satarupa22/MacromolecularLigandDB huggingface dataset:
Crystal structure of c-MET bound by compound 1 (PDB entry 7B3Q)
Macromolecule: Hepatocyte growth factor receptor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 299 residues
Sequence: GNTVHIDLSALNPELVQAVQHVVIGPSSLIVHFNEVIGRGHFGCVYHGTLLDNDGKKIHCAVKSLNRITDIGEVSQFLTEGIIMKDFSHPNVLSLLGICLRSEGSPLVVLPYMKHGDLRNFIRNETHNPTVKDLIGFGLQVAKGMKYLASKKFVHRDLAARNCMLDEKFTVKVADFGLARDMYDKEYYSVHNKTGAKLPVKWMALESLQTQKFTTKSDVWSFGVLLWELMTRGAPPYPDVNTFDITVYLLQGRRLLQPEYCPDPLYEVMLKCWHPKAEMRPSFSELVSRISAIFSTFIG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.75
R work: 0.171
R free: 0.192
Average B factor: 24.56
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 25 % PEG3350, 0.2 M (NH4)2SO4, 0.1 M Na-HEPES pH 7.5
Matthews coefficient: 2.59
Solvent content (%): 52.53
Ligand: 1-(phenylmethyl)-5~{H}-pyrrolo[3,2-c]pyridin-4-one (SV5)
Ligand formula: C14 H12 N2 O
Ligand molecular weight: 224.258
Ligand SMILES: c1ccc(cc1)Cn2ccc3c2C=CNC3=O
Ligand InChI: InChI=1S/C14H12N2O/c17-14-12-7-9-16(13(12)6-8-15-14)10-11-4-2-1-3-5-11/h1-9H,10H2,(H,15,17)
Release date: 2020-12-09
Crystal Structure of human phosphodiesterase 10 in complex with 6-cyclopropyl-N-(2-phenylpyrazol-3-yl)-3-(pyrimidin-5-ylamino)pyridine-2-carboxamide (PDB entry 5SEA)
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
R work: 0.1945
R free: 0.2277
Average B factor: 34.783
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: 2.66
Solvent content (%): 53.81
Ligand: 6-cyclopropyl-N-(1-phenyl-1H-pyrazol-5-yl)-3-[(pyrimidin-5-yl)amino]pyridine-2-carboxamide (IF5)
Ligand formula: C22 H19 N7 O
Ligand molecular weight: 397.433
Ligand SMILES: c1ccc(cc1)n2c(ccn2)NC(=O)c3c(ccc(n3)C4CC4)Nc5cncnc5
Ligand InChI: InChI=1S/C22H19N7O/c30-22(28-20-10-11-25-29(20)17-4-2-1-3-5-17)21-19(26-16-12-23-14-24-13-16)9-8-18(27-21)15-6-7-15/h1-5,8-15,26H,6-7H2,(H,28,30)
Release date: 2022-10-12
Ni-Carbonic Anhydrase II complexed with 3NPA after UV at 180 K (PDB entry 7Y2W)
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): 1.2
R work: 0.12813
R free: 0.15552
Average B factor: 17.146
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.8
Crystallization temperature (K): 293
Crystal growth procedure: 1.3 M sodium citrate, 50 mM Tris-HCl
Matthews coefficient: 2.09
Solvent content (%): 41.11
Ligand: NICKEL (II) ION (NI)
Ligand formula: Ni
Ligand molecular weight: 58.693
Ligand SMILES: [Ni+2]
Ligand InChI: InChI=1S/Ni/q+2
Release date: 2023-12-20
EGFR kinase domain mutant "TMLR" with compound 24 (PDB entry 5CAL)
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): 2.7
R work: 0.2047
R free: 0.2274
Average B factor: 67.19
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 292
Crystal growth procedure: PEG 10000, ethylene glycol
Matthews coefficient: 3.45
