satarupa22/MacromolecularLigandDB huggingface dataset:
HPK1 IN COMPLEX WITH COMPOUND 11 (PDB entry 7L24)
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: 288 residues
Sequence: DIFNRDPRDHYDLLQRLGGGTYGEVFKARDKVSGDLVALKMVKMEPDDDVSTLQKEILILKTCRHANIVAYHGSYLWLQKLWICMEFCGAGSLQDIYQVTGSLSELQISYVCREVLQGLAYLHSQKKIHRDIKGANILINDAGEVRLADFGISAQIGATLARRLAFIGTPYWMAPEVAAVALKGCYNELCDIWSLGITAIELAELQPPLFDVHPLRVLFLMTKSGYQPPRLKEKGKWSAAFHNFIKVTLTKSPKKRPSATKMLSHQLVSQPGLNRGLILDLLDKLKNP
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.68
R work: 0.2257
R free: 0.272
Average B factor: 82.986
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 293
Crystal growth procedure: UNDISCLOSED
Matthews coefficient: 2.65
Solvent content (%): 53.69
Ligand: 6-(2-fluoro-6-methoxyphenyl)-1-[4-(4-methylpiperazin-1-yl)phenyl]-1H-pyrazolo[4,3-c]pyridine (XHV)
Ligand formula: C24 H24 F N5 O
Ligand molecular weight: 417.479
Ligand SMILES: CN1CCN(CC1)c2ccc(cc2)n3c4cc(ncc4cn3)c5c(cccc5F)OC
Ligand InChI: InChI=1S/C24H24FN5O/c1-28-10-12-29(13-11-28)18-6-8-19(9-7-18)30-22-14-21(26-15-17(22)16-27-30)24-20(25)4-3-5-23(24)31-2/h3-9,14-16H,10-13H2,1-2H3
Release date: 2021-03-17
INPP5D PanDDA analysis group deposition -- Crystal Structure of the phosphatase and C2 domains of SHIP1 in complex with Z2856434894 (PDB entry 5RXM)
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): 1.46
R work: 0.1705
R free: 0.1992
Average B factor: 18.746
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: 2.07
Solvent content (%): 40.69
Ligand: ~{N},~{N}-dimethyl-4-[(propan-2-ylamino)methyl]aniline (GWV)
Ligand formula: C12 H20 N2
Ligand molecular weight: 192.301
Ligand SMILES: CC(C)NCc1ccc(cc1)N(C)C
Ligand InChI: InChI=1S/C12H20N2/c1-10(2)13-9-11-5-7-12(8-6-11)14(3)4/h5-8,10,13H,9H2,1-4H3
Release date: 2020-11-11
DDR1, 2-[8-(1H-indazole-5-carbonyl)-4-oxo-1-phenyl-1,3,8-triazaspiro[4.5]decan-3-yl]-N-methylacetamide, 1.440A, P1211, Rfree=24.1% (PDB entry 6FEW)
Macromolecule: Epithelial discoidin domain-containing receptor 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 321 residues
Sequence: PGAVGDGPPRVDFPRSRLRFKEKLGEGQFGEVHLCEVDSPQDLVSLDFPLNVRKGHPLLVAVKILRPDATKNARNDFLKEVKIMSRLKDPNIIRLLGVCVQDDPLCMITDYMENGDLNQFLSAHQLEDKAAEGAPGDPTISYPMLLHVAAQIASGMRYLATLNFVHRDLATRNCLVGENFTIKIADFGMSRNLYAGDYYRVQGRAVLPIRWMAWECILMGKFTTASDVWAFGVTLWEVLMLCRAQPFGQLTDEQVIENAGEFFRDQGRQVYLSRPPACPQGLYELMLRCWSRESEQRPPFSQLHRFLAEDALNTVHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.44
R work: 0.2171
R free: 0.2413
Average B factor: 31.1001
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 293
Crystal growth procedure: 11.5 mg/mL protein in 20mM HEPES/NaOH pH7.5, 5mM DTT, 5% glycerol, 0.1M NaCl mixed 3:1 in 600 nL with 0.1M Ca acetate, 12% PEG 8K, 0.1M Na cacodylate pH5.5
Matthews coefficient: 2.1
Solvent content (%): 41.33
Ligand: 2-[8-(2~{H}-indazol-5-ylcarbonyl)-4-oxidanylidene-1-phenyl-1,3,8-triazaspiro[4.5]decan-3-yl]-~{N}-methyl-ethanamide (D6W)
