satarupa22/MacromolecularLigandDB huggingface dataset:
Macrocyclic plasmin inhibitor (PDB entry 7UAH)
Macromolecule: Plasminogen
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.7
Sequence length: 250 residues
Sequence: AAPSFDCGKPQVEPKKCPGRVVGGCVAHPHSWPWQVSLRTRFGMHFCGGTLISPEWVLTAAHCLEKSPRPSSYKVILGAHQEVNLEPHVQEIEVSRLFLEPTRKDIALLKLSSPAVITDKVIPACLPSPNYVVADRTECFITGWGETQGTFGAGLLKEAQLPVIENKVCNRYEFLNGRVQSTELCAGHLAGGTDSCQGDAGGPLVCFEKDKYILQGVTSWGLGCARPNKPGVYVRVSRFVTWIEGVMRNN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.57
R work: 0.1749
R free: 0.1917
Average B factor: 24.1206
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5
Crystallization temperature (K): 293
Crystal growth procedure: 13-18% PEG 4000, 150 mM Ammonium sulfate, 100 mM MES, 10% 1,2-butanediol
Matthews coefficient: 2.12
Solvent content (%): 42.08
Ligand: (6S,9R,19S,22R)-N-{[4-(aminomethyl)phenyl]methyl}-22-[(3-chlorobenzene-1-sulfonyl)amino]-3,12,21-trioxo-2,6,9,13,20-pentaazatetracyclo[22.2.2.2~6,9~.2~14,17~]dotriaconta-1(26),14,16,24,27,29-hexaene-19-carboxamide (M63)
Ligand formula: C42 H49 Cl N8 O6 S
Ligand molecular weight: 829.406
Ligand SMILES: c1cc(cc(c1)Cl)S(=O)(=O)NC2Cc3ccc(cc3)NC(=O)CCN4CCN(CCC(=O)Nc5ccc(cc5)CC(NC2=O)C(=O)NCc6ccc(cc6)CN)CC4
Ligand InChI: InChI=1S/C42H49ClN8O6S/c43-33-2-1-3-36(26-33)58(56,57)49-38-25-30-10-14-35(15-11-30)47-40(53)17-19-51-22-20-50(21-23-51)18-16-39(52)46-34-12-8-29(9-13-34)24-37(48-42(38)55)41(54)45-28-32-6-4-31(27-44)5-7-32/h1-15,26,37-38,49H,16-25,27-28,44H2,(H,45,54)(H,46,52)(H,47,53)(H,48,55)/t37-,38+/m0/s1
Release date: 2023-03-15
Structural basis of tubulin detyrosination by vasohibins-SVBP enzyme complex and functional implications (PDB entry 6J4V)
Macromolecule: Tubulinyl-Tyr carboxypeptidase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.17.17
Sequence length: 251 residues
Sequence: GVLFHVNKSGFPIDSHTWERMWMHVAKVHPKGGEMVGAIRNAAFLAKPSIPQVPNYRLSMTIPDWLQAIQNYMKTLQYNHTGTQFFEIRKMRPLSGLMETAKEMTRESLPIKCLEAVILGIYLTNGQPSIERFPISFKTYFSGNYFHHVVLGIYCNGRYGSLGMSRRAELMDKPLTFRTLSDLIFDFEDSYKKYLHTVKKVKIGLYVPHEPHSFQPIEWKQLVLNVSKMLRADIRKELEKYARDMRMKILK
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.1
R work: 0.1688
R free: 0.1996
Crystallization method: EVAPORATION
Crystallization pH: 8.2
Crystallization temperature (K): 293
Crystal growth procedure: For crystallization of V2c-SVBP C58S in complex with the maTail peptide the components were mixed in a 1:3 molar ratio and incubated at room temperature for 24 h before setting up crystallization trials. The resulting V2c-SVBP S58C-maTail complex was crystallized in 1.4 M sodium/potassium phosphate, pH 8.2.