Solvent content (%): 64.36
Ligand: 2,2-dimethyl-3-[(4-{[2-methyl-1-(propan-2-yl)-1H-imidazo[4,5-c]pyridin-6-yl]amino}pyrimidin-2-yl)amino]propanamide (4Z8)
Ligand formula: C19 H26 N8 O
Ligand molecular weight: 382.463
Ligand SMILES: Cc1nc2cnc(cc2n1C(C)C)Nc3ccnc(n3)NCC(C)(C)C(=O)N
Ligand InChI: InChI=1S/C19H26N8O/c1-11(2)27-12(3)24-13-9-22-16(8-14(13)27)25-15-6-7-21-18(26-15)23-10-19(4,5)17(20)28/h6-9,11H,10H2,1-5H3,(H2,20,28)(H2,21,22,23,25,26)
Release date: 2015-10-28
Carbonic Anhydrase II in complex with the alkyl urea 3j (PDB entry 8FQZ)
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): 1.467
R work: 0.1644
R free: 0.1853
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.8
Crystallization temperature (K): 293
Crystal growth procedure: 1.6 M sodium citrate, 50 mM Tris base
Matthews coefficient: 2.07
Solvent content (%): 40.58
Ligand: ZINC ION (ZN)
Ligand formula: Zn
Ligand molecular weight: 65.409
Ligand SMILES: [Zn+2]
Ligand InChI: InChI=1S/Zn/q+2
Release date: 2023-02-01
Structure of human DNA polymerase beta complexed with dzA at N-1 of the template base paired with incoming dTTP (PDB entry 7MZ2)
Macromolecule: DNA polymerase beta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 326 residues
Sequence: TLNGGITDMLTELANFEKNVSQAIHKYNAYRKAASVIAKYPHKIKSGAEAKKLPGVGTKIAEKIDEFLATGKLRKLEKIRQDDTSSSINFLTRVSGIGPSAARKFVDEGIKTLEDLRKNEDKLNHHQRIGLKYFGDFEKRIPREEMLQMQDIVLNEVKKVDSEYIATVCGSFRRGAESSGDMDVLLTHPSFTSESTKQPKLLHQVVEQLQKVHFITDTLSKGETKFMGVCQLPSKNDEKEYPHRRIDIRLIPKDQYYCGVLYFTGSDIFNKNMRAHALEKGFTINEYTIRPLGVTGVAGEPLPVDSEKDIFDYIQWKYREPKDRSE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.088
R work: 0.1965
R free: 0.2428
Average B factor: 20.48
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 298
Crystal growth procedure: 14% to 23% PEG3400, and 350 mM sodium acetate in 50 mM imidazole (pH 7.5)
Matthews coefficient: 2.31
Solvent content (%): 46.69
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: 2022-05-25
Crystal structure of DYRK1AA in complex with 10-Bromo-substituted 11H-indolo[3,2-c]quinolone-6-carboxylic acid inhibitor 5t (PDB entry 4YLL)
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): 1.4
R work: 0.15053
R free: 0.17163
Average B factor: 14.565
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.6
Crystallization temperature (K): 277
Crystal growth procedure: 2 M ammonium sulfate, 0.1 M citrate, pH 5.6, 0.2 M potassium/sodium tartrate
Matthews coefficient: 2.5
Solvent content (%): 50.71
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: 2015-03-25
INPP5D PanDDA analysis group deposition -- Crystal Structure of the phosphatase and C2 domains of SHIP1 in complex with Z26548083 (PDB entry 5RXQ)
Macromolecule: Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.86
Sequence length: 463 residues
