satarupa22/MacromolecularLigandDB huggingface dataset:
Crystal structure of c-Met in complex with (R)-5-(8-fluoro-3-(1-fluoro-1-(3-methoxyquinolin-6-yl)ethyl)-[1,2,4]triazolo[4,3-a]pyridin-6-yl)-3-methylisoxazole (PDB entry 4XMO)
Macromolecule: Hepatocyte growth factor receptor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 309 residues
Sequence: QNTVHIDLSALNPELVQAVQHVVIGPSSLIVHFNEVIGRGHFGCVYHGTLLDNDGKKIHCAVKSLNRITDIGEVSQFLTEGIIMKDFSHPNVLSLLGICLRSEGSPLVVLPYMKHGDLRNFIRNETHNPTVKDLIGFGLQVAKGMKYLASKKFVHRDLAARNCMLDEKFTVKVADFGLARDMYDKEYYSVHNKTGAKLPVKWMALESLQTQKFTTKSDVWSFGVLLWELMTRGAPPYPDVNTFDITVYLLQGRRLLQPEYCPDPLYEVMLKCWHPKAEMRPSFSELVSRISAIFSTFIGEHYVHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.75
R work: 0.1865
R free: 0.2383
Average B factor: 26.896
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.8
Crystallization temperature (K): 298
Crystal growth procedure: 12% PEG 4000, 100 mM HEPES, pH 7.8, 6% isopropanol, 3% ethanol, 40 mM beta-mercaptoethanol
Matthews coefficient: 2.04
Solvent content (%): 39.75
Ligand: 6-{(1R)-1-fluoro-1-[8-fluoro-6-(3-methyl-1,2-oxazol-5-yl)[1,2,4]triazolo[4,3-a]pyridin-3-yl]ethyl}-3-methoxyquinoline (46G)
Ligand formula: C22 H17 F2 N5 O2
Ligand molecular weight: 421.399
Ligand SMILES: Cc1cc(on1)c2cc(c3nnc(n3c2)C(C)(c4ccc5c(c4)cc(cn5)OC)F)F
Ligand InChI: InChI=1S/C22H17F2N5O2/c1-12-6-19(31-28-12)14-9-17(23)20-26-27-21(29(20)11-14)22(2,24)15-4-5-18-13(7-15)8-16(30-3)10-25-18/h4-11H,1-3H3/t22-/m1/s1
Release date: 2015-03-11
Crystal structure of DUSP10 mutant_D59A (PDB entry 7Y4B)
Macromolecule: Dual specificity protein phosphatase 10
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.16
Sequence length: 149 residues
Sequence: SAELTPILPFLFLGNEQDAQDLDTMQRLNIGYVINVTTHLPLYHYEKGLFNYKRLPATASNKQNLRQYFEEAFEFIEEAHQCGKGLLIHCQAGVSRSATIVIAYLMKHTRMTMTDAYKFVKGKRPIISPNLNFMGQLLEFEEDLNNGVT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.86
R work: 0.1836
R free: 0.23
Average B factor: 41.58
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 283
Crystal growth procedure: 22.5%(w/v) PEG 3000, 100mM Tris base/Hydrochloric acid, 200mM Calcium acetate
Matthews coefficient: 2.37
Solvent content (%): 48.13
Release date: 2023-06-21
Crystal Structure of Human Scp1 bound to trans-proline peptidomimetic CTD phospho-Ser5 peptide (PDB entry 4YGY)
Macromolecule: Carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.16
Sequence length: 189 residues
Sequence: GSHGQYLLPEAKAQDSDKICVVINLDETLVHSSFKPVNNADFIIPVEIDGVVHQVYVLKRPHVDEFLQRMGELFECVLFTASLAKYADPVADLLDKWGAFRARLFRESCVFHRGNYVKDLSRLGRDLRRVLILDNSPASYVFHPDNAVPVASWFDNMSDTELHDLLPFFEQLSRVDDVYSVLRQPRPGS
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.36