Ligand formula: C24 H26 N6 O3
Ligand molecular weight: 446.502
Ligand SMILES: CNC(=O)CN1CN(C2(C1=O)CCN(CC2)C(=O)c3ccc4c(c3)c[nH]n4)c5ccccc5
Ligand InChI: InChI=1S/C24H26N6O3/c1-25-21(31)15-29-16-30(19-5-3-2-4-6-19)24(23(29)33)9-11-28(12-10-24)22(32)17-7-8-20-18(13-17)14-26-27-20/h2-8,13-14H,9-12,15-16H2,1H3,(H,25,31)(H,26,27)
Release date: 2018-11-28
Crystal Structure of Human NEIL1(242K) bound to duplex DNA containing THF (PDB entry 5ITU)
Macromolecule: Endonuclease 8-like 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.2.2
Sequence length: 400 residues
Sequence: MPEGPELHLASQFVNEACRALVFGGCVEKSSVSRNPEVPFESSAYRISASARGKELRLILSPLPGAQPQQEPLALVFRFGMSGSFQLVPREELPRHAHLRFYTAPPGPRLALCFVDIRRFGRWDLGGKWQPGRGPCVLQEYQQFRENVLRNLADKAFDRPICEALLDQRFFNGIGNYLRAEILYRLKIPPFEKARSVLEALQQHRPSPELTLSQKIRTKLQNPDLLELCHSVPKEVVQLGGKGYGSESGEEDFAAFRAWLRCYGMPGMSSLQDRHGRTIWFQGDPGPLAPKGRKSRKKKSKATQLSPEDRVEDALPPSKAPSRTRRAKRDLPKRTATQRPEGTSLQQDPEAPTVPKKGRRKGRQAASGHCRPRKVKADIPSLEPEGTSASAALGHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.41
R work: 0.21
R free: 0.26
Crystallization method: EVAPORATION
Crystallization pH: 6.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.1 M cacodylic acid (pH 7.0), 0.1 M NaCl, 0.05 M MgCl2 and 24% (w/v) PEG 8000
Matthews coefficient: 2.23
Solvent content (%): 44.92
Release date: 2016-07-06
Sucrose Binding Site in genetically engineered Carbonic anhydrase IX (PDB entry 4YWP)
Macromolecule: Carbonic anhydrase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 257 residues
Sequence: HWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHSFQVTFDDSQDKAVLKGGPLDGTYRLLQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDVGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTEGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLAECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.45
R work: 0.162
R free: 0.1899
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.8
Crystallization temperature (K): 298
Crystal growth procedure: 1.6 M sodium citrate, 50 mM Tris-HCL pH 7.4
Matthews coefficient: 2.1
Solvent content (%): 41.43
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: 2015-10-14
Crystal structure of PDE4D catalytic domain complexed with compound 17a (PDB entry 7F2K)
Macromolecule: Isoform 3 of cAMP-specific 3',5'-cyclic phosphodiesterase 4D
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.4.53
Sequence length: 507 residues
Sequence: MASNKFKRMLNRELTHLSEMSRSGNQVSEFISNTFLDKQHEVEIPSPTQKEKEKKKRPMSQISGVKKLMHSSSLTNSSIPRFGVKTEQEDVLAKELEDVNKWGLHVFRIAELSGNRPLTVIMHTIFQERDLLKTFKIPVDTLITYLMTLEDHYHADVAYHNNIHAADVVQSTHVLLSTPALEAVFTDLEILAAIFASAIHDVDHPGVSNQFLINTNSELALMYNDSSVLENHHLAVGFKLLQEENCDIFQNLTKKQRQSLRKMVIDIVLATDMSKHMNLLADLKTMVETKKVTSSGVLLLDNYSDRIQVLQNMVHCADLSNPTKPLQLYRQWTDRIMEEFFRQGDRERERGMEISPMCDKHNASVEKSQVGFIDYIVHPLWETWADLVHPDAQDILDTLEDNREWYQSTIPQSPSPAPDDPEEGRQGQTEKFQFELTLEEDGESDTEKDSGSQVEEDTSCSDSKTLCTQDSESTEIPLDEQVEEEAVGEEEESQPEACVIDDRSPDT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.10001966681
