satarupa22/MacromolecularLigandDB huggingface dataset:
The crystal structure of TrkA(F589L) kinase in complex with N-(3-cyclopropyl-5-((4-methylpiperazin-1-yl)methyl)phenyl)-4^6-methyl-14-oxo-5-oxa-13-aza-1(3,6)-imidazo[1,2-b]pyridazina-4(1,3)-benzenacyclotetradecaphan-2-yne-4^5-carboxamide (PDB entry 8J5W)
Macromolecule: High affinity nerve growth factor receptor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 313 residues
Sequence: SGLQGHIIENPQYFSDACVHHIKRRDIVLKWELGEGAFGKVFLAECHNLLPEQDKMLVAVKALKEASESARQDFQREAELLTMLQHQHIVRFFGVCTEGRPLLMVLEYMRHGDLNRFLRSHGPDAKLLAGGEDVAPGPLGLGQLLAVASQVAAGMVYLAGLHFVHRDLATRNCLVGQGLVVKIGDFGMSRDIYSTDYYRVGGRTMLPIRWMPPESILYRKFTTESDVWSFGVVLWEIFTYGKQPWYQLSNTEAIDCITQGRELERPRACPPEVYAIMRGCWQREPQQRHSIKDVHARLQALAQAPPVYLDVLG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.28041464539
R work: 0.216913692069
R free: 0.265992005805
Average B factor: 56.0588333871
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 289
Crystal growth procedure: 0.1M Na2HPO4/KH2PO4 (pH 6.2), 2M NaCl
Matthews coefficient: 2.61
Solvent content (%): 52.83
Ligand: N-(3-cyclopropyl-5-((4-methylpiperazin-1-yl)methyl)phenyl)-4^6-methyl-14-oxo-5-oxa-13-aza-1(3,6)-imidazo[1,2-b]pyridazina-4(1,3)-benzenacyclotetradecaphan-2-yne-4^5-carboxamide (A4U)
Ligand formula: C39 H45 N7 O3
Ligand molecular weight: 659.82
Ligand SMILES: Cc1c2cc(cc1C(=O)Nc3cc(cc(c3)C4CC4)CN5CCN(CC5)C)OCCCCCCCNC(=O)c6ccc7ncc(n7n6)C#C2
Ligand InChI: InChI=1S/C39H45N7O3/c1-27-30-10-11-33-25-41-37-13-12-36(43-46(33)37)39(48)40-14-6-4-3-5-7-19-49-34(23-30)24-35(27)38(47)42-32-21-28(20-31(22-32)29-8-9-29)26-45-17-15-44(2)16-18-45/h12-13,20-25,29H,3-9,14-19,26H2,1-2H3,(H,40,48)(H,42,47)
Release date: 2023-09-20
Crystal Structure of human phosphodiesterase 10 in complex with (2R)-2-[[3-cyano-2-[4-(2-ethoxyphenyl)phenyl]-6-fluoroquinolin-4-yl]amino]propanoic acid (PDB entry 5SJR)
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: 0.2093
R free: 0.2633
Average B factor: 45.797
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: 2.64
Solvent content (%): 53.35
Ligand: N-[3-cyano-2-(2'-ethoxy[1,1'-biphenyl]-4-yl)-6-fluoroquinolin-4-yl]-D-alanine (K63)
Ligand formula: C27 H22 F N3 O3
Ligand molecular weight: 455.48
Ligand SMILES: CCOc1ccccc1c2ccc(cc2)c3c(c(c4cc(ccc4n3)F)NC(C)C(=O)O)C#N
Ligand InChI: InChI=1S/C27H22FN3O3/c1-3-34-24-7-5-4-6-20(24)17-8-10-18(11-9-17)25-22(15-29)26(30-16(2)27(32)33)21-14-19(28)12-13-23(21)31-25/h4-14,16H,3H2,1-2H3,(H,30,31)(H,32,33)/t16-/m1/s1
Release date: 2022-10-12
Crystal structure of the human METTL3-METTL14 complex bound to Sinefungin (PDB entry 6Y4G)
Macromolecule: N6-adenosine-methyltransferase catalytic subunit
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1.348
Sequence length: 580 residues