R work: 0.1832
R free: 0.2462
Average B factor: 47.118
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 298
Crystal growth procedure: 30% PEG 3350, 0.2 M magnesium acetate
Matthews coefficient: 3.38
Solvent content (%): 63.6
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: 2015-09-16
Crystal structure of DYRK1A with harmine-derivatized AnnH-75 inhibitor (PDB entry 4YU2)
Macromolecule: Dual specificity tyrosine-phosphorylation-regulated kinase 1A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.12.1
Sequence length: 361 residues
Sequence: SMSSHKKERKVYNDGYDDDNYDYIVKNGEKWMDRYEIDSLIGKGSFGQVVKAYDRVEQEWVAIKIIKNKKAFLNQAQIEVRLLELMNKHDTEMKYYIVHLKRHFMFRNHLCLVFEMLSYNLYDLLRNTNFRGVSLNLTRKFAQQMCTALLFLATPELSIIHCDLKPENILLCNPKRSAIKIVDFGSSCQLGQRIYQYIQSRFYRSPEVLLGMPYDLAIDMWSLGCILVEMHTGEPLFSGANEVDQMNKIVEVLGIPPAHILDQAPKARKFFEKLPDGTWNLKKTKDGKREYKPPGTRKLHNILGVETGGPGGRRAGESGHTVADYLKFKDLILRMLDYDPKTRIQPYYALQHSFFKKTADE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.9
R work: 0.24302
R free: 0.27715
Average B factor: 75.108
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 9
Crystallization temperature (K): 277
Crystal growth procedure: 31% PEG 400, 0.2 M lithium sulfate, 0.1 M Tris, pH 9.0
Matthews coefficient: 3.26
Solvent content (%): 62.25
Ligand: TETRAETHYLENE GLYCOL (PG4)
Ligand formula: C8 H18 O5
Ligand molecular weight: 194.226
Ligand SMILES: C(COCCOCCOCCO)O
Ligand InChI: InChI=1S/C8H18O5/c9-1-3-11-5-7-13-8-6-12-4-2-10/h9-10H,1-8H2
Release date: 2015-03-25
The crystal structure of the human carbonic anhydrase II in complex with a nitroimidazole sulfamate inhibitor (PDB entry 5O07)
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): 1.8
R work: 0.1571
R free: 0.1954
Average B factor: 13.2664
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 293
Crystal growth procedure: 1.3 M SODIUM CITRATE, 100 MM TRIS-HCL
Matthews coefficient: 2.09
Solvent content (%): 41.07
Ligand: ZINC ION (ZN)
Ligand formula: Zn
Ligand molecular weight: 65.409
Ligand SMILES: [Zn+2]
Ligand InChI: InChI=1S/Zn/q+2
Release date: 2017-08-02
Phosphoinositide 3-Kinase gamma bound to an pyrrolopyridinone Inhibitor (PDB entry 6C1S)
Macromolecule: Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.1.153
Sequence length: 971 residues
