satarupa22/MacromolecularLigandDB huggingface dataset:
The structural basis of the histone demethylase KDM6B histone 3 lysine 27 specificity (PDB entry 5OY3)
Macromolecule: Lysine-specific demethylase 6B
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11
Sequence length: 509 residues
Sequence: DVVRASRNAKVKGKFRESYLSPAQSVKPKINTEEKLPREKLNPPTPSIYLESKRDAFSPVLLQFCTDPRNPITVIRGLAGSLRLNLGLFSTKTLVEASGEHTVEVRTQVQQPSDENWDLTGTRQIWPCESSRSHTTIAKYAQYQASSFQESLQEEKESEDEESEEPDSTTGTPPSSAPDPKNHHIIKFGTNIDLSDAKRWKPQLQELLKLPAFMRVTSTGNMLSHVGHTILGMNTVQLYMKVPGSRTPGHQENNNFCSVNINIGPGDCEWFAVHEHYWETISAFCDRHGVDYLTGSWWPILDDLYASNIPVYRFVQRPGDLVWINAGTVHWVQATGWCNNIAWNVGPLTAYQYQLALERYEWNEVKNVKSIVPMIHVSWNVARTVKISDPDLFKMIKFCLLQSMKHCQVQRESLVRAGKKIAYQGRVKDEPAYYCNECDVEVFNILFVTSENGSRNTYLVHCEGCARRRSAGLQGVVVLEQYRTEELAQAYDAFTLAPASTSRHHHHHH
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.136
R work: 0.165
R free: 0.2207
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.1M TRIS pH 7.5, 15%(v/v) Tert-butanol,
Matthews coefficient: 2.27
Solvent content (%): 45.82
Ligand: TERTIARY-BUTYL ALCOHOL (TBU)
Ligand formula: C4 H10 O
Ligand molecular weight: 74.122
Ligand SMILES: CC(C)(C)O
Ligand InChI: InChI=1S/C4H10O/c1-4(2,3)5/h5H,1-3H3
Release date: 2017-09-20
Crystal structure of the BRS domain of BRAF (PDB entry 5VR3)
Macromolecule: BRAF
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 88 residues
Sequence: GAMDPGGGGSSAADPAIPEEVWNIKQMIKLTQEHIEALLDKFGGEHNPPSIYLEAYEEYTSKLDALQQREQQLLESLGNGTDFSVSSS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.102
R work: 0.2095
R free: 0.2244
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293.15
Crystal growth procedure: 0.1 M Bis-Tris pH 6.5, 2.0 M ammonium sulphate
Matthews coefficient: 2.58
Solvent content (%): 52.44
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: 2018-02-14
Crystal Structure of Human Vaccinia-related kinase 2 (VRK-2) bound to JA-296 (PDB entry 8Q1Z)
Macromolecule: Serine/threonine-protein kinase VRK2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 324 residues
Sequence: SMPFPEGKVLDDMEGNQWVLGKKIGSGGFGLIYLAFPTNKPEKDARHVVKVEYQENGPLFSELKFYQRVAKKDCIKKWIERKQLDYLGIPLFYGSGLTEFKGRSYRFMVMERLGIDLQKISGQNGTFKKSTVLQLGIRMLDVLEYIHENEYVHGDIKAANLLLGYKNPDQVYLADYGLSYRYCPNGNHKQYQENPRKGHNGTIEFTSLDAHKGVALSRRSDVEILGYCMLRWLCGKLPWEQNLKDPVAVQTAKTNLLDELPQSVLKWAPSGSSCCEIAQFLVCAHSLAYDEKPNYQALKKILNPHGIPLGPLDFSTKGQSINVH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.85
R work: 0.19992
R free: 0.25075
Average B factor: 31.814
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 20% PEG3350 -- 0.2M potassium formate
Matthews coefficient: 2.25
Solvent content (%): 45.41
Ligand: 2-[4-[[4-[(3-~{tert}-butyl-1~{H}-pyrazol-5-yl)amino]pyrimidin-2-yl]amino]phenyl]ethanenitrile (IKD)