Sequence: MSDTWSSIQAHKKQLDSLRERLQRRRKQDSGHLDLRNPEAALSPTFRSDSPVPTAPTSGGPKPSTASAVPELATDPELEKKLLHHLSDLALTLPTDAVSICLAISTPDAPATQDGVESLLQKFAAQELIEVKRGLLQDDAHPTLVTYADHSKLSAMMGAVAEKKGPGEVAGTVTGQKRRAEQDSTTVAAFASSLVSGLNSSASEPAKEPAKKSRKHAASDVDLEIESLLNQQSTKEQQSKKVSQEILELLNTTTAKEQSIVEKFRSRGRAQVQEFCDYGTKEECMKASDADRPCRKLHFRRIINKHTDESLGDCSFLNTCFHMDTCKYVHYEIDACMDSEAPGSKDHTPSQELALTQSVGGDSSADRLFPPQWICCDIRYLDVSILGKFAVVMADPPWDIHMELPYGTLTDDEMRRLNIPVLQDDGFLFLWVTGRAMELGRECLNLWGYERVDEIIWVKTNQLQRIIRTGRTGHWLNHGKEHCLVGVKGNPQGFNQGLDCDVIVAEVRSTSHKPDEIYGMIERLSPGTRKIELFGRPHNVQPNWITLGNQLDGIHLLDPDVVARFKQRYPDGIISKPKNL
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.9
R work: 0.1834
R free: 0.2175
Average B factor: 32.94
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 295
Crystal growth procedure: 20% PEG 3350, 400mM Mg acetate
Ligand: SINEFUNGIN (SFG)
Ligand formula: C15 H23 N7 O5
Ligand molecular weight: 381.387
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)CC(CCC(C(=O)O)N)N)O)O)N
Ligand InChI: InChI=1S/C15H23N7O5/c16-6(1-2-7(17)15(25)26)3-8-10(23)11(24)14(27-8)22-5-21-9-12(18)19-4-20-13(9)22/h4-8,10-11,14,23-24H,1-3,16-17H2,(H,25,26)(H2,18,19,20)/t6-,7-,8+,10+,11+,14+/m0/s1
Release date: 2020-03-04
XChem group deposition -- Crystal Structure of human ACVR1 in complex with FM010935a (PDB entry 5S7F)
Macromolecule: Activin receptor type-1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.30
Sequence length: 301 residues
Sequence: SMQRTVARDITLLECVGKGRYGEVWRGSWQGENVAVKIFSSRDEKSWFRETELYNTVMLRHENILGFIASDMTSRHSSTQLWLITHYHEMGSLYDYLQLTTLDTVSCLRIVLSIASGLAHLHIEIFGTQGKPAIAHRDLKSKNILVKKNGQCCIADLGLAVMHSQSTNQLDVGNNPRVGTKRYMAPEVLDETIQVDCFDSYKRVDIWAFGLVLWEVARRMVSNGIVEDYKPPFYDVVPNDPSFEDMRKVVCVDQQRPNIPNRWFSDPTLTSLAKLMKECWYQNPSARLTALRIKKTLTKID
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.31
R work: 0.1498
R free: 0.1693
Average B factor: 17.214
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6
Crystallization temperature (K): 277
Crystal growth procedure: 0.1M citrate pH 6.0, 1.4M ammonium sulfate, 0.2M sodium/potassium tartrate
Matthews coefficient: 2.59
Solvent content (%): 52.59
Ligand: 4-methyl-3-[4-(1-methylpiperidin-4-yl)phenyl]-5-(3,4,5-trimethoxyphenyl)pyridine (LU8)
Ligand formula: C27 H32 N2 O3
Ligand molecular weight: 432.555
Ligand SMILES: Cc1c(cncc1c2cc(c(c(c2)OC)OC)OC)c3ccc(cc3)C4CCN(CC4)C
Ligand InChI: InChI=1S/C27H32N2O3/c1-18-23(21-8-6-19(7-9-21)20-10-12-29(2)13-11-20)16-28-17-24(18)22-14-25(30-3)27(32-5)26(15-22)31-4/h6-9,14-17,20H,10-13H2,1-5H3
Release date: 2021-06-23
uPA-BB2-30F (PDB entry 5ZAH)
Macromolecule: Urokinase-type plasminogen activator chain B
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.73
Sequence length: 253 residues
Sequence: IIGGEFTTIENQPWFAAIYRRHRGGSVTYVCGGSLISPCWVISATHCFIDYPKKEDYIVYLGRSRLNSNTQGEMKFEVENLILHKDYSADTLAHHNDIALLKIRSKEGRCAQPSRTIQTIALPSMYNDPQFGTSCEITGFGKEQSTDYLYPEQLKMTVVKLISHRECQQPHYYGSEVTTKMLCAADPQWKTDSCQGDSGGPLVCSLQGRMTLTGIVSWGRGCALKDKPGVYTRVSHFLPWIRSHTKEENGLAL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.98