Sequence: MPMASEESQAFQRQLTALIGYDVTDVSNVHDDELEFTRRGLVTPRMAEVASRDPKLYAMHPWVTSKPLPEYLWKKIANNCIFIVIHRSTTSQTIKVSPDDTPGAILQSFFTKMAKKKSLMDIPESQSEQDFVLRVCGRDEYLVGETPIKNFQWVRHCLKNGEEIHVVLDTPPDPALDEVRKEEWPLVDDCTGVTGYHEQLTIHGKDHESVFTVSLWDCDRKFRVKIRGIDIPVLPRNTDLTVFVEANIQHGQQVLCQRRTSPKPFTEEVLWNVWLEFSIKIKDLPKGALLNLQIYCGKAPALSSKASAESPSSESKGKVQLLYYVNLLLIDHRFLLRRGEYVLHMWQISGKGEDQGSFNADKLTSATNPDKENSMSISILLDNYCHPIALPKHQPTPDPEGDRVRAEMPNQLRKQLEAIIATDPLNPLTAEDKELLWHFRYESLKHPKAYPKLFSSVKWGQQEIVAKTYQLLARREVWDQSALDVGLTMQLLDCNFSDENVRAIAVQKLESLEDDDVLHYLLQLVQAVKFEPYHDSALARFLLKRGLRNKRIGHFLFWFLRSEIAQSRHYQQRFAVILEAYLRGCGTAMLHDFTQQVQVIEMLQKVTLDIKSLSAEKYDVSSQVISQLKQKLENLQNSQLPESFRVPYDPGLKAGALAIEKCKVMASKKKPLWLEFKCADPTALSNETIGIIFKHGDDLRQDMLILQILRIMESIWETESLDLCLLPYGCISTGDKIGMIEIVKDATTIAKIQQSTVGNTGAFKDEVLNHWLKEKSPTEEKFQAAVERFVYSCAGYCVATFVLGIGDRHNDNIMITETGNLFHIDFGHILGNYKSFLGINKERVPFVLTPDFLFVMGTSGKKTSPHFQKFQDICVKAYLALRHHTNLLIILFSMMLMTGMPQLTSKEDIEYIRDALTVGKNEEDAKKYFLDQIEVCRDKGWTVQFNWFLHLVLGIKQGEKHSALEHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.31
R work: 0.197
R free: 0.257
Average B factor: 87.57
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 298
Crystal growth procedure: 25% PEG3350, 200MM Lithium Sulfate, 10 MM DTT, 10 MM EDTA, 100 MM Tris
Matthews coefficient: 2.35
Solvent content (%): 47.69
Ligand: {4-[2-(5,6-dimethoxypyridin-3-yl)-5-oxo-5,7-dihydro-6H-pyrrolo[3,4-b]pyridin-6-yl]-1H-pyrazol-1-yl}acetonitrile (EFV)
Ligand formula: C19 H16 N6 O3
Ligand molecular weight: 376.369
Ligand SMILES: COc1cc(cnc1OC)c2ccc3c(n2)CN(C3=O)c4cnn(c4)CC#N
Ligand InChI: InChI=1S/C19H16N6O3/c1-27-17-7-12(8-21-18(17)28-2)15-4-3-14-16(23-15)11-25(19(14)26)13-9-22-24(10-13)6-5-20/h3-4,7-10H,6,11H2,1-2H3
Release date: 2018-06-27
Crystal Structure of Human Indoleamine 2,3-dioxygenagse 1 (hIDO1) Complexed with 6-Bromo-N-(((1S,2S)-2-chlorocyclohexyl)methyl)-1H-indazol-4-amine (39) (PDB entry 7E0U)
Macromolecule: Indoleamine 2,3-dioxygenase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.13.11.52
Sequence length: 392 residues
Sequence: SKEYHIDEEVGFALPNPQENLPDFYNDWMFIAKHLPDLIESGQLRERVEKLNMLSIDHLTDHKSQRLARLVLGCITMAYVWGKGHGDVRKVLPRNIAVPYCQLSKKLELPPILVYADCVLANWKKKDPNKPLTYENMDVLFSFRDGDCSKGFFLVSLLVEIAAASAIKVIPTVFKAMQMQERDTLLKALLEIASCLEKALQVFHQIHDHVNPKAFFSVLRIYLSGWKGNPQLSDGLVYEGFWEDPKEFAGGSAGQSSVFQCFDVLLGIQQTAGGGHAAQFLQDMRRYMPPAHRNFLCSLESNPSVREFVLSKGDAGLREAYDACVKALVSLRSYHLQIVTKYILIPASQQPKENKTSEDPSKEEAKGTGGTDLMNFLKTVRSTTEKSLLKEG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.278
R work: 0.1897
R free: 0.2482
Average B factor: 63.9333
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 15% to 23% PEG 8000, 0.2M ammonium acetate
Matthews coefficient: 2.84
Solvent content (%): 56.67
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: 2021-07-21
Co-crystal Structure of Lipid Kinase PI3K alpha with a selective phosphatidylinositol-3 kinase alpha inhibitor (PDB entry 4ZOP)
Macromolecule: Phosphatidylinositol 3-kinase regulatory subunit alpha
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 290 residues