Sequence: SMEQPEPDMITIFIGTWNMGNAPPPKKITSWFLSKGQGKTRDDSADYIPHDIYVIGTQEDPLSEKEWLEILKHSLQEITSVTFKTVAIHTLWNIRIVVLAKPEHENRISHICTDNVKTGIANTLGNKGAVGVSFMFNGTSLGFVNSHLTSGSEKKLRRNQNYMNILRFLALGDKKLSPFNITHRFTHLFWFGDLNYRVDLPTWEAETIIQKIKQQQYADLLSHDQLLTERREQKVFLHFEEEEITFAPTYRFERLTRDKYAYTKQKATGMKYNLPSWCDRVLWKSYPLVHVVCQSYGSTSDIMTSDHSPVFATFEAGVTSQFVSKNGPGTVDSQGQIEFLRCYATLKTKSQTKFYLEFHSSCLESFVKSQEGENEEGSEGELVVKFGETLPKLKPIISDPEYLLDQHILISIKSSDSDESYGEGCIALRLEATETQLPIYTPLTHHGELTGHFQGEIKLQTSQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.65
R work: 0.176
R free: 0.2134
Average B factor: 21.44
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 30 mM sodium nitrate, 30 mM dibasic sodium phosphate, 30 mM ammonium sulfate, 100 mM MES/imidazole, pH 6.5, 20% PEG500 MME, 10% PEG20000
Matthews coefficient: 2.06
Solvent content (%): 40.4
Ligand: N-(3-cyanophenyl)-2-methylpropanamide (WL4)
Ligand formula: C11 H12 N2 O
Ligand molecular weight: 188.226
Ligand SMILES: CC(C)C(=O)Nc1cccc(c1)C#N
Ligand InChI: InChI=1S/C11H12N2O/c1-8(2)11(14)13-10-5-3-4-9(6-10)7-12/h3-6,8H,1-2H3,(H,13,14)
Release date: 2020-11-11
Human Cyclophilin D Complexed with an Inhibitor at room temperature (PDB entry 4ZSD)
Macromolecule: Peptidyl-prolyl cis-trans isomerase F, mitochondrial
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 5.2.1.8
Sequence length: 164 residues
Sequence: GNPLVYLDVDANGKPLGRVVLELKADVVPKTAENFRALCTGEKGFGYKGSTFHRVIPSFMCQAGDFTNHNGTGGKSIYGSRFPDENFTLKHVGPGVLSMANAGPNTNGSQFFICTIKTDWLDGKHVVFGHVIEGMDVVKKIESFGSKSGRTSKKIVITDCGQLS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.45
R work: 0.1338
R free: 0.1554
Average B factor: 12.549
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.3
Crystallization temperature (K): 291
Crystal growth procedure: 30% PEG4000
Matthews coefficient: 2.11
Solvent content (%): 41.59
Ligand: 1-(4-aminobenzyl)-3-[(2S)-4-(methylsulfanyl)-1-{(2R)-2-[2-(methylsulfanyl)phenyl]pyrrolidin-1-yl}-1-oxobutan-2-yl]urea (7I6)
Ligand formula: C24 H32 N4 O2 S2
Ligand molecular weight: 472.666
Ligand SMILES: CSCCC(C(=O)N1CCCC1c2ccccc2SC)NC(=O)NCc3ccc(cc3)N
Ligand InChI: InChI=1S/C24H32N4O2S2/c1-31-15-13-20(27-24(30)26-16-17-9-11-18(25)12-10-17)23(29)28-14-5-7-21(28)19-6-3-4-8-22(19)32-2/h3-4,6,8-12,20-21H,5,7,13-16,25H2,1-2H3,(H2,26,27,30)/t20-,21+/m0/s1
Release date: 2015-08-12
Crystal structure of IRAK4 in complex with compound 14 (PDB entry 5UIT)
Macromolecule: Interleukin-1 receptor-associated kinase 4
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 323 residues
Sequence: MHHHHHHGGENLYFQGENKSLEVSDTRFHSFSFYELKNVTNNFDERPISVGGNKMGEGGFGVVYKGYVNNTTVAVKKLAAMVDITTEELKQQFDQEIKVMAKCQHENLVELLGFSSDGDDLCLVYVYMPNGSLLDRLSCLDGTPPLSWHMRCKIAQGAANGINFLHENHHIHRDIKSANILLDEAFTAKISDFGLARASEKFAQTVMTSRIVGTTAYMAPEALRGEITPKSDIYSFGVVLLEIITGLPAVDEHREPQLLLDIKEEIEDEEKTIEDYIDKKMNDADSTSVEAMYSVASQCLHEKKNKRPDIKKVQQLLQEMTAS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.84