R work: 0.168
R free: 0.268
Average B factor: 66.14
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 298
Crystal growth procedure: 50mM sodium citrate pH 4.6, 1.95M (NH4)2SO4, 0.03% NaN3, 5% PEG 400
Matthews coefficient: 2.14
Solvent content (%): 42.43
Ligand: 3-azanyl-5-(azepan-1-yl)-N-carbamimidoyl-6-(2-methoxypyrimidin-5-yl)pyrazine-2-carboxamide (30I)
Ligand formula: C17 H23 N9 O2
Ligand molecular weight: 385.424
Ligand SMILES: COc1ncc(cn1)c2c(nc(c(n2)C(=O)NC(=N)N)N)N3CCCCCC3
Ligand InChI: InChI=1S/C17H23N9O2/c1-28-17-21-8-10(9-22-17)11-14(26-6-4-2-3-5-7-26)24-13(18)12(23-11)15(27)25-16(19)20/h8-9H,2-7H2,1H3,(H2,18,24)(H4,19,20,25,27)
Release date: 2018-12-19
EED in complex with PRC2 allosteric inhibitor compound 7 (PDB entry 7QJU)
Macromolecule: Polycomb protein EED
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 366 residues
Sequence: GKCKYSFKCVNSLKEDHNQPLFGVQFNWHSKEGDPLVFATVGSNRVTLYECHSQGEIRLLQSYVDADADENFYTCAWTYDSNTSHPLLAVAGSRGIIRIINPITMQCIKHYVGHGNAINELKFHPRDPNLLLSVSKDHALRLWNIQTDTLVAIFGGVEGHRDEVLSADYDLLGEKIMSCGMDHSLKLWRINSKRMMNAIKESYDYNPNKTNRPFISQKIHFPDFSTRDIHRNYVDCVRWLGDLILSKSCENAIVCWKPGKMEDDIDKIKPSESNVTILGRFDYSQCDIWYMRFSMDFWQKMLALGNQVGKLYVWDLEVEDPHKAKCTTLTHHKCGAAIRQTSFSRDSSILIAVCDDASIWRWDRLR
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.1867
R free: 0.2131
Average B factor: 26.08
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M Tris pH 8.0, 16% PEG 8000
Matthews coefficient: 2.29
Solvent content (%): 46.2
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: 2022-04-13
Crystal Structure of Ephrin A2 (EphA2) Receptor Protein Kinase with compound 66 (PDB entry 5IA2)
Macromolecule: Ephrin type-A receptor 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 306 residues
Sequence: GDPNQAVLKFTTEIHPSCVTRQKVIGAGEFGEVYKGMLKTSSGKKEVPVAIKTLKAGYTEKQRVDFLGEAGIMGQFSHHNIIRLEGVISKYKPMMIITEYMENGALDKFLREKDGEFSVLQLVGMLRGIAAGMKYLANMNYVHRDLAARNILVNSNLVCKVSDFGLSRVLEDDPEATYTTSGGKIPIRWTAPEAISYRKFTSASDVWSFGIVMWEVMTYGERPYWELSNHEVMKAINDGFRLPTPMDCPSAIYQLMMQCWQQERARRPKFADIVSILDKLIRAPDSLKTLADFDPRVSIRLPSTSG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.619
R work: 0.1625
R free: 0.1988
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 37.5 % MPD_P1k_P3350, 0.1 M Amino Acids, 0.1 M MES pH 7.0
Matthews coefficient: 1.98
Solvent content (%): 37.76
Ligand: 7-(5-hydroxy-2-methylphenyl)-8-(2-methoxyphenyl)-1-methyl-1H-imidazo[2,1-f]purine-2,4(3H,8H)-dione (L66)
Ligand formula: C22 H19 N5 O4
Ligand molecular weight: 417.417
Ligand SMILES: Cc1ccc(cc1c2cn3c4c(nc3n2c5ccccc5OC)N(C(=O)NC4=O)C)O
Ligand InChI: InChI=1S/C22H19N5O4/c1-12-8-9-13(28)10-14(12)16-11-26-18-19(25(2)22(30)24-20(18)29)23-21(26)27(16)15-6-4-5-7-17(15)31-3/h4-11,28H,1-3H3,(H,24,29,30)
Release date: 2016-11-09