Sequence: MHNLQYLPPKPPKPTTVANNGMNNNMSLQDAEWYWGDISREEVNEKLRDTADGTFLVRDASTKMHGDYTLTLRKGGNNKLIKIFHRDGKYGFSDPLTFSSVVELINHYRNESLAQYNPKLDVKLLYPVSKYQQDQVVKEDNIEAVGKKLHEYNTQFQEKSREYDRLYEEYTRTSQEIQMKRTAIEAFNETIKIFEEQCQTQERYSKEYIEKFKREGNEKEIQRIMHNYDKLKSRISEIIDSRRRLEEDLKKQAAEYREIDKRMNSIKPDLIQLRKTRDQYLMWLTQKGVR
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.62
R work: 0.1926
R free: 0.258
Average B factor: 68.91
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 303
Crystal growth procedure: 12% PEG 3350, 120MM KSCN, 6UL PROTEIN TO 4UL WELL WITH STREAK SEEDING AT 18C , PH 7.5, VAPOR DIFFUSION, HANGING DROP
Matthews coefficient: 2.35
Solvent content (%): 47.69
Ligand: (2S,3R)-N~1~-(8-tert-butyl-4,5-dihydro[1,3]thiazolo[4,5-h]quinazolin-2-yl)-3-methylpyrrolidine-1,2-dicarboxamide (4Q2)
Ligand formula: C20 H26 N6 O2 S
Ligand molecular weight: 414.524
Ligand SMILES: CC1CCN(C1C(=O)N)C(=O)Nc2nc3c(s2)-c4c(cnc(n4)C(C)(C)C)CC3
Ligand InChI: InChI=1S/C20H26N6O2S/c1-10-7-8-26(14(10)16(21)27)19(28)25-18-23-12-6-5-11-9-22-17(20(2,3)4)24-13(11)15(12)29-18/h9-10,14H,5-8H2,1-4H3,(H2,21,27)(H,23,25,28)/t10-,14+/m1/s1
Release date: 2016-05-18
Human Carbonic Anhydrase I in complex with 3,4-dihydro-1H-benzo[c][1,2]oxaborinin-1-ol pH 7.0 (PDB entry 8Q7G)
Macromolecule: Carbonic anhydrase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 261 residues
Sequence: MASPDWGYDDKNGPEQWSKLYPIANGNNQSPVDIKTSETKHDTSLKPISVSYNPATAKEIINVGHSFHVNFEDNDNRSVLKGGPFSDSYRLFQFHFHWGSTNEHGSEHTVDGVKYSAELHVAHWNSAKYSSLAEAASKADGLAVIGVLMKVGEANPKLQKVLDALQAIKTKGKRAPFTNFDPSTLLPSSLDFWTYPGSLTHPPLYESVTWIICKESISVSSEQLAQFRSLLSNVEGDNAVPMQHNNRPTQPLKGRTVRASF
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.43
R work: 0.1927
R free: 0.2175
Average B factor: 23.904
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 28-31% PEG4000, 0.2 M Sodium acetate, 0.1 M Tris pH 8.5-9.0
Matthews coefficient: 2.34
Solvent content (%): 47.51
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: 2024-08-28
PKG I's Carboxyl Terminal Cyclic Nucleotide Binding Domain (CNB-B) in a complex with RP-cGMP (PDB entry 5L0N)
Macromolecule: cGMP-dependent protein kinase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.12
Sequence length: 135 residues
Sequence: GSTGLIKHTEYMEFLKSVPTFQSLPEEILSKLADVLEETHYENGEYIIRQGARGDTFFIISKGTVNVTREDSPSEDPVFLRTLGKGDWFGEKALQGEDVRTANVIAAEAVTCLVIDRDSFKHLIGGLDDVSNKAY
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.285
R work: 0.1671
R free: 0.1821
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 4
Crystallization temperature (K): 277
Crystal growth procedure: 0.8 M Lithium sulfate monohydrate.  0.1 M Sodium acetate trihydrate pH 4.0,  4% v/v Polyethylene glycol 200