Matthews coefficient: 3.1
Solvent content (%): 60.32
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: 2019-05-01
EGFR kinase domain mutant "TMLR" with compound 33 (PDB entry 5CAQ)
Macromolecule: Epidermal growth factor receptor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 331 residues
Sequence: GSGEAPNQALLRILKETEFKKIKVLGSGAFGTVYKGLWIPEGEKVKIPVAIKELREATSPKANKEILDEAYVMASVDNPHVCRLLGICLTSTVQLIMQLMPFGCLLDYVREHKDNIGSQYLLNWCVQIAKGMNYLEDRRLVHRDLAARNVLVKTPQHVKITDFGRAKLLGAAAAEYHAEGGKVPIKWMALESILHRIYTHQSDVWSYGVTVWELMTFGSKPYDGIPASEISSILEKGERLPQPPICTIDVYMIMVKCWMIDADSRPKFRELIIEFSKMARDPQRYLVIQGDERMHLPSPTDSNFYRALMDEEDMDDVVDADEYLIPQQGNS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.5
R work: 0.1831
R free: 0.2244
Average B factor: 58.96
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 292
Crystal growth procedure: PEG 10000, erthylene glycol
Matthews coefficient: 3.46
Solvent content (%): 64.46
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: 2015-10-28
Crystal structure of an engineered helicase domain construct for human Bloom syndrome protein (BLM) (PDB entry 7AUC)
Macromolecule: Bloom syndrome protein,Bloom syndrome protein
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.4.12
Sequence length: 562 residues
Sequence: MGSAWSHPQFEKSSGLEVLFQGPHMSRNLKHERFQSLSFPHTKEMMKIFHKKFGLHNFRTNQLEAINAALLGEDCFILMPTGGGKSLCYQLPACVSPGVTVVISPLRSLIVDQVQKLTSLDIPATYLTGDKTDSEATNIYLQLSKKDPIIKLLYVTPEKICASNRLISTLENLYERKLLARFVIDEAHCVSQWGHDFRQDYKRMNMLRQKFPSVPVMALTATANPRVQKDILTQLKILRPQVFSMSFNRHNLKYYVLPKKPKKVAFDCLEWIRKHHPYDSGIIYCLSRRECDTMADTLQRDGLAALAYHAGLSDSARDEVQQKWINQDGCQVICATIAFGMGIDKPDVRFVIHASLPKSVEGYYQESGRAGRDGEISHCLLFYTYHDVTRLKRLIMMEKDGNHHTRETHFNNLYSMVHYCENITECRRIQLLAYFGENGFNPDFCKKHPDVSCDNCCKTKGSGGSKALVAKVSQREEMVKKCLGELTEVCKSLGKVFGVHYFNIFNTVTLKKLAESLSSDPEVLLQIDGVTEDKLEKYGAEVISVLQKYSEWTSPAEDSSPG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.53
R work: 0.1891
R free: 0.2084
Average B factor: 32.6
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277.15
Crystal growth procedure: Morpheus-HT, condition A8, Molecular Dimensions
0.06 M divalents, 37.5% Buffer System 2 and 37.5% Precipitant Mix 4
Divalents = 0.3M magnesium chloride, 0.3M calcium chloride
Buffer system 2 = 1M sodium HEPES, MOPS (acid) pH 7.5
75% Precipitant Mix 4 = 25% w/v MPD, 25% v/v PEG1000, 25% w/v PEG 3350
Matthews coefficient: 2.38
Solvent content (%): 48.39
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: 2020-12-16
Crystal structure of human PCAF bromodomain in complex with fragment MB093 (fragment 7) (PDB entry 5FE5)
Macromolecule: Histone acetyltransferase KAT2B
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1.48
Sequence length: 119 residues
Sequence: SMGKEKSKEPRDPDQLYSTLKSILQQVKSHQSAWPFMEPVKRTEAPGYYEVIRFPMDLKTMSERLKNRYYVSKKLFMADLQRVFTNCKEYNPPESEYYKCANILEKFFFSKIKEAGLID
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.12