R work: 0.208256947539
R free: 0.256955453423
Average B factor: 27.2593589744
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 277
Crystal growth procedure: 0.1 M HEPES (pH 7.4), 0.1 M MgCl2, 15% PEG3350, 10% isopropanol, and 25% ethylene glycol
Matthews coefficient: 1.65
Solvent content (%): 25.63
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: 2021-10-20
Crystal structure of human phosphodiesterase 2A with 1-(2-chloro-5-isobutoxy-phenyl)-N,4-dimethyl-[1,2,4]triazolo[4,3-a]quinoxaline-8-carboxamide (PDB entry 6C7F)
Macromolecule: cGMP-dependent 3',5'-cyclic phosphodiesterase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.4.17
Sequence length: 342 residues
Sequence: SAMDDEYTKLLHDGIQPVAAIDSNFASFTYTPRSLPEDDTSMAILSMLQDMNFINNYKIDCPTLARFCLMVKKGYRDPPYHNWMHAFSVSHFCYLLYKNLELTNYLEDIEIFALFISCMCHDLDHRGTNNSFQVASKSVLAALYSSEGSVMERHHFAQAIAILNTHGCNIFDHFSRKDYQRMLDLMRDIILATDLAHHLRIFKDLQKMAEVGYDRNNKQHHRLLLCLLMTSCDLSDQTKGWKTTRKIAELIYKEFFSQGDLEKAMGNRPMEMMDREKAYIPELQISFMEHIAMPIYKLLQDLFPKAAELYERVASNREHWTKVSHKFTIRGLPSNNSLDFLD
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.82
R work: 0.1952
R free: 0.2463
Average B factor: 36.7351
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8.4
Crystallization temperature (K): 293
Crystal growth procedure: 17-19% PEG3350, 0.2 M magnesium chloride, 0.1 M Tris, pH 8.4
Matthews coefficient: 2.21
Solvent content (%): 44.45
Ligand: 1-[2-chloro-5-(2-methylpropoxy)phenyl]-N,4-dimethyl[1,2,4]triazolo[4,3-a]quinoxaline-8-carboxamide (EOS)
Ligand formula: C22 H22 Cl N5 O2
Ligand molecular weight: 423.895
Ligand SMILES: Cc1c2nnc(n2c3cc(ccc3n1)C(=O)NC)c4cc(ccc4Cl)OCC(C)C
Ligand InChI: InChI=1S/C22H22ClN5O2/c1-12(2)11-30-15-6-7-17(23)16(10-15)21-27-26-20-13(3)25-18-8-5-14(22(29)24-4)9-19(18)28(20)21/h5-10,12H,11H2,1-4H3,(H,24,29)
Release date: 2018-08-15
CDK2 liganded with para chloro ANS (PDB entry 7UG1)
Macromolecule: Cyclin-dependent kinase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.22
Sequence length: 306 residues
Sequence: GPLGSPEFMENFQKVEKIGEGTYGVVYKARNKLTGEVVALKKIRLDTETEGVPSTAIREISLLKELNHPNIVKLLDVIHTENKLYLVFEFLHQDLKKFMDASALTGIPLPLIKSYLFQLLQGLAFCHSHRVLHRDLKPQNLLINTEGAIKLADFGLARAFGVPVRTYTHEVVTLWYRAPEILLGCKYYSTAVDIWSLGCIFAEMVTRRALFPGDSEIDQLFRIFRTLGTPDEVVWPGVTSMPDYKPSFPKWARQDFSKVVPPLDEDGRSLLSQMLHYDPNKRISAKAALAHPFFQDVTKPVPHLRL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.84
R work: 0.1821
R free: 0.2422
Average B factor: 25.7971
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 291
Crystal growth procedure: 50 mM sodium/potassium phosphate, pH 7.5, 50 mM HEPES, pH 7.5, 5% v/v PEG3350
Matthews coefficient: 1.91
Solvent content (%): 35.56
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: 2023-04-12