Matthews coefficient: 2.04
Solvent content (%): 39.7
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: 2017-08-02
Crystal Structure of human phosphodiesterase 10 in complex with 6-cyclopropyl-3-methoxy-N-[2-(3-pyridin-3-yl-1H-1,2,4-triazol-5-yl)ethyl]pyrazine-2-carboxamide (PDB entry 5SIZ)
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): 2.1
R work: 0.1772
R free: 0.2228
Average B factor: 39.22
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 (%): 52.82
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
Crystal structure of Tdp1 catalytic domain in complex with Zenobia fragment ZT1982 (single soak) (PDB entry 6DJD)
Macromolecule: Tyrosyl-DNA phosphodiesterase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.4
Sequence length: 461 residues
Sequence: SGEGQDIWDMLDKGNPFQFYLTRVSGVKPKYNSGALHIKDILSPLFGTLVSSAQFNYCFDVDWLVKQYPPEFRKKPILLVHGDKREAKAHLHAQAKPYENISLCQAKLDIAFGTHHTKMMLLLYEEGLRVVIHTSNLIHADWHQKTQGIWLSPLYPRIADGTHKSGESPTHFKADLISYLMAYNAPSLKEWIDVIHKHDLSETNVYLIGSTPGRFQGSQKDNWGHFRLKKLLKDHASSMPNAESWPVVGQFSSVGSLGADESKWLCSEFKESMLTLGKESKTPGKSSVPLYLIYPSVENVRTSLEGYPAGGSLPYSIQTAEKQNWLHSYFHKWSAETSGRSNAMPHIKTYMRPSPDFSKIAWFLVTSANLSKAAWGALEKNGTQLMIRSYELGVLFLPSAFGLDSFKVKQKFFAGSQEPMATFPVPYDLPPELYGSKDRPWIWNIPYVKAPDTHGNMWVPS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.777
R work: 0.1864
R free: 0.2272
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 292
Crystal growth procedure: 0.1 M MOPS/HEPES-Na pH 7.5
10% w/v PEG 8000
20% v/v ethylene glycol
0.03M sodium fluoride
0.03M sodium bromide
0.03M sodium iodide
Matthews coefficient: 2.45
Solvent content (%): 49.88
Ligand: 4-hydroxyquinoline-3-carboxylic acid (GJP)
Ligand formula: C10 H7 N O3
Ligand molecular weight: 189.167
Ligand SMILES: c1ccc2c(c1)c(c(cn2)C(=O)O)O
Ligand InChI: InChI=1S/C10H7NO3/c12-9-6-3-1-2-4-8(6)11-5-7(9)10(13)14/h1-5H,(H,11,12)(H,13,14)
Release date: 2019-05-29
Inactive Fe-PP1 (PDB entry 6G0J)
Macromolecule: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.16
Sequence length: 331 residues
Sequence: GMSDSEKLNLDSIIGRLLEVQGSRPGKNVQLTENEIRGLCLKSREIFLSQPILLELEAPLKICGDIHGQYYDLLRLFEYGGFPPESNYLFLGDYVDRGKQSLETICLLLAYKIKYPENFFLLRGNHECASINRIYGFYDECKRRYNIKLWKTFTDCFNCLPIAAIVDEKIFCCHGGLSPDLQSMEQIRRIMRPTDVPDQGLLCDLLWSDPDKDVQGWGENDRGVSFTFGAEVVAKFLHKHDLDLICRAHQVVEDGYEFFAKRQLVTLFSAPNYCGEFDNAGAMMSVDETLMCSFQILKPADKNKGKYGQFSGLNPGGRPITPPRNSAKAKK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.1
R work: 0.20107
R free: 0.2364
Average B factor: 36.462
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8
Crystallization temperature (K): 291
Crystal growth procedure: 28% w/v PEG 3350, 0.1 M TRIS-Cl,pH 8.0 RT, 1 M Lithium Chloride.
