1544
R free: 0.1718
Average B factor: 26.1433
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 85-90mM HEPES pH 7.5, 17-18% PEG4000
Matthews coefficient: 2.51
Solvent content (%): 50.95
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: 2021-12-01
Crystal structure of IRE1 in complex with G-3053 (PDB entry 6XDD)
Macromolecule: Serine/threonine-protein kinase/endoribonuclease IRE1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 434 residues
Sequence: GSSPSLEQDDGDEETSVVIVGKISFCPKDVLGHGAEGTIVYRGMFDNRDVAVKRILPECFSFADREVQLLRESDEHPNVIRYFCTEKDRQFQYIAIELCAATLQEYVEQKDFAHLGLEPITLLQQTTSGLAHLHSLNIVHRDLKPHNILISMPNAHGKIKAMISDFGLCKKLAVGRHSFSRRSGVPGTEGWIAPEMLSEDCKENPTYTVDIFSAGCVFYYVISEGSHPFGKSLQRQANILLGACSLDCLHPEKHEDVIARELIEKMIAMDPQKRPSAKHVLKHPFFWSLEKQLQFFQDVSDRIEKESLDGPIVKQLERGGRAVVKMDWRENITVPLQTDLRKFRTYKGGSVRDLLRAMRNKKHHYRELPAEVRETLGSLPDDFVCYFTSRFPHLLAHTYRAMELCSHERLFQPYYFHEPPEPQPPVTPDALGNS
Oligomeric state: Homo 2-mer
Stoichiometry: A2
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.4
R work: 0.1984
R free: 0.2381
Average B factor: 63.8392
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 10% 2-propanol, 0.1 M sodium citrate tribasic dihydrate pH 5.0, and 26% PEG400, 4% pentaerythritol ethoxylate (3/4 EO/OH), 4% 1,3-Propanediol
Matthews coefficient: 2.93
Solvent content (%): 58.04
Ligand: 4-[(trans-4-aminocyclohexyl)amino]-N-(6-chloro-3-{[(2,5-difluorophenyl)sulfonyl]amino}-2-fluorophenyl)thieno[3,2-d]pyrimidine-7-carboxamide (N97)
Ligand formula: C25 H22 Cl F3 N6 O3 S2
Ligand molecular weight: 611.059
Ligand SMILES: c1cc(c(cc1F)S(=O)(=O)Nc2ccc(c(c2F)NC(=O)c3csc4c3ncnc4NC5CCC(CC5)N)Cl)F
Ligand InChI: InChI=1S/C25H22ClF3N6O3S2/c26-16-6-8-18(35-40(37,38)19-9-12(27)1-7-17(19)28)20(29)22(16)34-25(36)15-10-39-23-21(15)31-11-32-24(23)33-14-4-2-13(30)3-5-14/h1,6-11,13-14,35H,2-5,30H2,(H,34,36)(H,31,32,33)/t13-,14-
Release date: 2021-04-21
Structure based design of RIP1 kinase inhibitors (PDB entry 6C4D)
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: GGSGQPDMSLNVIKMKSSDFLESAELDSGGFGKVSLAFHRTQGLMIMKTVYKGPNCIEHNEALLEEAKMMNRLRHSRVVKLLGVIIEEGKYSLVMEYMEKGNLMHVLKAEMSTPLSVKGRIILEIIEGMAYLHGKGVIHKDLKPENILVDNDFHIKIADLGLASFKMWSKLNNEEHNELREVDGTAKKNGGTLYYMAPEHLNDVNAKPTEKSDVYSFAVVLWAIFANKEPYENAIAEQQLIMAIKSGNRPDVDDITEYCPREIISLMKLCWEANPEARPTFPGIEEKFRPFYLSQLE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.52
R work: 0.23625
R free: 0.29643
Average B factor: 71.72
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 7.2
Crystallization temperature (K): 277
Crystal growth procedure: 0.25 M ammonium iodide, 0.03 M glycyl-glycyl-glycine and polyethylene glycol (PEG) 3350 15-25%
Matthews coefficient: 2.24
Solvent content (%): 45.18
Ligand: (3S)-3-(2-benzyl-3-chloro-7-oxo-2,4,5,7-tetrahydro-6H-pyrazolo[3,4-c]pyridin-6-yl)-5-methyl-4-oxo-2,3,4,5-tetrahydro-1,5-benzoxazepine-8-carbonitrile (EJP)
Ligand formula: C24 H20 Cl N5 O3
Ligand molecular weight: 461.9
Ligand SMILES: CN1c2ccc(cc2OCC(C1=O)N3CCc4c(nn(c4Cl)Cc5ccccc5)C3=O)C#N
Ligand InChI: InChI=1S/C24H20ClN5O3/c1-28-18-8-7-16(12-26)11-20(18)33-14-19(23(28)31)29-10-9-17-21(24(29)32)27-30(22(17)25)13-15-5-3-2-4-6-15/h2-8,11,19H,9-10,13-14H2,1H3/t19-/m0/s1
Release date: 2018-03-21
High-resolution crystal structure of the UBC core domain of UBE2E1/UbcH6 (PDB entry 5LBN)
Macromolecule: Ubiquitin-conjugating enzyme E2 E1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2.23
Sequence length: 158 residues
Sequence: GSMSKNSKLLSTSAKRIQKELADITLDPPPNCSAGPKGDNIYEWRSTILGPPGSVYEGGVFFLDITFTPEYPFKPPKVTFRTRIYHCNINSQGVICLDILKDNWSPALTISKVLLSICSLLTDCNPADPLVGSIATQYMTNRAEHDRMARQWTKRYAT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.42
R work: 0.1543
R free: 0.183
Average B factor: 17.7812
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 0.1M Sodium citrate pH 6 and 8% (w/v) PEG 8000
Matthews coefficient: 2.1
Solvent content (%): 39.8
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: 2018-02-14