R work: 0.1809
R free: 0.218
Average B factor: 41.71
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 295
Crystal growth procedure: 1.6-1.8 M Ammonium Citrate, pH7.0
Matthews coefficient: 2.58
Solvent content (%): 52.39
Ligand: 1-{[(2S)-5-oxopyrrolidin-2-yl]methoxy}-7-[(propan-2-yl)oxy]isoquinoline-6-carboxamide (8CD)
Ligand formula: C18 H21 N3 O4
Ligand molecular weight: 343.377
Ligand SMILES: CC(C)Oc1cc2c(ccnc2OCC3CCC(=O)N3)cc1C(=O)N
Ligand InChI: InChI=1S/C18H21N3O4/c1-10(2)25-15-8-13-11(7-14(15)17(19)23)5-6-20-18(13)24-9-12-3-4-16(22)21-12/h5-8,10,12H,3-4,9H2,1-2H3,(H2,19,23)(H,21,22)/t12-/m0/s1
Release date: 2017-05-24
CRYSTAL STRUCTURE OF B-RAF IN COMPLEX WITH BI 882370 (PDB entry 5CSX)
Macromolecule: Serine/threonine-protein kinase B-raf
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 282 residues
Sequence: GPRDSSDDWEIPDGQITVGQRIGSGSFGTVYKGKWHGDVAVKMLNVTAPTPQQLQAFKNEVGVLRKTRHVNILLFMGYSTKPQLAIVTQWCEGSSLYHHLHASETKFEMKKLIDIARQTARGMDYLHAKSIIHRDLKSNNIFLHEDNTVKIGDFGLATVKSRWSGSHQFEQLSGSILWMAPEVIRMQDSNPYSFQSDVYAFGIVLYELMTGQLPYSNINNRDQIIEMVGRGSLSPDLSKVRSNCPKRMKRLMAECLKKKRDERPSFPRILAEIEELARELSG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.51
R work: 0.2174
R free: 0.2825
Average B factor: 33.445
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 277
Crystal growth procedure: PEG 3350
Matthews coefficient: 2.39
Solvent content (%): 48.58
Ligand: N-(3-{5-[(1-ethylpiperidin-4-yl)(methyl)amino]-3-(pyrimidin-5-yl)-1H-pyrrolo[3,2-b]pyridin-1-yl}-2,4-difluorophenyl)propane-1-sulfonamide (54J)
Ligand formula: C28 H33 F2 N7 O2 S
Ligand molecular weight: 569.669
Ligand SMILES: CCCS(=O)(=O)Nc1ccc(c(c1F)n2cc(c3c2ccc(n3)N(C)C4CCN(CC4)CC)c5cncnc5)F
Ligand InChI: InChI=1S/C28H33F2N7O2S/c1-4-14-40(38,39)34-23-7-6-22(29)28(26(23)30)37-17-21(19-15-31-18-32-16-19)27-24(37)8-9-25(33-27)35(3)20-10-12-36(5-2)13-11-20/h6-9,15-18,20,34H,4-5,10-14H2,1-3H3
Release date: 2016-03-09
Crystal structure of the R64D mutant of Bauhinia Bauhinioides Kallikrein Inhibitor complexed with Human Kallikrein 4 (PDB entry 7JQO)
Macromolecule: Kallikrein-4
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21
Sequence length: 223 residues
Sequence: IINGEDCSPHSQPWQAALVMENELFCSGVLVHPQWVLSAAHCFQNSYTIGLGLHSLEADQEPGSQMVEASLSVRHPEYNRPLLANDLMLIKLDESVSESDTIRSISIASQCPTAGNSCLVSGWGLLANGRMPTVLQCVNVSVVSEEVCSKLYDPLYHPSMFCAGGGQDQKDSCNGDSGGPLICNGYLQGLVSFGKAPCGQVGVPGVYTNLCKFTEWIEKTVQA
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.6
R work: 0.1123
R free: 0.1518
Average B factor: 25.21
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 2.0M Ammounium Sulfate, 2% PEG400, 10mM CdCl2
Matthews coefficient: 3.21
Solvent content (%): 61.7
Ligand: NONAETHYLENE GLYCOL (2PE)