Structure of CDK2 in complex with FP24322, a Helicon Polypeptide (PDB entry 7UXK)
Macromolecule: Cyclin-dependent kinase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.22
Sequence length: 299 residues
Sequence: GMENFQKVEKIGEGTYGVVYKARNKLTGEVVALKKIRLDTETEGVPSTAIREISLLKELNHPNIVKLLDVIHTENKLYLVFEFLHQDLKKFMDASALTGIPLPLIKSYLFQLLQGLAFCHSHRVLHRDLKPQNLLINTEGAIKLADFGLARAFGVPVRTYTHEVVTLWYRAPEILLGCKYYSTAVDIWSLGCIFAEMVTRRALFPGDSEIDQLFRIFRTLGTPDEVVWPGVTSMPDYKPSFPKWARQDFSKVVPPLDEDGRSLLSQMLHYDPNKRISAKAALAHPFFQDVTKPVPHLRL
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.63
R work: 0.261
R free: 0.3
Average B factor: 70
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 291.15
Crystal growth procedure: Crystallization buffer: 0.1 M BICINE pH 9.2, 2% v/v 1,4-Dioxane, 6% w/v PEG 20000
Matthews coefficient: 2.21
Solvent content (%): 44.27
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: 2022-12-28
Crystal structure of the p97 D2 domain in a helical split-washer conformation (PDB entry 6G2Z)
Macromolecule: Transitional endoplasmic reticulum ATPase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.4.6
Sequence length: 306 residues
Sequence: GPGSALRETVVEVPQVTWEDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANECQANFISIKGPELLTMWFGESEANVREIFDKARQAAPCVLFFDELDSIAKARGGNIGDGGGAADRVINQILTEMDGMSTKKNVFIIGATNRPDIIDPAILRPGRLDQLIYIPLPDEKSRVAILKANLRKSPVAKDVDLEFLAKMTNGFSGADLTEICQRACKLAIRESIESEIRRERERQTNPSAMEVEEDDPVPEIRRDHFEEAMRFARRSVSDNDIRKYEMFAQTLQQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.923
R work: 0.2234
R free: 0.2467
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.08M L-Na-Glutamate; 0.08M Alanine (racemic); 0.08M Glycine; 0.08M Lysine HCl (racemic); 0.08M Serine (racemic), 0.08M Tris, 0.08M BICINE, 10% v/v MPD; 10% PEG 1000; 10% w/v PEG 3350 at pH 8.5
Matthews coefficient: 2.38
Solvent content (%): 48.22
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: 2019-04-10
Crystal Structure of IRAK-4 (PDB entry 4RMZ)
Macromolecule: Interleukin-1 receptor-associated kinase 4
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 307 residues
Sequence: ENKSLEVSDTRFHSFSFYELKNVTNNFDERPISVGGNKMGEGGFGVVYKGYVNNTTVAVKKLAAMVDITTEELKQQFDQEIKVMAKCQHENLVELLGFSSDGDDLCLVYVYMPNGSLLDRLSCLDGTPPLSWHMRCKIAQGAANGINFLHENHHIHRDIKSANILLDEAFTAKISDFGLARASEKFAQTVMTSRIVGTTAYMAPEALRGEITPKSDIYSFGVVLLEIITGLPAVDEHREPQLLLDIKEEIEDEEKTIEDYIDKKMNDADSTSVEAMYSVASQCLHEKKNKRPDIKKVQQLLQEMTAS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.2
R work: 0.2357
R free: 0.29575
Average B factor: 41.829
Crystallization method: EVAPORATION
Crystallization pH: 6.4
Crystallization temperature (K): 293
Crystal growth procedure: 2.6 - 2.9 M ammonium sulfate, PH 6.4-7.9 , EVAPORATION, temperature 293K
Matthews coefficient: 2.6
Solvent content (%): 52.77
Ligand: 3-nitro-N-[1-phenyl-5-(piperidin-1-ylmethyl)-1H-benzimidazol-2-yl]benzamide (T20)