Ligand formula: C19 H21 N7
Ligand molecular weight: 347.417
Ligand SMILES: CC(C)(C)c1cc([nH]n1)Nc2ccnc(n2)Nc3ccc(cc3)CC#N
Ligand InChI: InChI=1S/C19H21N7/c1-19(2,3)15-12-17(26-25-15)23-16-9-11-21-18(24-16)22-14-6-4-13(5-7-14)8-10-20/h4-7,9,11-12H,8H2,1-3H3,(H3,21,22,23,24,25,26)
Release date: 2023-08-16
The crystal structure of H-Ras and SOS in complex with ligands (PDB entry 4US0)
Macromolecule: GTPase HRas
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.5.2
Sequence length: 185 residues
Sequence: MHHHHHHGGGENLYFQGSHMTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHQYREQIKRVKDSDDVPMVLVGNKCDLAARTVESRQAQDLARSYGIPYIETSAKTRQGVEDAFYTLVREIRQH
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.17
R work: 0.1856
R free: 0.2123
Average B factor: 42.1
Matthews coefficient: 3.57
Solvent content (%): 65.59
Ligand: 1-ETHYL-PYRROLIDINE-2,5-DIONE (NEN)
Ligand formula: C6 H9 N O2
Ligand molecular weight: 127.141
Ligand SMILES: CCN1C(=O)CCC1=O
Ligand InChI: InChI=1S/C6H9NO2/c1-2-7-5(8)3-4-6(7)9/h2-4H2,1H3
Release date: 2015-03-04
Crystal structure of HPK1 kinase domain T165E,S171E phosphomimetic mutant in complex with 3-[6-chloro-4-(9-methyl-1-oxa-4,9-diazaspiro[5.5]undec-4-yl)-7H-pyrrolo[2,3-d]pyrimidin-5-yl]benzonitrile (PDB entry 8FH4)
Macromolecule: Mitogen-activated protein kinase kinase kinase kinase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 331 residues
Sequence: MASHHHHHHDYDGATTENLYFQGSMDVVDPDIFNRDPRDHYDLLQRLGGGTYGEVFKARDKVSGDLVALKMVKMEPDDDVSTLQKEILILKTCRHANIVAYHGSYLWLQKLWICMEFCGAGSLQDIYQVTGSLSELQISYVCREVLQGLAYLHSQKKIHRDIKGANILINDAGEVRLADFGISAQIGAELARRLEFIGTPYWMAPEVAAVALKGGYNELCDIWSLGITAIELAELQPPLFDVHPLRVLFLMTKSGYQPPRLKEKGKWSAAFHNFIKVTLTKSPKKRPSATKMLSHQLVSQPGLNRGLILDLLDKLKNPGKGPSIGDIEDEE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.827
R work: 0.1874
R free: 0.2152
Average B factor: 31.69
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 286.15
Crystal growth procedure: 15 mg/mL protein + reservoir (0.1 M Tris, pH 8.0, 17.5% 1,6-hexanediol, 10 mM magnesium sulfate, 24 mM barium acetate)
Matthews coefficient: 2.2
Solvent content (%): 44.18
Ligand: (3P)-3-[6-chloro-4-(9-methyl-1-oxa-4,9-diazaspiro[5.5]undecan-4-yl)-7H-pyrrolo[2,3-d]pyrimidin-5-yl]benzonitrile (XXF)
Ligand formula: C22 H23 Cl N6 O
Ligand molecular weight: 422.911
Ligand SMILES: CN1CCC2(CC1)CN(CCO2)c3c4c(c([nH]c4ncn3)Cl)c5cccc(c5)C#N
Ligand InChI: InChI=1S/C22H23ClN6O/c1-28-7-5-22(6-8-28)13-29(9-10-30-22)21-18-17(16-4-2-3-15(11-16)12-24)19(23)27-20(18)25-14-26-21/h2-4,11,14H,5-10,13H2,1H3,(H,25,26,27)
Release date: 2023-04-05
Structure of the proprotein convertase furin complexed to meta-guanidinomethyl-Phac-RVR-Amba in presence of EDTA (PDB entry 5JXJ)
Macromolecule: Furin