Crystal structure of N-terminal catalytic domain of human PLAAT3 (PDB entry 7ZOM)
Macromolecule: Phospholipase A and acyltransferase 3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1
Sequence length: 132 residues
Sequence: MRAPIPEPKPGDLIEIFRPFYRHWAIYVGDGYVVHLAPPSEVAGAGAASVMSALTDKAIVKKELLYDVAGSDKYQVNNKHDDKYSPLPCSKIIQRAEELVGQEVLYKLTSENCEHFVNELRYGVARSDQVRD
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.601
R work: 0.1846
R free: 0.2091
Average B factor: 38.16
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 0.1M Hepes-NaOH pH7.0-7.5, 45-70% MPD
Matthews coefficient: 2.65
Solvent content (%): 53.61
Ligand: (4S)-2-METHYL-2,4-PENTANEDIOL (MPD)
Ligand formula: C6 H14 O2
Ligand molecular weight: 118.174
Ligand SMILES: CC(CC(C)(C)O)O
Ligand InChI: InChI=1S/C6H14O2/c1-5(7)4-6(2,3)8/h5,7-8H,4H2,1-3H3/t5-/m0/s1
Release date: 2023-04-26
ARHGEF2 PanDDA analysis group deposition -- ARHGEF2 and RhoA in complex with Z1270393711 (PDB entry 7G8S)
Macromolecule: Transforming protein RhoA
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.5.2
Sequence length: 185 residues
Sequence: SMAAIRKKLVIVGDGACGKTCLLIVFSKDQFPEVYVPTVFENYVADIEVDGKQVELALWDTAGQEDYDRLRPLSYPDTDVILMCFSIDSPDSLENIPEKWTPEVKHFCPNVPIILVGNKKDLRNDEHTRRELAKMKQEPVKPEEGRDMANRIGAFGYMECSAKTKDGVREVFEMATRAALQARRG
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.6
R work: 0.1933
R free: 0.2216
Average B factor: 32.14
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 293
Crystal growth procedure: 100 mM Tris, 2.6M sodium formate
Matthews coefficient: 2.5
Solvent content (%): 50.84
Ligand: FORMIC ACID (FMT)
Ligand formula: C H2 O2
Ligand molecular weight: 46.025
Ligand SMILES: C(=O)O
Ligand InChI: InChI=1S/CH2O2/c2-1-3/h1H,(H,2,3)
Release date: 2023-07-12
Crystal structure of the catalytic domain of human diphosphoinositol pentakisphosphate kinase 2 (PPIP5K2) in complex with AMP-PNP and 5-(PCP)-IP5 (PDB entry 5DGH)
Macromolecule: Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.4.21
Sequence length: 330 residues
Sequence: GSFTERQIVVGICSMAKKSKSKPMKEILERISLFKYITVVVFEEEVILNEPVENWPLCDCLISFHSKGFPLDKAVAYAKLRNPFVINDLNMQYLIQDRREVYSILQAEGILLPRYAILNRDPNNPKECNLIEGEDHVEVNGEVFQKPFVEKPVSAEDHNVYIYYPTSAGGGSQRLFRKIGSRSSVYSPESNVRKTGSYIYEEFMPTDGTDVKVYTVGPDYAHAEARKSPALDGKVERDSEGKEVRYPVILNAREKLIAWKVCLAFKQTVCGFDLLRANGQSYVCDVNGFSFVKNSMKYYDDCAKILGNIVMRELAPQFHIPWSIPLEAED
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.1
R work: 0.18671
R free: 0.2314
Average B factor: 24.654
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7
Crystallization temperature (K): 277
Crystal growth procedure: 12% (w/v) PEG 3350, 20 mM MgCl2, 0.1 M HEPES, pH 7.0, 1 mM AMP-PNP and 2 mM CdCl2. The crystals were transferred to a stabilizing buffer containing 22% (w/v) PEG 3350, 10 mM MgCl2, 0.1 M sodium acetate, pH 5.2 at 4 oC overnight. The crystals were soaked under the above stabilizing buffer for three days with 2 mM compound.