Ligand formula: C18 H38 O10
Ligand molecular weight: 414.488
Ligand SMILES: C(COCCOCCOCCOCCOCCOCCOCCOCCO)O
Ligand InChI: InChI=1S/C18H38O10/c19-1-3-21-5-7-23-9-11-25-13-15-27-17-18-28-16-14-26-12-10-24-8-6-22-4-2-20/h19-20H,1-18H2
Release date: 2021-07-21
Crystal structure of CSF-1R kinase domain with sulfatinib (PDB entry 8JOT)
Macromolecule: Macrophage colony-stimulating factor 1 receptor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 354 residues
Sequence: MKKGHHHHHHGQKPKYQVRWKIIESYEGNSYTFIDPTQLPYNEKWEFPRNNLQFGKTLGAGAFGKVVEATAFGLGKEDAVLKVAVKMLKSTAHADEKEALMSELKIMSHLGQHENIVNLLGACTHGGPVLVITEYCTYGDLLNFLRRKAEAMLGPSLSPGQDPEGGVDYKNIHLEKLDKEDGRPLELRDLLHFSSQVAQGMAFLASKNCIHRDVAARNVLLTNGHVAKIGDFGLARDIMNDSNYIVKGNARLPVKWMAPESIFDSVYTVQSDVWSYGILLWEIFSLGLNPYPGILVNSKFYKLVKDGYQMAQPAFAPKNIYSIMQACWALEPTHRPTFQQITSFLQEQAQEDRR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.69
R work: 0.179
R free: 0.2071
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 277.15
Crystal growth procedure: 19% PEG8K, 0.2 M MgCl and 0.1 M Tris, pH 7.5
Matthews coefficient: 2.47
Solvent content (%): 50.22
Ligand: N-(2-(dimethylamino)ethyl)-1-(3-((4-((2-methyl-1H-indol-5-yl)oxy)pyrimidin-2-yl)amino)phenyl)methanesulfonamide (UKI)
Ligand formula: C24 H28 N6 O3 S
Ligand molecular weight: 480.583
Ligand SMILES: Cc1cc2cc(ccc2[nH]1)Oc3ccnc(n3)Nc4cccc(c4)CS(=O)(=O)NCCN(C)C
Ligand InChI: InChI=1S/C24H28N6O3S/c1-17-13-19-15-21(7-8-22(19)27-17)33-23-9-10-25-24(29-23)28-20-6-4-5-18(14-20)16-34(31,32)26-11-12-30(2)3/h4-10,13-15,26-27H,11-12,16H2,1-3H3,(H,25,28,29)
Release date: 2024-03-27
The Discovery of A-893, A New Cell-Active Benzoxazinone Inhibitor of Lysine Methyltransferase SMYD2 (PDB entry 4YND)
Macromolecule: N-lysine methyltransferase SMYD2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1
Sequence length: 461 residues
Sequence: MSYYHHHHHHDYDIPTTENLYFQGAMDPMRAEGLGGLERFCSPGKGRGLRALQPFQVGDLLFSCPAYAYVLTVNERGNHCEYCFTRKEGLSKCGRCKQAFYCNVECQKEDWPMHKLECSPMVVFGENWNPSETVRLTARILAKQKIHPERTPSEKLLAVKEFESHLDKLDNEKKDLIQSDIAALHHFYSKHLGFPDNDSLVVLFAQVNCNGFTIEDEELSHLGSAIFPDVALMNHSCCPNVIVTYKGTLAEVRAVQEIKPGEEVFTSYIDLLYPTEDRNDRLRDSYFFTCECQECTTKDKDKAKVEIRKLSDPPKAEAIRDMVRYARNVIEEFRRAKHYKSPSELLEICELSQEKMSSVFEDSNVYMLHMMYQAMGVCLYMQDWEGALQYGQKIIKPYSKHYPLYSLNVASMWLKLGRLYMGLEHKAAGEKALKKAIAIMEVAHGKDHPYISEIKQEIESH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.79
R work: 0.1979
R free: 0.2532
Average B factor: 33.04
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 290
Crystal growth procedure: The protein ligand complex was made using a slight molar excess of S adenomethionine (SAM) and A-893 from concentrated DMSO stocks. Co-crystals were grown using the hanging drop format with a 1:1 v/v drop composition of the protein complex: well solution (20% w/v PEG 10,000, 0.1 HEPES pH 7.5) at 17C.