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.75
Sequence length: 482 residues
Sequence: DVYQEPTDPKFPQQWYLSGVTQRDLNVKAAWAQGYTGHGIVVSILDDGIEKNHPDLAGNYDPGASFDVNDQDPDPQPRYTQMNDNRHGTRCAGEVAAVANNGVCGVGVAYNARIGGVRMLDGEVTDAVEARSLGLNPNHIHIYSASWGPEDDGKTVDGPARLAEEAFFRGVSQGRGGLGSIFVWASGNGGREHDSCNCDGYTNSIYTLSISSATQFGNVPWYSEACSSTLATTYSSGNQNEKQIVTTDLRQKCTESHTGTSASAPLAAGIIALTLEANKNLTWRDMQHLVVQTSKPAHLNANDWATNGVGRKVSHSYGYGLLDAGAMVALAQNWTTVAPQRKCIIDILTEPKDIGKRLEVRKTVTACLGEPNHITRLEHAQARLTLSYNRRGDLAIHLVSPMGTRSTLLAARPHDYSADGFNDWAFMTTHSWDEDPSGEWVLEIENTSEANNYGTLTKFTLVLYGTASGSLVPRGSHHHHHH
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.0
R work: 0.1668
R free: 0.1889
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293.15
Crystal growth procedure: crystallization solution: 100 mM MES, 200 mM K/NaH2PO4, pH 5.5-6.0, 3-4 M NaCl, 3% DMSO; reservoir solution: 3-4 M NaCl
Matthews coefficient: 3.69
Solvent content (%): 66.65
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: 2016-10-05
Native state mass spectrometry, surface plasmon resonance and X-ray crystallography correlate strongly as a fragment screening combination (PDB entry 5FNG)
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): 2.05
R work: 0.17576
R free: 0.22918
Average B factor: 21.689
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystal growth procedure: 15 MG/ML PROTEIN WITH 2.7 M AMMONIUM SULFATE, 100 MM TRIS PH 8.5 AT 8 C IN SITTING DROPS.
Matthews coefficient: 2.1
Solvent content (%): 41.4
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: 2016-03-02
TorsinA-LULL1 complex, H. sapiens, bound to VHH-BS2 (PDB entry 5J1S)
Macromolecule: Torsin-1A-interacting protein 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 239 residues
Sequence: MSSVNSYYSSPAQQVPKNPALEAFLAQFSQLEDKFPGQSSFLWQRGRKFLQKHLNASNPTEPATIIFTAAREGRETLKCLSHHVADAYTSSQKVSPIQIDGAGRTWQDSDTVKLLVDLELSYGFENGQKAAVVHHFESFPAGSTLIFYKYCDHENAAFKDVALVLTVLLEEETLEASVGPRETEEKVRDLLWAKFTNSDTPTSFNHMDSDKLSGLWSRISHLVLPVQPVSSIEEQGCLF
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.399
R work: 0.1433
R free: 0.1879
Average B factor: 33.1887
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 291
Crystal growth procedure: 13 % PEG 6000
5 % MPD
100 mM MES, pH 6.5
Matthews coefficient: 2.48
Solvent content (%): 50.38
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: 2016-08-17
human PDE10A, 6-Chloro-5,8-dimethyl-2-[2-(2-methyl-5-pyrrolidin-1-yl-2H-[1,2,4]triazol-3-yl)-ethyl]-[1,2,4]triazolo[1,5-a]pyridine, 2.20A, H3, Rfree=23.5% (PDB entry 5EDI)
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: 319 residues