Ligand formula: C26 H25 N5 O3
Ligand molecular weight: 455.508
Ligand SMILES: c1ccc(cc1)n2c3ccc(cc3nc2NC(=O)c4cccc(c4)N(=O)=O)CN5CCCCC5
Ligand InChI: InChI=1S/C26H25N5O3/c32-25(20-8-7-11-22(17-20)31(33)34)28-26-27-23-16-19(18-29-14-5-2-6-15-29)12-13-24(23)30(26)21-9-3-1-4-10-21/h1,3-4,7-13,16-17H,2,5-6,14-15,18H2,(H,27,28,32)
Release date: 2016-01-13
Carbonic Anhydrase IX-mimic in complex with Beta-Galactose_2C (PDB entry 7RRF)
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: 0.1529
R free: 0.1693
Average B factor: 17.9886
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 pH 7.8
Matthews coefficient: 2.12
Solvent content (%): 42.09
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: 2022-08-24
ARHGEF2 PanDDA analysis group deposition -- ARHGEF2 and RhoA in complex with Z1041785508 (PDB entry 7G80)
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): 1.671
R work: 0.2032
R free: 0.2301
Average B factor: 35.59
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: 2.55
Solvent content (%): 51.72
Ligand: 5-(1,3-thiazol-2-yl)-1H-1,2,4-triazole (K34)
Ligand formula: C5 H4 N4 S
Ligand molecular weight: 152.177
Ligand SMILES: c1csc(n1)c2[nH]ncn2
Ligand InChI: InChI=1S/C5H4N4S/c1-2-10-5(6-1)4-7-3-8-9-4/h1-3H,(H,7,8,9)
Release date: 2023-07-12
Discovery of Spirohydantoins as Selective, Orally Bioavailable Inhibitors of p300/CBP Histone Acetyltransferases (PDB entry 7LJE)
Macromolecule: Histone acetyltransferase p300
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1.48
Sequence length: 348 residues
Sequence: KFSAKRLPSTRLGTFLENRVNDFLRRQNHPESGEVTVRVVHASDKTVEVKPGMKARFVDSGEMAESFPYRTKALFAFEEIDGVDLCFFGMHVQEYGSDCPPPNQRRVYISYLDSVHFFRPKCLRTAVYHEILIGYLEYVKKLGYTTGHIWACPPSEGDDYIFHCHPPDQKIPKPKRLQEWYKKMLDKAVSERIVHDYKDIFKQATEDRLTSAKELPYFEGDFWPNVLEESIKELEQKTSKNKSSLSRGNKKKPGMPNVSNDLSQKLYATMEKHKEVFFVIRLIAGPAANSLPPIVDPDPLIPCDLMDGRDAFLTLARDRHLEFSSLRRAQWSTGCMLVELHTQSQDRF
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.607
R work: 0.2115
R free: 0.2651
Average B factor: 44.98
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 5.5
Crystallization temperature (K): 290
Crystal growth procedure: 25% PEG 3350, 0.2 M Ammonium Acetate, 0.1 M Bis-Tris HCl pH 5.5
Matthews coefficient: 2.11
Solvent content (%): 41.72
Ligand: 2-[4-[(3'R,4S)-3'-fluoro-1-[2-[(4-fluorophenyl)methyl-[(1S)-2,2,2-trifluoro-1-methyl-ethyl]amino]-2-oxo-ethyl]-2,5-dioxo-spiro[imidazolidine-4,1'-indane]-5'-yl]pyrazol-1-yl]-N-methyl-acetamide (Y2P)
Ligand formula: C29 H27 F5 N6 O4
Ligand molecular weight: 618.554
Ligand SMILES: CC(C(F)(F)F)N(Cc1ccc(cc1)F)C(=O)CN2C(=O)C3(CC(c4c3ccc(c4)c5cnn(c5)CC(=O)NC)F)NC2=O
Ligand InChI: InChI=1S/C29H27F5N6O4/c1-16(29(32,33)34)39(12-17-3-6-20(30)7-4-17)25(42)15-40-26(43)28(37-27(40)44)10-23(31)21-9-18(5-8-22(21)28)19-11-36-38(13-19)14-24(41)35-2/h3-9,11,13,16,23H,10,12,14-15H2,1-2H3,(H,35,41)(H,37,44)/t16-,23+,28-/m0/s1