Matthews coefficient: 2.1
Solvent content (%): 41.53
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: 2015-05-20
X-ray structure of the complex between human alpha-thrombin and modified 15-mer DNA aptamer containing 5-(3-(2-(1H-indol-3-yl)acetamide-N-yl)-1-propen-1-yl)-2'-deoxyuridine residue (PDB entry 6EO6)
Macromolecule: GA63A - TBA MODIFIED APTAMER
Type: DNA, polydeoxyribonucleotide
Source organism: synthetic construct
Sequence length: 15 residues
Sequence: GGTUGGTGTGGTTGG
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.69
R work: 0.14531
R free: 0.16832
Average B factor: 30.399
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 281
Crystal growth procedure: 18% W/V PEG4000, 20% V/V 2-PROPANOL,
 0.2 M SODIUM CITRATE
Matthews coefficient: 4.16
Solvent content (%): 70.44
Ligand: D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide (0G6)
Ligand formula: C21 H34 Cl N6 O3
Ligand molecular weight: 453.986
Ligand SMILES: c1ccc(cc1)CC(C(=O)N2CCCC2C(=O)NC(CCCNC(=[NH2+])N)C(CCl)O)N
Ligand InChI: InChI=1S/C21H33ClN6O3/c22-13-18(29)16(8-4-10-26-21(24)25)27-19(30)17-9-5-11-28(17)20(31)15(23)12-14-6-2-1-3-7-14/h1-3,6-7,15-18,29H,4-5,8-13,23H2,(H,27,30)(H4,24,25,26)/p+1/t15-,16+,17+,18-/m1/s1
Release date: 2017-10-25
Crystal Structure of Drosophilia DHX36 helicase in complex with GAGCACTGC (PDB entry 5N8R)
Macromolecule: CG9323, isoform A
Type: Protein, polypeptide(L)
Source organism: Drosophila melanogaster
EC number: 3.6.1.3
Sequence length: 944 residues
Sequence: MQRDRDSSGSNARKGNRPPGLRGKDIGLYYRNLARQQKKDRGENAESKEPQIRLGCNVSAPSGVLERVKELMEDYSRAPSRQNVDDKNVDAKFQQQFRHLLSVNFEEFVAETKERNADLDWVNPKLDERLQLELGQRQLEENAKKRLEARKKLPTMKYADDIIQAVRENQVILIVGSTGCGKTTQVPQILLDDAISRGCASSCRIICTQPRRISAIAIAEWVSYERCESLGNSVGYQIRLESRKARERASITYCTTGVLLQQLQSDPLMHNLSVLILDEIHERSVETDLLMGLLKVILPHRPDLKVILMSATVREQDFCDYFNNCPMFRIEGVMFPVKMLYLEDVLSKTNYEFQKFRDRRPKRDPPERRMKHEAMIEPYLRRIRNSYDSRVLDKLRLPESEGCEDIDFIADLVYYICENEPEGAILVFLPGYDKISQLYNILDKPKTSKGQRWRDHMAVFPLHSLMQSGEQQAVFRRPPAGQRKVIISTIIAETSVTIDDVVYVINSGRTKATNYDIETNIQSLDEVWVTKANTQQRRGRAGRVRPGICYNLFSRAREDRMDDIPTPEILRSKLESIILSLKLLHIDDPYRFLQTLINAPNPEAIKMGVELLKRIEALDQTGTLTPLGMHLAKLPIDPQMGKMILMSALFCCLDPITSAAAALSFKSPFYSPLGKESRVDEIKRRMARNMRSDHLMVHNTIIAYRDSRYSHAERDFCYKNFLSSMTLQQLERMKNQFSELLYNYKFLASSNCKDAASNKNSEKIPLLRAIIGAGLYPNMAHLRKSRQIKNRVRAIHTMATDDGRRVNFHPSSVNSGESGFDSAYFVYFQRQKSTDLFLLDSTMVFPMALIIFGDGVEAGVTQNTPYLCVAKTYYFKCNRETADVVIQLRSNLEKLLLKKALYPAPIEENGYEKQLIKAIELLLSLDERLGEDYISSDEIDDIVD
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.2
R work: 0.1761
R free: 0.2186
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 298
Crystal growth procedure: 0.1M MES monohydrate-imidazole
20mM sodium formate
20mM ammonium acetate
20mM sodium citrate tribasic hydrate
20mM sodium oxamate
20mM potassium sodium tartrate tetrahydrate
Matthews coefficient: 2.69
Solvent content (%): 54.3
Release date: 2018-03-14
Crystal structure of Human HPSE1 in complex with inhibitor (PDB entry 7YJC)
Macromolecule: Heparanase 50 kDa subunit
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.2.1.166
Sequence length: 386 residues
Sequence: KKFKNSTYSRSSVDVLYTFANCSGLDLIFGLNALLRTADLQWNSSNAQLLLDYCSSKGYNISWELGNEPNSFLKKADIFINGSQLGEDFIQLHKLLRKSTFKNAKLYGPDVGQPRRKTAKMLKSFLKAGGEVIDSVTWHHYYLNGRTATREDFLNPDVLDIFISSVQKVFQVVESTRPGKKVWLGETSSAYGGGAPLLSDTFAAGFMWLDKLGLSARMGIEVVMRQVFFGAGNYHLVDENFDPLPDYWLSLLFKKLVGTKVLMASVQGSKRRKLRVYLHCTNTDNPRYKEGDLTLYAINLHNVTKYLRLPYPFSNKQVDKYLLRPLGPHGLLSKSVQLNGLTLKMVDDQTLPPLMEKPLRPGSSLGLPAFSYSFFVIRNAKVAACI
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.3
R work: 0.273
R free: 0.33932
Average B factor: 42.901
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 6.3
Crystallization temperature (K): 293
Crystal growth procedure: 20% w/v Polyethylene glycol 3,350,  200 mM Ammonium chloride; pH 6.3
Matthews coefficient: 2.39
Solvent content (%): 48.59
Ligand: (5~{S},6~{R},7~{S},8~{S})-6,7,8-tris(oxidanyl)-5,6,7,8-tetrahydroimidazo[1,2-a]pyridine-5-carboxylic acid (IVO)
Ligand formula: C8 H10 N2 O5
Ligand molecular weight: 214.175
Ligand SMILES: c1cn2c(n1)C(C(C(C2C(=O)O)O)O)O
Ligand InChI: InChI=1S/C8H10N2O5/c11-4-3(8(14)15)10-2-1-9-7(10)6(13)5(4)12/h1-6,11-13H,(H,14,15)/t3-,4+,5-,6+/m0/s1
Release date: 2022-12-07