Sequence: TSEEWQGLMQFTLPVRLCREIELFHFDIGPFENMWPGIFVYMVHRSCGTSCFELEKLCRFIMSVKKNYRRVPYHNWKHAVTVAHCMYAILQNNHTLFTDLERKGLLIACLCHDLDHRGFSNSYLQKFDHPLAALYSTSTMEQHHFSQTVSILQLEGHNIFSTLSSSEYEQVLEIIRKAIIATDLALYFGNRKQLEEMYQTGSLNLNNQSHRDRVIGLMMTACDLCSVTKLWPVTKLTANDIYAEFWAEGDEMKKLGIQPIPMMDRDKKDEVPQGQLGFYNAVAIPCYTTLTQILPPTEPLLKACRDNLSQWEKVIRGEE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.2
R work: 0.1857
R free: 0.2347
Average B factor: 53.039
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 295
Crystal growth procedure: 0.1 M HEPES-NaOH pH 7.5, 30% PEG550MME, 50mM MgCl2
Matthews coefficient: 2.86
Solvent content (%): 56.92
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 Mdm2 bound to a stapled peptide (PDB entry 6H22)
Macromolecule: E3 ubiquitin-protein ligase Mdm2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2.27
Sequence length: 97 residues
Sequence: GPLGSSQIPASEQETLVRPKPLLLKLLKSVGAQKDTYTMKEVLFYLGQYIMTKRLYDAAQQHIVYCSNDLLGDLFGVPSFSVKEHRKIYTMIYRNLV
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.006
R work: 0.2107
R free: 0.2384
Average B factor: 30.0421
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 292.15
Crystal growth procedure: 1.1 M sodium malonate dibasic, 0.1 M HEPES pH 7.0, 0.5% v/v Jeffamine ED-2003
Matthews coefficient: 2.17
Solvent content (%): 43.42
Ligand: 12-(dimethylamino)-3,10-diethyl-N,N,N-trimethyl-3,10-dihydrodibenzo[3,4:7,8]cycloocta[1,2-d:5,6-d']bis([1,2,3]triazole)-5-aminium (FL5)
Ligand formula: C25 H31 N8
Ligand molecular weight: 443.567
Ligand SMILES: CCn1c-2c(nn1)-c3ccc(cc3-c4c(nnn4CC)-c5c2cc(cc5)N(C)C)[N+](C)(C)C
Ligand InChI: InChI=1S/C25H31N8/c1-8-31-24-20-14-16(30(3)4)10-12-18(20)22-25(32(9-2)29-26-22)21-15-17(33(5,6)7)11-13-19(21)23(24)27-28-31/h10-15H,8-9H2,1-7H3/q+1/b22-18+,23-19+,24-20+,25-21+
Release date: 2019-07-31
Homo Sapiens Fatty Acid Synthetase, Thioesterase Domain at 1.7 Angstroms Resolution (PDB entry 4Z49)
Macromolecule: Fatty acid synthase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.2.14
Sequence length: 282 residues
Sequence: SLLVNPEGPTLMRLNSVQSSERPLFLVHPIEGSTTVFHSLASRLSIPTYGLQCTRAAPLDSIHSLAAYYIDCIRQVQPEGPYRVAGYSYGACVAFEMCSQLQAQQSPAPTHNSLFLFDGSPTYVLAYTQSYRAKLTPGCEAEAETEAICFFVQQFTDMEHNRVLEALLPLKGLEERVAAAVDLIIKSHQGLDRQELSFAARSFYYKLRAAEQYTPKAKYHGNVMLLRAKTGGAYGEDLGADYNLSQVCDGKVSVHVIEGDHRTLLEGSGLESIISIIHSSLA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.7
R work: 0.171
R free: 0.2123
Average B factor: 20.85
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 20% PEG-3350, 0.2M potassium chloride
Matthews coefficient: 2.24
Solvent content (%): 45.03
Ligand: POTASSIUM ION (K)
Ligand formula: K
Ligand molecular weight: 39.098
Ligand SMILES: [K+]
Ligand InChI: InChI=1S/K/q+1
Release date: 2016-03-16
Crystal structure of human phosphodiesterase 12 (PDB entry 4ZKF)
Macromolecule: 2',5'-phosphodiesterase 12
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.4