R work: 0.20513
R free: 0.2511
Average B factor: 45.8
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277.15
Crystal growth procedure: 21-35% PEG 3350, 0.1 M Bis-Tris pH 5.5-7.0 or 21-40% medium-molecular-weight PEG smears (MMW PEG smears) buffered either with 0.1 M Bis-Tris pH 6.0-7.5 or 0.1 M Tris pH 7.5-8.8
Matthews coefficient: 3.39
Solvent content (%): 63.71
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: 2016-01-13
Crystal structure of PDE5A in complex with inhibitor L12 (PDB entry 7FAR)
Macromolecule: cGMP-specific 3',5'-cyclic phosphodiesterase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.4.35
Sequence length: 349 residues
Sequence: SYHASAAEEETRELQSLAAAVVPSAQTLKITDFSFSDFELSDLETALCTIRMFTDLNLVQNFQMKHEVLCRWILSVKKNYRKNVAYHNWRHAFNTAQCMFAALKAGKIQNKLTDLEILALLIAALSHDLDHRGVNNSYIQRSEHPLAQLYCHSIMEHHHFDQCLMILNSPGNQILSGLSIEEYKTTLKIIKQAILATDLALYIKRRGEFFELIRKNQFNLEDPHQKELFLAMLMTACDLSAITKPWPIQQRIAELVATEFFDQGDRERKELNIEPTDLMNREKKNKIPSMQVGFIDAICLQLYEALTHVSEDCFPLLDGCRKNRQKWQALAEQQEKMLINGESGQAKRN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.40006470991
R work: 0.212773636809
R free: 0.249946221896
Average B factor: 50.2141933494
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 0.2 M magnesium sulfate, 0.1 M sodium cacodylate, pH 6.5, 17% PEG3350
Matthews coefficient: 2.59
Solvent content (%): 52.51
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: 2022-05-18
Crystal structure of the human neutralizing antibody Fab fragment T025 bound to TBEV EDIII (Siberian Subtype) (PDB entry 7LSG)
Macromolecule: T025 Fab Heavy Chain
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 232 residues
Sequence: QVQLVESGGGVVQPGRSLRLSCAASGFTFSNYGMHWVRQAPGKGLDWVAVISYDAISKSYADSVEGRFTISRDNSKNTLYLQMNSLRAEDSAVYYCAKSPTAIDPPFDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDKTHHHHHH
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.86
R work: 0.1867
R free: 0.2123
Average B factor: 34.93
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 295
Crystal growth procedure: 5% (+/-)-2-Methyl-2,4-pentanediol, 0.1M HEPES pH 7.5, 10% PEG 10000
Matthews coefficient: 2.87
Solvent content (%): 57.18
Release date: 2021-04-07
Crystal structure of JAK3 in complex with Compound 10 (FM475) (PDB entry 6GL9)
Macromolecule: Tyrosine-protein kinase JAK3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 294 residues
Sequence: SMQDPTIFEERHLKYISQLGKGNFGSVELCRYDPLGDNTGALVAVKQLQHSGPDQQRDFQREIQILKALHSDFIVKYRGVSYGPGRQSLRLVMEYLPSGCLRDFLQRHRARLDASRLLLYSSQICKGMEYLGSRRCVHRALAARNILVESEAHVKIADFGLAKLLPLDKDYYVVREPGQSPIFWYAPESLSDNIFSRQSDVWSFGVVLYELFTYCDKSCSPSAEFLRMMGSERDVPALSRLLELLEEGQRLPAPPACPAEVHELMKLCWAPSPQDRPSFSALGPQLDMLWSGSR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.7
R work: 0.20688
R free: 0.2438
Average B factor: 24.922
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277.15
Crystal growth procedure: 24-30% PEG 3350, 0.1 M MES, pH 5.5-6.0 and 0.1-0.2 M MgCl2