Matthews coefficient: 2.66
Solvent content (%): 53.8
Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER (ANP)
Ligand formula: C10 H17 N6 O12 P3
Ligand molecular weight: 506.196
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(NP(=O)(O)O)O)O)O)N
Ligand InChI: InChI=1S/C10H17N6O12P3/c11-8-5-9(13-2-12-8)16(3-14-5)10-7(18)6(17)4(27-10)1-26-31(24,25)28-30(22,23)15-29(19,20)21/h2-4,6-7,10,17-18H,1H2,(H,24,25)(H2,11,12,13)(H4,15,19,20,21,22,23)/t4-,6-,7-,10-/m1/s1
Release date: 2016-08-10
The crystal structure of human CtsL in complex with 14a (PDB entry 7W33)
Macromolecule: Procathepsin L
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.22.15
Sequence length: 333 residues
Sequence: MNPTLILAAFCLGIASATLTFDHSLEAQWTKWKAMHNRLYGMNEEGWRRAVWEKNMKMIELHNQEYREGKHSFTMAMNAFGDMTSEEFRQVMNGFQNRKPRKGKVFQEPLFYEAPRSVDWREKGYVTPVKNQGQCGSCWAFSATGALEGQMFRKTGRLISLSEQNLVDCSGPQGNEGCNGGLMDYAFQYVQDNGGLDSEESYPYEATEESCKYNPKYSVANDTGFVDIPKQEKALMKAVATVGPISVAIDAGHESFLFYKEGIYFEPDCSSEDMDHGVLVVGYGFESTESDNNKYWLVKNSWGEEWGMGGYVKMAKDRRNHCGIASAASYPTV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.39
R work: 0.2222
R free: 0.261
Average B factor: 68.5029
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 4.1
Crystallization temperature (K): 289.15
Crystal growth procedure: 100mM sodium acetate (pH 4.1), 15% (w/v) PEG 2000, protein concentration 8 mg/ml
Matthews coefficient: 1.83
Solvent content (%): 32.86
Ligand: N-[(2S)-3-(4-fluorophenyl)-1-oxidanylidene-1-[[(2R,3S)-3-oxidanyl-4-oxidanylidene-1-[(3S)-2-oxidanylidenepiperidin-3-yl]-4-[(phenylmethyl)amino]butan-2-yl]amino]propan-2-yl]-1-benzofuran-2-carboxamide (89B)
Ligand formula: C34 H35 F N4 O6
Ligand molecular weight: 614.663
Ligand SMILES: c1ccc(cc1)CNC(=O)C(C(CC2CCCNC2=O)NC(=O)C(Cc3ccc(cc3)F)NC(=O)c4cc5ccccc5o4)O
Ligand InChI: InChI=1S/C34H35FN4O6/c35-25-14-12-21(13-15-25)17-27(39-33(43)29-19-23-9-4-5-11-28(23)45-29)32(42)38-26(18-24-10-6-16-36-31(24)41)30(40)34(44)37-20-22-7-2-1-3-8-22/h1-5,7-9,11-15,19,24,26-27,30,40H,6,10,16-18,20H2,(H,36,41)(H,37,44)(H,38,42)(H,39,43)/t24-,26+,27-,30-/m0/s1
Release date: 2023-05-31
Crystal structure of c-Met kinase domain in complex with LXM108 (PDB entry 5HTI)
Macromolecule: Hepatocyte growth factor receptor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 319 residues
Sequence: MGSSHHHHHHGDSDISSPLLQNTVHIDLSALNPELVQAVQHVVIGPSSLIVHFNEVIGRGHFGCVYHGTLLDNDGKKIHCAVKSLNRITDIGEVSQFLTEGIIMKDFSHPNVLSLLGICLRSEGSPLVVLPYMKHGDLRNFIRNETHNPTVKDLIGFGLQVAKGMKYLASKKFVHRDLAARNCMLDEKFTVKVADFGLARDMYDKEYYSVHNKTGAKLPVKWMALESLQTQKFTTKSDVWSFGVLLWELMTRGAPPYPDVNTFDITVYLLQGRRLLQPEYCPDPLYEVMLKCWHPKAEMRPSFSELVSRISAIFSTFIG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.66
R work: 0.181
R free: 0.2056
Average B factor: 23.6161
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.1
Crystallization temperature (K): 293
Crystal growth procedure: 10-11% PEG5000MME, 11% isopropanol, 0.1M HEPES pH 7.1
Matthews coefficient: 2.19
Solvent content (%): 43.9
Ligand: N-[3-fluoro-4-({7-[2-(morpholin-4-yl)ethoxy]-1,6-naphthyridin-4-yl}oxy)phenyl]-N'-(4-fluorophenyl)cyclopropane-1,1-dicarboxamide (66L)