Sequence length: 462 residues
Sequence: GIDPFTKYKVERNPPAFTELQLPRYIMAGFPVCPKLSLEFGDPASSLFRWYKEAKPGAAEPEVGVPSSLSPSSPSSSWTETDVEERVYTPSNADIGLRLKLHCTPGDGQRFGHSRELESVCVVEAGPGTCTFDHRHLYTKKVTEDALIRTVSYNILADTYAQTEFSRTVLYPYCAPYALELDYRQNLIQKELTGYNADVICLQEVDRAVFSDSLVPALEAFGLEGVFRIKQHEGLATFYRKSKFSLLSQHDISFYEALESDPLHKELLEKLVLYPSAQEKVLQRSSVLQVSVLQSTKDSSKRICVANTHLYWHPKGGYIRLIQMAVALAHIRHVSCDLYPGIPVIFCGDFNSTPSTGMYHFVINGSIPEDHEDWASNGEEERCNMSLTHFFKLKSACGEPAYTNYVGGFHGCLDYIFIDLNALEVEQVIPLPSHEEVTTHQALPSVSHPSDHIALVCDLKWK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.82
R work: 0.1657
R free: 0.1897
Average B factor: 22.36
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: PEG 3350, sodium chloride
Matthews coefficient: 2.31
Solvent content (%): 46.68
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: 2015-06-17
Selective and potent inhibition of the glycosidase human amylase by the short and extremely compact peptide piHA from mRNA display (PDB entry 5KEZ)
Macromolecule: ACE-DTY-PRO-TYR-SER-CYS-TRP-VAL-ARG-HIS-NH2
Type: Protein, polypeptide(L)
Source organism: synthetic construct
Sequence length: 11 residues
Sequence: XYPYSCWVRHX
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.83
R work: 0.177
R free: 0.208
Crystallization method: EVAPORATION
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: 53%-57% MPD, 0.1 M Na Cacodylate, pH 7.5
Matthews coefficient: 2.42
Solvent content (%): 49.18
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: 2017-03-29
Structure of Cyclophilin D Peptidyl-Prolyl Isomerase Domain bound to Macrocyclic Inhibitor B3 (PDB entry 7TH1)
Macromolecule: Peptidyl-prolyl cis-trans isomerase F, mitochondrial
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 5.2.1.8
Sequence length: 165 residues
Sequence: NANPLVYLDVDANGKPLGRVVLELKADVVPKTAENFRALCTGEKGFGYKGSTFHRVIPSFMCQAGDFTNHNGTGGKSIYGSRFPDENFTLKHVGPGVLSMANAGPNTNGSQFFICTIKTDWLDGKHVVFGHVIEGMDVVKKIESFGSKSGRTSKKIVITDCGQLS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.52
R work: 0.169
R free: 0.1886
Average B factor: 18.44
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.3
Crystallization temperature (K): 298
Crystal growth procedure: 28% PEG 3350
0.5 M KH2PO4
Protein and inhibitor were mixed in ratio 1:3
1 uL of protein:inhibitor complex was mixed with 1 uL mother liquor
Matthews coefficient: 2.19
Solvent content (%): 43.9
Ligand: (4S,7S,11R,13E,19S)-N-[2-(2-aminoethoxy)ethyl]-7-benzyl-4-[(3-methylphenyl)methyl]-3,6,12,15,21-pentaoxo-1,3,4,5,6,7,8,9,10,12,15,16,17,18,19,20,21,22-octadecahydro-2H-7,11-methano-2,5,11,16,20-benzopentaazacyclotetracosine-19-carboxamide (I5J)
Ligand formula: C44 H55 N7 O7
Ligand molecular weight: 793.95