Matthews coefficient: 1.95
Solvent content (%): 36.89
Ligand: (~{E})-3-[3-(3-cyclohexyl-3,5,8,10-tetrazatricyclo[7.3.0.0^{2,6}]dodeca-1(9),2(6),4,7,11-pentaen-4-yl)phenyl]prop-2-enenitrile (F3W)
Ligand formula: C23 H21 N5
Ligand molecular weight: 367.446
Ligand SMILES: c1cc(cc(c1)c2nc3cnc4c(c3n2C5CCCCC5)cc[nH]4)C=CC#N
Ligand InChI: InChI=1S/C23H21N5/c24-12-5-7-16-6-4-8-17(14-16)23-27-20-15-26-22-19(11-13-25-22)21(20)28(23)18-9-2-1-3-10-18/h4-8,11,13-15,18H,1-3,9-10H2,(H,25,26)/b7-5+
Release date: 2018-06-27
Crystal structure of zebrafish Sirtuin 5 in complex with 3(S)-(naphthylthio)succinyl-CPS1 peptide (PDB entry 6FLG)
Macromolecule: 3(S)-(naphthylthio)succinyl-CPS1 peptide
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 8 residues
Sequence: XVLXEYGV
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.5
R work: 0.24158
R free: 0.31055
Average B factor: 78.898
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.7
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M HEPES 7.7, 20% PEG3350
Matthews coefficient: 2.7
Solvent content (%): 54.5
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: 2018-04-18
Factor Xa complex with GTC000102 (PDB entry 4ZHA)
Macromolecule: Coagulation factor X
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.6
Sequence length: 134 residues
Sequence: EEMKKGHLERECMEETCSYEEAREVFEDSDKTNEFWNKYKDGDQCETSPCQNQGKCKDGLGEYTCTCLEGFEGKNCELFTRKLCSLDNGDCDQFCHEEQNSVVCSCARGYTLADNGKACIPTGPYPCGKQTLER
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.86
R work: 0.1953
R free: 0.2382
Average B factor: 33.901
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 16-20% PEG 6K, 50 mM Mes-NaOH (pH 5.7-6.0), 5 mM CaCl2, and 50 mM NaCl
Matthews coefficient: 1.85
Solvent content (%): 33.59
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: 2016-01-13
Crystal structure of the G291R mutant of human phosphoglucomutase 1 (PDB entry 5HSH)
Macromolecule: Phosphoglucomutase-1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 5.4.2.2
Sequence length: 562 residues
Sequence: MVKIVTVKTQAYQDQKPGTSGLRKRVKVFQSSANYAENFIQSIISTVEPAQRQEATLVVGGDGRFYMKEAIQLIARIAAANGIGRLVIGQNGILSTPAVSCIIRKIKAIGGIILTASHNPGGPNGDFGIKFNISNGGPAPEAITDKIFQISKTIEEYAVCPDLKVDLGVLGKQQFDLENKFKPFTVEIVDSVEAYATMLRSIFDFSALKELLSGPNRLKIRIDAMHGVVGPYVKKILCEELGAPANSAVNCVPLEDFGGHHPDPNLTYAADLVETMKSGEHDFGAAFDGDRDRNMILGKHGFFVNPSDSVAVIAANIFSIPYFQQTGVRGFARSMPTSGALDRVASATKIALYETPTGWKFFGNLMDASKLSLCGEESFGTGSDHIREKDGLWAVLAWLSILATRKQSVEDILKDHWQKYGRNFFTRYDYEEVEAEGANKMMKDLEALMFDRSFVGKQFSANDKVYTVEKADNFEYSDPVDGSISRNQGLRLIFTDGSRIVFRLSGTGSAGATIRLYIDSYEKDVAKINQDPQVMLAPLISIALKVSQLQERTGRTAPTVIT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.65
R work: 0.23
R free: 0.2733
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 9.7
Crystallization temperature (K): 292
Crystal growth procedure: ~1.0M Sodium Citrate, 0.1M CHES Buffer pH 9.7.