Release date: 2021-03-17
Crystal structure of human GPX4-U46C with oxidized Cys-46 (PDB entry 7L8Q)
Macromolecule: Phospholipid hydroperoxide glutathione peroxidase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.11.1.12
Sequence length: 192 residues
Sequence: MGSSHHHHHHSSGLVPRGSHMLEAASRDDWRCARSMHEFSAKDIDGHMVNLDKYRGFVCIVTNVASQCGKTEVNYTQLVDLHARYAECGLRILAFPCNQFGKQEPGSNEEIKEFAAGYNVKFDMFSKICVNGDDAHPLWKWMKIQPKGKGILGNAIKWNFTKFLIDKNGCVVKRYGPMEEPLVIEKDLPHYF
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.48
R work: 0.154
R free: 0.1821
Average B factor: 22.5835
Crystallization method: MICROBATCH
Crystallization pH: 5
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M potassium thiocyanate, 0.1 M sodium acetate, and 20% (w/v) PEG 8000
Matthews coefficient: 1.65
Solvent content (%): 25.66
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: 2021-12-29
Binary complex crystal structure of DNA polymerase Beta with A:A mismatch at the primer terminus (PDB entry 5J0O)
Macromolecule: DNA polymerase beta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 335 residues
Sequence: MSKRKAPQETLNGGITDMLTELANFEKNVSQAIHKYNAYRKAASVIAKYPHKIKSGAEAKKLPGVGTKIAEKIDEFLATGKLRKLEKIRQDDTSSSINFLTRVSGIGPSAARKFVDEGIKTLEDLRKNEDKLNHHQRIGLKYFGDFEKRIPREEMLQMQDIVLNEVKKVDSEYIATVCGSFRRGAESSGDMDVLLTHPSFTSESTKQPKLLHQVVEQLQKVHFITDTLSKGETKFMGVCQLPSKNDEKEYPHRRIDIRLIPKDQYYCGVLYFTGSDIFNKNMRAHALEKGFTINEYTIRPLGVTGVAGEPLPVDSEKDIFDYIQWKYREPKDRSE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2
R work: 0.2097
R free: 0.264
Average B factor: 33.4081
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 291
Crystal growth procedure: 50 mM Imidazole, pH 7.5, 350 mM Sodium Acetate, 16-18 % PEG3350
Matthews coefficient: 2.42
Solvent content (%): 49.11
Ligand: SODIUM ION ()
Ligand formula: Na
Ligand molecular weight: 22.99
Ligand SMILES: [Na+]
Ligand InChI: InChI=1S/Na/q+1
Release date: 2016-10-26
Crystal Structure of BACE1 in complex with N-{3-[(4R)-2-amino-4-(prop-1-yn-1-yl)-5,6-dihydro-4H-1,3-oxazin-4-yl]-4-fluorophenyl}-5-cyanopyridine-2-carboxamide (PDB entry 7D2X)
Macromolecule: Beta-secretase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.23.46
Sequence length: 416 residues
Sequence: GSHMLPRETDEEPEEPGRRGSFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHPFLHRYYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTVRANIAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTHVPNLFSLQLCGAGFPLNQSEVLASVGGSMIIGGIDHSLYTGSLWYTPIRREWYYEVIIVRVEINGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVKSIKAASSTEKFPDGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRITILPQQYLRPVEDVATSQDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSACHVHDEFRTAAVEGPFVTLDMEDCGYNIPQTDEST
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.45
R work: 0.1846