Matthews coefficient: 2.57
Solvent content (%): 52.15
Ligand: FE (III) ION (FE)
Ligand formula: Fe
Ligand molecular weight: 55.845
Ligand SMILES: [Fe+3]
Ligand InChI: InChI=1S/Fe/q+3
Release date: 2018-11-21
Structure of human Usb1 with uridine 5'-monophosphate (PDB entry 5V1M)
Macromolecule: U6 snRNA phosphodiesterase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.4
Sequence length: 191 residues
Sequence: GAHMGNWATHVYVPYEAKEEFLDLLDVLLPHAQTYVPRLVRMKVFHLSLSQSVVLRHHWILPFVQALKARMTSFHRFFFTANQVKIYTNQEKTRTFIGLEVTSGHAQFLDLVSEVDRVMEEFNLTTFYQDPSFHLSLAWCVGDARLQLEGQCLQELQAIVDGFEDAEVLLRVHTEQVRCKSGNKFFSMPLK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.47
R work: 0.159
R free: 0.1944
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 289
Crystal growth procedure: 20% w/v PEG 20,000, 20% v/v glycerol, 100 mM bis-tris base, 50 mM HCl, and 10 mM disodium 5' UMP
Matthews coefficient: 2.27
Solvent content (%): 45.9
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: 2017-08-16
Caspase-3 Mutant - T152V (PDB entry 6BHA)
Macromolecule: Caspase-3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.22.56
Sequence length: 175 residues
Sequence: MENTENSVDSKSIKNLEPKIIHGSESMDSGISLDNSYKMDYPEMGLCIIINNKNFHKSTGMTSRSGTDVDAANLRETFRNLKYEVRNKNDLTREEIVELMRDVSKEDHSKRSSFVCVLLSHGEEGIIFGTNGPVDLKKITNFFRGDRCRSLVGKPKLFIIQACRGTELDCGIETD
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.603
R work: 0.1597
R free: 0.1843
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 291
Crystal growth procedure: Crystals were obtained at 18 C by the hanging drop vapor diffusion method using 4 mL drops that contained equal volumes of protein and reservoir solutions over a 0.5 mL solution of 100 mM sodium citrate, pH 4.9-5.2, 8-18 % PEG 6000 (w/v), 10 mM DTT, and 3 mM NaN3. Crystals appeared within 3-5 days and were briefly immersed in a cryogenic solution containing 10% MPD (2-methylpentane-2,4-diol) and 90% reservoir solution.
Matthews coefficient: 2.17
Solvent content (%): 43.23
Release date: 2018-02-21
Crystal Structure of cGMP-dependent Protein Kinase (PDB entry 7T4T)
Macromolecule: cGMP-dependent protein kinase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.12
Sequence length: 469 residues
Sequence: STGLIKHTEYMEFLKSVPTFQSLPEEILSKLADVLEETHYENGEYIIRQGARGDTFFIISKGTVNVTREDSPSEDPVFLRTLGKGDWFGEKALQGEDVRTANVIAAEAVTCLVIDRDSFKHLIGGLDDVSNKAYEDAEAKAKYEAEAAFFANLKLSDFNIIDTLGVGGFGRVELVQLKSEESKTFAMKILKKRHIVDTRQQEHIRSEKQIMQGAHSDFIVRLYRTFKDSKYLYMLMEACLGGELWTILRDRGSFEDSTTRFYTACVVEAFAYLHSKGIIYRDLKPENLILDHRGYAKLVDFGFAKKIGFGKKTWTFCGTPEYVAPEIILNKGHDISADYWSLGILMYELLTGSPPFSGPDPMKTYNIILRGIDMIEFPKKIAKNAANLIKKLCRDNPSERLGNLKNGVKDIQKHKWFEGFNWEGLRKGTLTPPIIPSVASPTDTSNFDSFPEDNDEPPPDDNSGWDIDF
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.08
R work: 0.188
R free: 0.221
Average B factor: 54.31
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 8
Crystallization temperature (K): 295
Crystal growth procedure: 0.1M Bis Tris propane pH 7.5 0.2M Sodium sulfate 20% PEG 3350
Matthews coefficient: 2.69
Solvent content (%): 54.33
Ligand: CYCLIC GUANOSINE MONOPHOSPHATE (PCG)
Ligand formula: C10 H12 N5 O7 P
Ligand molecular weight: 345.205