Ligand formula: C31 H29 F2 N5 O5
Ligand molecular weight: 589.589
Ligand SMILES: c1cc(ccc1NC(=O)C2(CC2)C(=O)Nc3ccc(c(c3)F)Oc4ccnc5c4cnc(c5)OCCN6CCOCC6)F
Ligand InChI: InChI=1S/C31H29F2N5O5/c32-20-1-3-21(4-2-20)36-29(39)31(8-9-31)30(40)37-22-5-6-27(24(33)17-22)43-26-7-10-34-25-18-28(35-19-23(25)26)42-16-13-38-11-14-41-15-12-38/h1-7,10,17-19H,8-9,11-16H2,(H,36,39)(H,37,40)
Release date: 2017-02-01
Crystal structure of TRIM24 PHD-bromodomain complexed with N-(6-{3-[4-(dimethylamino)butoxy]-5-propoxyphenoxy}-1,3-dimethyl-2-oxo-2,3-dihydro-1H-1,3-benzodiazol-5-yl)-3,4-dimethoxybenzene-1-sulfonamide (8i) (PDB entry 4YC9)
Macromolecule: Transcription intermediary factor 1-alpha
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 6.3.2
Sequence length: 184 residues
Sequence: SPNEDWCAVCQNGGELLCCEKCPKVFHLSCHVPTLTNFPSGEWICTFCRDLSKPEVEYDCDAPSHNSEKKKTEGLVKLTPIDKRKCERLLLFLYCHEMSLAFQDPVPLTVPDYYKIIKNPMDLSTIKKRLQEDYSMYSKPEDFVADFRLIFQNCAEFNEPDSEVANAGIKLENYFEELLKNLYP
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.82
R work: 0.155
R free: 0.2035
Average B factor: 36.339
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 298
Crystal growth procedure: 2.2-2.4M ammonium sulfate, 0.1M HEPES buffer pH 7.5, 2% PEG400 and 8-9% glycerol
Matthews coefficient: 2.27
Solvent content (%): 45.9
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: 2015-06-24
Human protein kinase CK2 alpha in complex with ferulic acid (PDB entry 6HOQ)
Macromolecule: Casein kinase II subunit alpha
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 336 residues
Sequence: MSGPVPSRARVYTDVNTHRPREYWDYESHVVEWGNQDDYQLVRKLGRGKYSEVFEAINITNNEKVVVKILKPVKKKKIKREIKILENLRGGPNIITLADIVKDPVSRTPALVFEHVNNTDFKQLYQTLTDYDIRFYMYEILKALDYCHSMGIMHRDVKPHNVMIDHEHRKLRLIDWGLAEFYHPGQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRKEPFFHGHDNYDQLVRIAKVLGTEDLYDYIDKYNIELDPRFNDILGRHSRKRWERFVHSENQHLVSPEALDFLDKLLRYDHQSRLTAREAMEHPYFYTVVKDQARMGS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.55
R work: 0.1604
R free: 0.1849
Average B factor: 25.4688
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 293
Crystal growth procedure: 32% PEG4000, 0.2 M Lithium Sulfate
Matthews coefficient: 1.98
Solvent content (%): 37.96
Ligand: 3-(4-HYDROXY-3-METHOXYPHENYL)-2-PROPENOIC ACID (FER)
Ligand formula: C10 H10 O4
Ligand molecular weight: 194.184
Ligand SMILES: COc1cc(ccc1O)C=CC(=O)O
Ligand InChI: InChI=1S/C10H10O4/c1-14-9-6-7(2-4-8(9)11)3-5-10(12)13/h2-6,11H,1H3,(H,12,13)/b5-3+
Release date: 2019-10-02
Human 8-oxoguanine glycosylase interrogating fully intrahelical oxoG lesion DNA (PDB entry 6W13)
Macromolecule: N-glycosylase/DNA lyase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.2.2
Sequence length: 317 residues
Sequence: GSEGHRTLASTPALWASIPCPRSELRLDLVLPSGQSFRWREQSPAHWSGVLADQVWTLTQTEEQLHCTVYRGDKSQASRPTPDELEAVRKYFQLDVTLAQLYHHWGSVDSHFQQVAQKFQGVRLLRQDPIECLFSFICSSNNNIARITGMVERLCQAFGPRLIQLDDVTYHGFPSLQALAGPEVEAHLRKLGLGYRARCVSASARAILEEQGGLAWLQQLRESSYEEAHKALCILPGVGTKVADWICLMALDKPQAVPVDVHMWHIAQRDYSWHPTTSQAKGPSPQTNKELGNFFRSLWGPYAGWAQAVLFSADLRQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.38