Ligand SMILES: Cc1cccc(c1)CC2C(=O)NCc3ccccc3CC(=O)NC(CCNC(=O)C=CC(=O)N4CCCC(C4)(C(=O)N2)Cc5ccccc5)C(=O)NCCOCCN
Ligand InChI: InChI=1S/C44H55N7O7/c1-31-9-7-12-33(25-31)26-37-42(56)48-29-35-14-6-5-13-34(35)27-39(53)49-36(41(55)47-21-24-58-23-19-45)17-20-46-38(52)15-16-40(54)51-22-8-18-44(30-51,43(57)50-37)28-32-10-3-2-4-11-32/h2-7,9-16,25,36-37H,8,17-24,26-30,45H2,1H3,(H,46,52)(H,47,55)(H,48,56)(H,49,53)(H,50,57)/b16-15+/t36-,37-,44-/m0/s1
Release date: 2022-08-24
PanDDA analysis group deposition -- Crystal structure of PTP1B in complex with compound_FMSOA000675b (PDB entry 5QEL)
Macromolecule: Tyrosine-protein phosphatase non-receptor type 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 321 residues
Sequence: MEMEKEFEQIDKSGSWAAIYQDIRHEASDFPSRVAKLPKNKNRNRYRDVSPFDHSRIKLHQEDNDYINASLIKMEEAQRSYILTQGPLPNTVGHFWEMVWEQKSRGVVMLNRVMEKGSLKCAQYWPQKEEKEMIFEDTNLKLTLISEDIKSYYTVRQLELENLTTQETREILHFHYTTWPDFGVPESPASFLNFLFKVRESGSLSPEHGPVVVHCSAGIGRSGTFCLADTCLLLMDKRKDPSSVDIKKVLLEMRKFRMGLIQTADQLRFSYLAVIEGAKFIMGDSSVQDQWKELSHEDLEPPPEHIPPPPRPPKRILEPHN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.654
R work: 0.1872
R free: 0.2125
Average B factor: 39.4399
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: well solution: 0.3 M magnesium acetate, 0.1 M HEPES pH 7.5, 0.1% beta-mercaptoethanol, 13-14% PEG 8000, 2% ethanol
Matthews coefficient: 3.31
Solvent content (%): 62.87
Ligand: 5-(pyrrolidin-1-yl)pyridine-2-carbonitrile (JKS)
Ligand formula: C10 H11 N3
Ligand molecular weight: 173.214
Ligand SMILES: c1cc(ncc1N2CCCC2)C#N
Ligand InChI: InChI=1S/C10H11N3/c11-7-9-3-4-10(8-12-9)13-5-1-2-6-13/h3-4,8H,1-2,5-6H2
Release date: 2018-10-10
Crystal structure of beta-catenin and the MDM2 p53-binding domain in complex with H330, a Helicon Polypeptide (PDB entry 8EIC)
Macromolecule: E3 ubiquitin-protein ligase Mdm2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2.27
Sequence length: 95 residues
Sequence: SQIPASEQETLVRPKPLLLKLLKSVGAQKDTYTMKEVLFYLGQYIMTKRLYDEKQQHIVYCSNDLLGDLFGVPSFSVKEHRKIYTMIYRNLVVVN
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.62
R work: 0.2258
R free: 0.2694
Average B factor: 71.399
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 4M Sodium formate
Matthews coefficient: 2.3
Solvent content (%): 46.45
Ligand: N,N'-(1,4-phenylene)diacetamide (WHL)
Ligand formula: C10 H12 N2 O2
Ligand molecular weight: 192.214
Ligand SMILES: CC(=O)Nc1ccc(cc1)NC(=O)C
Ligand InChI: InChI=1S/C10H12N2O2/c1-7(13)11-9-3-5-10(6-4-9)12-8(2)14/h3-6H,1-2H3,(H,11,13)(H,12,14)
Release date: 2023-10-25
Oxidized SHP2 forms a disulfide bond between Cys367 and Cys459 (PDB entry 6ATD)
Macromolecule: Tyrosine-protein phosphatase non-receptor type 11
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 528 residues