Matthews coefficient: 2.94
Solvent content (%): 58.12
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: 2016-04-27
PanDDA analysis group deposition -- Crystal Structure of JMJD1B in complex with XS040486b (PDB entry 5RAK)
Macromolecule: Lysine-specific demethylase 3B
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11
Sequence length: 372 residues
Sequence: MHHHHHHSSGVDLGTENLYFQSMTSHSWLCDGRLLCLHDPSNKNNWKIFRECWKQGQPVLVSGVHKKLKSELWKPEAFSQEFGDQDVDLVNCRNCAIISDVKVRDFWDGFEIICKRLRSEDGQPMVLKLKDWPPGEDFRDMMPTRFEDLMENLPLPEYTKRDGRLNLASRLPSYFVRPDLGPKMYNAYGLITAEDRRVGTTNLHLDVSDAVNVMVYVGIPIGEGAHDEEVLKTIDEGDADEVTKERIHDHKEKPGALWHIYAAKDAEKIRELLRKVGEEQGQENPPDHDPIHDQSWYLDQTLRKRLYEEYGVQGWAIVQFLGDAVFIPAGAPHQVHNLYSCIKVAEDFVSPEHVKHCFRLTQEFRHLSNTHT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.69
R work: 0.1817
R free: 0.2127
Average B factor: 31.198
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.1M bis-tris pH 5.5 21% PEG3350  0.3M magnesium chloride
Matthews coefficient: 2.8
Solvent content (%): 56.06
Ligand: 3-(pyridin-3-yl)aniline (N6Y)
Ligand formula: C11 H10 N2
Ligand molecular weight: 170.21
Ligand SMILES: c1cc(cc(c1)N)c2cccnc2
Ligand InChI: InChI=1S/C11H10N2/c12-11-5-1-3-9(7-11)10-4-2-6-13-8-10/h1-8H,12H2
Release date: 2020-04-22
Crystal structure of Mg-free KRAS-G12D bound to GDP (PDB entry 7EYX)
Macromolecule: Isoform 2B of GTPase KRas
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.5.2
Sequence length: 169 residues
Sequence: STEYKLVVVGADGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKCDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQGVDDAFYTLVREIRKHKEK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.82
R work: 0.1731
R free: 0.2124
Average B factor: 18.86
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 298
Crystal growth procedure: 30% (w/v) PEG-8000, 
0.1M Acetate pH 4.5, 0.2M Li2SO4 (final pH 4.7)
Matthews coefficient: 1.75
Solvent content (%): 29.68
Ligand: GUANOSINE-5'-DIPHOSPHATE (GDP)
Ligand formula: C10 H15 N5 O11 P2
Ligand molecular weight: 443.201
Ligand SMILES: c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
Ligand InChI: InChI=1S/C10H15N5O11P2/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(25-9)1-24-28(22,23)26-27(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1
Release date: 2021-06-16
Structure of the FSP1 protein from Human (PDB entry 8JSC)
Macromolecule: Ferroptosis suppressor protein 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.6.5
Sequence length: 372 residues
Sequence: GSQVSVESGALHVVIVGGGFGGIAAASQLQALNVPFMLVDMKDSFHHNVAALRASVETGFAKKTFISYSVTFKDNFRQGLVVGIDLKNQMVLLQGGEALPFSHLILATGSTGPFPGKFNEVSSQQAAIQAYEDMVRQVQRSRFIVVVGGGSAGVEMAAEIKTEYPEKEVTLIHSQVALADKELLPSVRQEVKEILLRKGVQLLLSERVSNLEELPLNEYREYIKVQTDKGTEVATNLVILCTGIKINSSAYRKAFESRLASSGALRVNEHLQVEGHSNVYAIGDCADVRTPKMAYLAGLHANIAVANIVNSVKQRPLQAYKPGALTFLLSMGRNDGVGQISGFYVGRLMVRLTKSRDLFVSTSWKTMRQSPP
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.16
R work: 0.1866
R free: 0.2267
Average B factor: 18.72
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 289.15
Crystal growth procedure: PEG 3350, Ammonium nitrate.