R work: 0.2137
R free: 0.2711
Average B factor: 52.078
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 100 mM sodium cacodylate, pH 6.1, 200 mM MgOAc, and 17 % polyethylene glycol 8000
Matthews coefficient: 3.16
Solvent content (%): 65.42
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: 2020-09-23
X-ray structure of furin in complex with the dichlorophenylpyridine-based inhibitor 1 (PDB entry 7QY0)
Macromolecule: Furin
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.75
Sequence length: 480 residues
Sequence: DVYQEPTDPKFPQQWYLSGVTQRDLNVKAAWAQGYTGHGIVVSILDDGIEKNHPDLAGNYDPGASFDVNDQDPDPQPRYTQMNDNRHGTRCAGEVAAVANNGVCGVGVAYNARIGGVRMLDGEVTDAVEARSLGLNPNHIHIYSASWGPEDDGKTVDGPARLAEEAFFRGVSQGRGGLGSIFVWASGNGGREHDSCNCDGYTNSIYTLSISSATQFGNVPWYSEACSSTLATTYSSGNQNEKQIVTTDLRQKCTESHTGTSASAPLAAGIIALTLEANKNLTWRDMQHLVVQTSKPAHLNANDWATNGVGRKVSHSYGYGLLDAGAMVALAQNWTTVAPQRKCIIDILTEPKDIGKRLEVRKTVTACLGEPNHITRLEHAQARLTLSYNRRGDLAIHLVSPMGTRSTLLAARPHDYSADGFNDWAFMTTHSWDEDPSGEWVLEIENTSEANNYGTLTKFTLVLYGTASGSLVPRGSHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.54
R work: 0.1493
R free: 0.1725
Average B factor: 26.16
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293.15
Crystal growth procedure: CRYSTALLIZATION SOLUTION: 100mM MES, 200mM K/NAH2PO4, PH 5.5, 2 M NACL; RESERVOIR SOLUTION: 3.0-3.2M NACL
Matthews coefficient: 3.72
Solvent content (%): 66.91
Ligand: N-[[1-[[2-[3,5-bis(chloranyl)phenyl]-6-[6-[4-(2-methoxyethyl)piperazin-4-ium-1-yl]pyridin-3-yl]oxy-pyridin-4-yl]methyl]piperidin-1-ium-4-yl]methyl]ethanamide (I0T)
Ligand formula: C32 H42 Cl2 N6 O3
Ligand molecular weight: 629.62
Ligand SMILES: CC(=O)NCC1CC[NH+](CC1)Cc2cc(nc(c2)Oc3ccc(nc3)N4CC[NH+](CC4)CCOC)c5cc(cc(c5)Cl)Cl
Ligand InChI: InChI=1S/C32H40Cl2N6O3/c1-23(41)35-20-24-5-7-39(8-6-24)22-25-15-30(26-17-27(33)19-28(34)18-26)37-32(16-25)43-29-3-4-31(36-21-29)40-11-9-38(10-12-40)13-14-42-2/h3-4,15-19,21,24H,5-14,20,22H2,1-2H3,(H,35,41)/p+2
Release date: 2022-04-20
Crystal Structure of human JMJD2D complexed with KDOPP7 (PDB entry 5F5C)
Macromolecule: Lysine-specific demethylase 4D
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11
Sequence length: 346 residues
Sequence: YFQSMETMKSKANCAQNPNCNIMIFHPTKEEFNDFDKYIAYMESQGAHRAGLAKIIPPKEWKARETYDNISEILIATPLQQVASGRAGVFTQYHKKKKAMTVGEYRHLANSKKYQTPPHQNFEDLERKYWKNRIYNSPIYGADISGSLFDENTKQWNLGHLGTIQDLLEKECGVVIEGVNTPYLYFGMWKTTFAWHTEDMDLYSINYLHLGEPKTWYVVPPEHGQRLERLARELFPGSSRGCGAFLRHKVALISPTVLKENGIPFNRITQEAGEFMVTFPYGYHAGFNHGFNCAEAINFATPRWIDYGKMASQCSCGEARVTFSMDAFVRILQPERYDLWKRGQDR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.88
R work: 0.1715
R free: 0.2108
Average B factor: 13.863
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.8
Crystallization temperature (K): 293
Crystal growth procedure: 26% PEG3350 , 0.1M HEPES pH 6.8 , 0.2M ammonium sulfate
Matthews coefficient: 2.41
Solvent content (%): 49.05
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: 2015-12-30