Ligand SMILES: c1nc2c(n1C3C(C4C(O3)COP(=O)(O4)O)O)N=C(NC2=O)N
Ligand InChI: InChI=1S/C10H12N5O7P/c11-10-13-7-4(8(17)14-10)12-2-15(7)9-5(16)6-3(21-9)1-20-23(18,19)22-6/h2-3,5-6,9,16H,1H2,(H,18,19)(H3,11,13,14,17)/t3-,5-,6-,9-/m1/s1
Release date: 2023-06-14
Crystal structure of human MTH1(G2K/D120N mutant) in complex with 2-oxo-dATP at pH 7.7 (PDB entry 8I1I)
Macromolecule: 7,8-dihydro-8-oxoguanine triphosphatase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.1.55
Sequence length: 156 residues
Sequence: MKASRLYTLVLVLQPQRVLLGMKKRGFGAGRWNGFGGKVQEGETIEDGARRELQEESGLTVDALHKVGQIVFEFVGEPELMDVHVFCTDSIQGTPVESDEMRPCWFQLDQIPFKDMWPDNSYWFPLLLQKKKFHGYFKFQGQDTILDYTLREVDTV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.2
R work: 0.1355
R free: 0.1633
Average B factor: 20.6
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: sodium citrate, tris, NaCl
Matthews coefficient: 1.9
Solvent content (%): 35.15
Ligand: [[(2R,3S,5R)-5-(6-azanyl-2-oxidanylidene-1H-purin-9-yl)-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate (6U4)
Ligand formula: C10 H16 N5 O13 P3
Ligand molecular weight: 507.181
Ligand SMILES: C1C(C(OC1N2C=NC3=C(NC(=O)N=C32)N)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O
Ligand InChI: InChI=1S/C10H16N5O13P3/c11-8-7-9(14-10(17)13-8)15(3-12-7)6-1-4(16)5(26-6)2-25-30(21,22)28-31(23,24)27-29(18,19)20/h3-6,16H,1-2H2,(H,21,22)(H,23,24)(H2,18,19,20)(H3,11,13,14,17)/t4-,5+,6+/m0/s1
Release date: 2023-03-22
Crystal structure of PTPN2 with a PROTAC (PDB entry 8U0H)
Macromolecule: PTPN2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 324 residues
Sequence: MAMPTTIEREFEELDTQRRWQPLYLEIRNESHDYPHRVAKFPENRNRNRYRDVSPYDHSRVKLQNAENDYINASLVDIEEAQRSYILTQGPLPNTCCHFWLMVWQQKTKAVVMLNRIVEKESVKCAQYWPTDDQEMLFKETGFSVKLLSEDVKSYYTVHLLQLENINSGETRTISHFHYTTWPDFGVPESPASFLNFLFKVRESGSLNPDHGPAVIHCSAGIGRSGTFSLVDTCLVLMEKGDDINIKQVLLNMRKYRMGLIQTPDQLRFSYMAIIEGAKCIKGDSSIQKRWKELSKEDLSPAFDHSPNKIMTEKYNHHHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.93
R work: 0.1726
R free: 0.1917
Average B factor: 38.32
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.9
Crystallization temperature (K): 296
Crystal growth procedure: 0.49M Sodium phosphate monobasic monohydrate, 0.91M Potassium phosphate dibasic
Matthews coefficient: 2.41
Solvent content (%): 49.06
Ligand: (5P)-3-(carboxymethoxy)-4-chloro-5-(3-{[(4S)-1-({3-[2-(4-{3-[(3R)-2,6-dioxopiperidin-3-yl]-2-oxo-2,3-dihydro-1,3-benzoxazol-6-yl}piperidin-1-yl)acetamido]phenyl}methanesulfonyl)-2,2-dimethylpiperidin-4-yl]amino}phenyl)thiophene-2-carboxylic acid (UB0)
Ligand formula: C46 H49 Cl N6 O12 S2
Ligand molecular weight: 977.497
Ligand SMILES: CC1(CC(CCN1S(=O)(=O)Cc2cccc(c2)NC(=O)CN3CCC(CC3)c4ccc5c(c4)OC(=O)N5C6CCC(=O)NC6=O)Nc7cccc(c7)c8c(c(c(s8)C(=O)O)OCC(=O)O)Cl)C
Ligand InChI: InChI=1S/C46H49ClN6O12S2/c1-46(2)22-32(48-31-8-4-6-29(20-31)41-39(47)40(64-24-38(56)57)42(66-41)44(59)60)15-18-52(46)67(62,63)25-26-5-3-7-30(19-26)49-37(55)23-51-16-13-27(14-17-51)28-9-10-33-35(21-28)65-45(61)53(33)34-11-12-36(54)50-43(34)58/h3-10,19-21,27,32,34,48H,11-18,22-25H2,1-2H3,(H,49,55)(H,56,57)(H,59,60)(H,50,54,58)/t32-,34+/m0/s1
Release date: 2024-09-04