R free: 0.2285
Average B factor: 39.417
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.2 M sodium citrate tribasic pH 6.5, 0.2 M ammonium iodide, 19.6% w/v PEG 5000MME
Matthews coefficient: 2.73
Solvent content (%): 54.87
Ligand: IODIDE ION (IOD)
Ligand formula: I
Ligand molecular weight: 126.904
Ligand SMILES: [I-]
Ligand InChI: InChI=1S/HI/h1H/p-1
Release date: 2021-03-31
ALK-5 kinase inhibitor complex (PDB entry 5USQ)
Macromolecule: TGF-beta receptor type-1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.30
Sequence length: 299 residues
Sequence: TIARTIVLQESIGKGRFGEVWRGKWRGEEVAVKIFSSREERSWFREAEIYQTVMLRHENILGFIAADNKDNGTWTQLWLVSDYHEHGSLFDYLNRYTVTVEGMIKLALSTASGLAHLHMEIVGTQGKPAIAHRDLKSKNILVKKNGTCCIADLGLAVRHDSATDTIDIAPNHRVGTKRYMAPEVLDDSINMKHFESFKRADIYAMGLVFWEIARRCSIGGIHEDYQLPYYDLVPSDPSVEEMRKVVCEQKLRPNIPNRWQSCEALRVMAKIMRECWYANGAARLTALRIKKTLSQLSQQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.55
R work: 0.1792
R free: 0.2305
Average B factor: 28.686
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 9.2
Crystallization temperature (K): 293
Crystal growth procedure: 16 % PEG 8000
100mM CHES pH 9.2
Matthews coefficient: 2.16
Solvent content (%): 42.95
Ligand: N-[2-(5-chloro-2-fluorophenyl)pyridin-4-yl]-2-[(piperidin-4-yl)methyl]-2H-pyrazolo[4,3-b]pyridin-7-amine (8LY)
Ligand formula: C23 H22 Cl F N6
Ligand molecular weight: 436.912
Ligand SMILES: c1cc(c(cc1Cl)c2cc(ccn2)Nc3ccnc4c3nn(c4)CC5CCNCC5)F
Ligand InChI: InChI=1S/C23H22ClFN6/c24-16-1-2-19(25)18(11-16)21-12-17(5-9-27-21)29-20-6-10-28-22-14-31(30-23(20)22)13-15-3-7-26-8-4-15/h1-2,5-6,9-12,14-15,26H,3-4,7-8,13H2,(H,27,29)
Release date: 2017-04-12
CDK2/CyclinA in complex with SU9516 (PDB entry 6GUC)
Macromolecule: Cyclin-dependent kinase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.22
Sequence length: 302 residues
Sequence: GPGSMENFQKVEKIGEGTYGVVYKARNKLTGEVVALKKIRLDTETEGVPSTAIREISLLKELNHPNIVKLLDVIHTENKLYLVFEFLHQDLKKFMDASALTGIPLPLIKSYLFQLLQGLAFCHSHRVLHRDLKPQNLLINTEGAIKLADFGLARAFGVPVRTYTHEVVTLWYRAPEILLGCKYYSTAVDIWSLGCIFAEMVTRRALFPGDSEIDQLFRIFRTLGTPDEVVWPGVTSMPDYKPSFPKWARQDFSKVVPPLDEDGRSLLSQMLHYDPNKRISAKAALAHPFFQDVTKPVPHLRL
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.0
R work: 0.19165
R free: 0.22315
Average B factor: 44.106
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277
Crystal growth procedure: PROTEIN AT 5MG PER ML. 0.6 TO 0.8M KCL, 0.9 TO 1.2M (NH402SO4, AND 100MM HEPES (PH 7.0), 0.5mM Inhibitor
Matthews coefficient: 2.94
Solvent content (%): 58.12
Ligand: (3Z)-3-(1H-IMIDAZOL-5-YLMETHYLENE)-5-METHOXY-1H-INDOL-2(3H)-ONE (SU9)
Ligand formula: C13 H11 N3 O2
Ligand molecular weight: 241.245
Ligand SMILES: COc1ccc2c(c1)C(=Cc3cnc[nH]3)C(=O)N2
Ligand InChI: InChI=1S/C13H11N3O2/c1-18-9-2-3-12-10(5-9)11(13(17)16-12)4-8-6-14-7-15-8/h2-7H,1H3,(H,14,15)(H,16,17)/b11-4-
Release date: 2018-12-05