Sequence: GHMTSRRWFHPNITGVEAENLLLTRGVDGSFLARPSKSNPGDFTLSVRRNGAVTHIKIQNTGDYYDLYGGEKFATLAELVQYYMEHHGQLKEKNGDVIELKYPLNCADPTSERWFHGHLSGKEAEKLLTEKGKHGSFLVRESQSHPGDFVLSVRTGDDKGESNDGKSKVTHVMIRCQELKYDVGGGERFDSLTDLVEHYKKNPMVETLGTVLQLKQPLNTTRINAAEIESRVRELSKLAETTDKVKQGFWEEFETLQQQECKLLYSRKEGQRQENKNKNRYKNILPFDHTRVVLHDGDPNEPVSDYINADIIMPEFETKCNNSKPKKSYIATQGCLQNTVNDFWRMVFQENSRVIVMTTKEVERGKSKCVKYWPDEYALKEYGVMRVRNVKESAAHDYTLRELKLSKVGQGNTERTVWQYHFRTWPDHGVPSDPGGVLDFLEEVHHKQESIMDAGPVVVHCSAGIGRTGTFIVIDILIDIIREKGVDCDIDVPKTIQMVRSQRSGMVQTEAQYRFIYMAVQHYIETLQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.5
R work: 0.1947
R free: 0.2453
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 9.1
Crystallization temperature (K): 277
Crystal growth procedure: 0.2 M sodium phosphate, 20% (w/v) PEG 3350
Matthews coefficient: 2.29
Solvent content (%): 46.28
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: 2018-07-11
Human Sirt6 in complex with ADP-ribose and the activator isoquercetin (PDB entry 6QCE)
Macromolecule: NAD-dependent protein deacetylase sirtuin-6
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.5.1
Sequence length: 302 residues
Sequence: GIDPFTADKGKCGLPEIFDPPEELERKVWELARLVWQSSSVVFHTGAGISTASGIPDFRGPHGVWTMEERGLAPKFDTTFESARPTQTHMALVQLERVGLLRFLVSQNVDGLHVRSGFPRDKLAELHGNMFVEECAKCKTQYVRDTVVGTMGLKATGRLCTVAKARGLRACRGELRDTILDWEDSLPDRDLALADEASRNADLSITLGTSLQIRPSGNLPLATKRRGGRLVIVNLQPTKHDRHADLRIHGYVDEVMTRLMKHLGLEIPAWDGPRVLERALPPLPRPPTPKLEPKEESPTRIN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.9
R work: 0.15164
R free: 0.18692
Average B factor: 44.115
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.7
Crystallization temperature (K): 293
Crystal growth procedure: 1.6 M (NH4)2SO4, 10% PEG 400, and Bis-Tris buffer pH 5.7
Matthews coefficient: 2.63
Solvent content (%): 53.34
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: 2019-12-25
Human DNA polymerase lambda- Apoenzyme and complex with 6 paired DNA (PDB entry 5DDM)
Macromolecule: DNA polymerase lambda
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 335 residues
Sequence: MAQPSSQKATNHNLHITEKLEVLAKAYSVQGDKWRALGYAKAINALKSFHKPVTSYQEACSIPGIGKRMAEKIIEILESGHLRKLDHISESVPVLELFSNIWGAGTKTAQMWYQQGFRSLEDIRSQASLTTQQAIGLKHYSDFLERMPREEATEIEQTVQKAAQAFNSGLLCVACGSYRRGKATCGDVDVLITHPDGRSHRGIFSRLLDSLRQEGFLTDDLVSQEENGQQQKYLGVCRLPGPGRRHRRLDIIVVPYSEFACALLYFTGSAHFNRSMRALAKTKGMSLSEHALSTAVVRNTHGCKVGPGRVLPTPTEKDVFRLLGLPYREPAERDW
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.802
R work: 0.2013
R free: 0.2391
Average B factor: 41.23
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.1M Lithium Sulfate monohydrate, 0.1M HEPES-Sodium, 0.1M Potassium Sodium Tartrate
Matthews coefficient: 2.55
Solvent content (%): 51.76
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: 2016-02-24