Matthews coefficient: 2.11
Solvent content (%): 41.68
Ligand: 6-HYDROXY-FLAVIN-ADENINE DINUCLEOTIDE (6FA)
Ligand formula: C27 H33 N9 O16 P2
Ligand molecular weight: 801.549
Ligand SMILES: Cc1cc2c(c(c1C)O)N=C3C(=O)NC(=O)N=C3N2CC(C(C(COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)n5cnc6c5ncnc6N)O)O)O)O)O
Ligand InChI: InChI=1S/C27H33N9O16P2/c1-9-3-11-15(18(39)10(9)2)32-17-24(33-27(44)34-25(17)43)35(11)4-12(37)19(40)13(38)5-49-53(45,46)52-54(47,48)50-6-14-20(41)21(42)26(51-14)36-8-31-16-22(28)29-7-30-23(16)36/h3,7-8,12-14,19-21,26,37-42H,4-6H2,1-2H3,(H,45,46)(H,47,48)(H2,28,29,30)(H,34,43,44)/t12-,13+,14+,19-,20+,21+,26+/m0/s1
Release date: 2024-03-13
Aspartyl/Asparaginyl beta-hydroxylase (AspH)oxygenase and TPR domains in complex with manganese, N-oxalylglycine and factor X substrate peptide fragment(39mer-4Ser) (PDB entry 5JQY)
Macromolecule: Aspartyl/asparaginyl beta-hydroxylase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11.16
Sequence length: 429 residues
Sequence: KPKLLNKFDKTIKAELDAAEKLRKRGKIEEAVNAFKELVRKYPQSPRARYGKAQCEDDLAEKRRSNEVLRGAIETYQEVASLPDVPADLLKLSLKRRSDRQQFLGHMRGSLLTLQRLVQLFPNDTSLKNDLGVGYLLIGDNDNAKKVYEEVLSVTPNDGFAKVHYGFILKAQNKIAESIPYLKEGIESGDPGTDDGRFYFHLGDAMQRVGNKEAYKWYELGHKRGHFASVWQRSLYNVNGLKAQPWWTPKETGYTELVKSLERNWKLIRDEGLAVMDKAKGLFLPEDENLREKGDWSQFTLWQQGRRNENACKGAPKTCTLLEKFPETTGCRRGQIKYSIMHPGTHVWPHTGPTNCRLRMHLGLVIPKEGCKIRCANETKTWEEGKVLIFDDSFEHEVWQDASSFRLIFIVDVWHPELTPQQRRSLPAI
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.99
R work: 0.1914
R free: 0.2053
Average B factor: 43.6616
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8
Crystallization temperature (K): 277
Crystal growth procedure: 100mM SPG buffer, 25% PEG 1500, 2mM NOG, 1mM MnCl2, 18mg/ml protein
Matthews coefficient: 2.7
Solvent content (%): 54.5
Ligand: MANGANESE (II) ION (MN)
Ligand formula: Mn
Ligand molecular weight: 54.938
Ligand SMILES: [Mn+2]
Ligand InChI: InChI=1S/Mn/q+2
Release date: 2017-05-24
Crystal structure of human DCAF1 WD40 repeats (Q1250L) in complex with compound 15 (PDB entry 8OOD)
Macromolecule: DDB1- and CUL4-associated factor 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 367 residues
Sequence: GGGREPKQRRQAPINFTSRLNRRASFPKYGGVDGGCFDRHLIFSRFRPISVFREANEDESGFTCCAFSARERFLMLGTCTGQLKLYNVFSGQEEASYNCHNSAITHLEPSRDGSLLLTSATWSQPLSALWGMKSVFDMKHSFTEDHYVEFSKHSQDRVIGTKGDIAHIYDIQTGNKLLTLFNPDLANNYKRNCATFNPTDDLVLNDGVLWDVRSALAIHKFDKFNMNISGVFHPNGLEVIINTEIWDLRTFHLLHTVPALDQCRVVFNHTGTVMYGAMLQADDEDDLMEERMKSPFGSSFRTFNATDYKPIATIDVKRNIFDLCTDTKDCYLAVIENQGSMDALNMDTVCRLYEVGRQRLAEDEDEE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.497
R work: 0.17
R free: 0.186
Average B factor: 20.866
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: 2.13M LiSO4, 0.1M Tris pH 7.5
Matthews coefficient: 2.67
Solvent content (%): 53.95
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: 2023-05-24
Crystal structure of SOS1-HRas-peptidomimetic2 (PDB entry 8BE6)
Macromolecule: GTPase HRas
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.5.2
Sequence length: 186 residues
Sequence: MGSSHHHHHHSSGLVPRGSHMTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHQYREQIKRVKDSDDVPMVLVGNKCDLAARTVESRQAQDLARSYGIPYIETSAKTRQGVEDAFYTLVREIRQH
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.89880249261
R work: 0.220464709466
R free: 0.272647863941
Average B factor: 85.7265821798
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 277
Crystal growth procedure: sodium formate 3 M, Tris 100mM pH 8.0
Matthews coefficient: 3.22
Solvent content (%): 61.75
Release date: 2023-04-26
FGFR1 kinase domain (residues 458-765) with mutations C488A, C584S in complex with 38. (PDB entry 7OZB)
Macromolecule: Fibroblast growth factor receptor 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 309 residues
Sequence: GAGVSEYELPEDPRWELPRDRLVLGKPLGEGAFGQVVLAEAIGLDKDKPNRVTKVAVKMLKSDATEKDLSDLISEMEMMKMIGKHKNIINLLGACTQDGPLYVIVEYASKGNLREYLQARRPPGLEYSYNPSHNPEEQLSSKDLVSCAYQVARGMEYLASKKCIHRDLAARNVLVTEDNVMKIADFGLARDIHHIDYYKKTTNGRLPVKWMAPEALFDRIYTHQSDVWSFGVLLWEIFTLGGSPYPGVPVEELFKLLKEGHRMDKPSNCTNELYMMMRDCWHAVPSQRPTFKQLVEDLDRIVALTSNQE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.71
R work: 0.2088
R free: 0.2442
Average B factor: 39.414
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.7
Crystallization temperature (K): 291
Crystal growth procedure: 0.185M ammonium sulfate, 20% v/v ethylene glycol, 17% w/v PEG 8000, 0.1M PCPT
Matthews coefficient: 2.65
Solvent content (%): 53.66
Ligand: 4-[3-(4-piperazin-4-ium-1-ylphenyl)-1H-indazol-6-yl]phenol (47I)
Ligand formula: C23 H23 N4 O
Ligand molecular weight: 371.455
Ligand SMILES: c1cc(ccc1c2c3ccc(cc3[nH]n2)c4ccc(cc4)O)N5CC[NH2+]CC5
Ligand InChI: InChI=1S/C23H22N4O/c28-20-8-3-16(4-9-20)18-5-10-21-22(15-18)25-26-23(21)17-1-6-19(7-2-17)27-13-11-24-12-14-27/h1-10,15,24,28H,11-14H2,(H,25,26)/p+1
Release date: 2021-12-01
HUMAN JAK3 KINASE DOMAIN WITH 1-(4-((2-((1-methyl-1H-pyrazol-4-yl)amino)quinazolin-8-yl)amino)piperidin-1-yl)ethan-1-one (PDB entry 7Q6H)
Macromolecule: Tyrosine-protein kinase JAK3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 327 residues
Sequence: MGHHHHHHAQLYACQDPTIFEERHLKYISQLGKGNFGSVELCRYDPLGDNTGALVAVKQLQHSGPDQQRDFQREIQILKALHSDFIVKYRGVSYGPGRQSLRLVMEYLPSGCLRDFLQRHRARLDASRLLLYSSQICKGMEYLGSRRCVHRDLAARNILVESEAHVKIADFGLAKLLPLDKDYYVVREPGQSPIFWYAPESLSDNIFSRQSDVWSFGVVLYELFTYCDKSCSPSAEFLRMMGSERDVPALSRLLELLEEGQRLPAPPACPAEVHELMKLCWAPSPQDRPSFSALGPQLDMLWSGSRGCETHAFTAHPEGKHHSLSFS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.749
R work: 0.1827
R free: 0.2202
Average B factor: 32.526
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 293
Crystal growth procedure: 8-20% PEG3350 and 0.2-0.3M ammonium sulphate (AS). 2% phenylurea
Matthews coefficient: 2.13
Solvent content (%): 42.32
Ligand: 1-[4-[[2-[(1-methylpyrazol-4-yl)amino]quinazolin-8-yl]amino]piperidin-1-yl]ethanone (934)
Ligand formula: C19 H23 N7 O
Ligand molecular weight: 365.432
Ligand SMILES: CC(=O)N1CCC(CC1)Nc2cccc3c2nc(nc3)Nc4cnn(c4)C
Ligand InChI: InChI=1S/C19H23N7O/c1-13(27)26-8-6-15(7-9-26)22-17-5-3-4-14-10-20-19(24-18(14)17)23-16-11-21-25(2)12-16/h3-5,10-12,15,22H,6-9H2,1-2H3,(H,20,23,24)
Release date: 2022-02-02