satarupa22/MacromolecularLigandDB huggingface dataset:
Crystal structure of the p300 acetyltransferase catalytic core with propionyl-coenzyme A. (PDB entry 5LKX)
Macromolecule: Histone acetyltransferase p300,Histone acetyltransferase p300
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1.48
Sequence length: 578 residues
Sequence: GAMAGKAVPMQSKKKIFKPEELRQALMPTLEALYRQDPESLPFRQPVDPQLLGIPDYFDIVKSPMDLSTIKRKLDTGQYQEPWQYVDDIWLMFNNAWLYNRKTSRVYKYCSKLSEVFEQEIDPVMQSLGYCCGRKLEFSPQTLCCYGKQLCTIPRDATYYSYQNRYHFCEKCFNEIQGESVSLGDDPSQPQTTINKEQFSKRKNDTLDPELFVECTECGRKMHQICVLHHEIIWPAGFVCDGCLKKSARTRKENKFSAKRLPSTRLGTFLENRVNDFLRRQNHPESGEVTVRVVHASDKTVEVKPGMKARFVDSGEMAESFPYRTKALFAFEEIDGVDLCFFGMHVQEYGSDCPPPNQRRVYISYLDSVHFFRPKCLRTAVYHEILIGYLEYVKKLGYTTGHIWACPPSEGDDYIFHCHPPDQKIPKPKRLQEWFKKMLDKAVSERIVHDYKDIFKQATEDRLTSAKELPYFEGDFWPNVLEESIKESGGSGSQKLYATMEKHKEVFFVIRLIAGPAANSLPPIVDPDPLIPCDLMDGRDAFLTLARDKHLEFSSLRRAQWSTMCMLVELHTQSQDRF
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.52
R work: 0.20671
R free: 0.23944
Average B factor: 55.942
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277
Crystal growth procedure: Tris, PEG MME 2000, DMSO
Matthews coefficient: 3.1
Solvent content (%): 60.27
Ligand: ZINC ION (ZN)
Ligand formula: Zn
Ligand molecular weight: 65.409
Ligand SMILES: [Zn+2]
Ligand InChI: InChI=1S/Zn/q+2
Release date: 2016-11-02
Human Sirt6 in complex with ADP-ribose and fragment 4-hydroxybenzamide (PDB entry 8AK8)
Macromolecule: NAD-dependent protein deacetylase sirtuin-6
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1.286
Sequence length: 302 residues
Sequence: GIDPFTADKGKCGLPEIFDPPEELERKVWELARLVWQSSSVVFHTGAGISTASGIPDFRGPHGVWTMEERGLAPKFDTTFESARPTQTHMALVQLERVGLLRFLVSQNVDGLHVRSGFPRDKLAELHGNMFVEECAKCKTQYVRDTVVGTMGLKATGRLCTVAKARGLRACRGELRDTILDWEDSLPDRDLALADEASRNADLSITLGTSLQIRPSGNLPLATKRRGGRLVIVNLQPTKHDRHADLRIHGYVDEVMTRLMKHLGLEIPAWDGPRVLERALPPLPRPPTPKLEPKEESPTRIN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.73
R work: 0.1615
R free: 0.1929
Average B factor: 37.573
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.7
Crystallization temperature (K): 293
Crystal growth procedure: 1.6 M (NH4)2SO4, 10% PEG 400, and Bis-Tris buffer pH 5.7
Matthews coefficient: 2.6
Solvent content (%): 52.68
Ligand: [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL
[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE (AR6)
Ligand formula: C15 H23 N5 O14 P2
Ligand molecular weight: 559.316
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)O)O)O)O)O)N
Ligand InChI: InChI=1S/C15H23N5O14P2/c16-12-7-13(18-3-17-12)20(4-19-7)14-10(23)8(21)5(32-14)1-30-35(26,27)34-36(28,29)31-2-6-9(22)11(24)15(25)33-6/h3-6,8-11,14-15,21-25H,1-2H2,(H,26,27)(H,28,29)(H2,16,17,18)/t5-,6-,8-,9-,10-,11-,14-,15+/m1/s1
Release date: 2023-08-16
Crystal structure of human PTPN2 in complex with allosteric inhibitor (PDB entry 9C56)
Macromolecule: Tyrosine-protein phosphatase non-receptor type 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 315 residues
Sequence: GMPTTIEREFEELDTQRRWQPLYLEIRNESHDYPHRVAKFPENRNRNRYRDVSPYDHSRVKLQNAENDYINASLVDIEEAQRSYILTQGPLPNTCCHFWLMVWQQKTKAVVMLNRIVEKESVKCAQYWPTDDQEMLFKETGFSVKLLSEDVKSYYTVHLLQLENINSGETRTISHFHYTTWPDFGVPESPASFLNFLFKVRESGSLNPDHGPAVIHCSAGIGRSGTFSLVDTCLVLMEKGDDINIKQVLLNMRKYRMGLIQTPDQLRFSYMAIIEGAKCIKGDSSIQKRWKELSKEDLSPAFDHSPNKIMTEKYN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.43
R work: 0.1986
R free: 0.2461
Average B factor: 53.67
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 100mM MES/imidazole pH6.5, 8% w/v PEG 8000, 16% v/v ethylene glycol, 35mM sodium l-glutamate, 35mM dl-alanine, 35mM glycine, 35mM dl-lysine HCl, 35mM dl-serine
Matthews coefficient: 2.34
Solvent content (%): 47.51
Ligand: 3-(3,5-DIBROMO-4-HYDROXY-BENZOYL)-2-ETHYL-BENZOFURAN-6-SULFONIC ACID [4-(THIAZOL-2-YLSULFAMOYL)-PHENYL]-AMIDE (FRJ)
Ligand formula: C26 H19 Br2 N3 O7 S3
Ligand molecular weight: 741.448
Ligand SMILES: CCc1c(c2ccc(cc2o1)S(=O)(=O)Nc3ccc(cc3)S(=O)(=O)Nc4nccs4)C(=O)c5cc(c(c(c5)Br)O)Br
Ligand InChI: InChI=1S/C26H19Br2N3O7S3/c1-2-21-23(24(32)14-11-19(27)25(33)20(28)12-14)18-8-7-17(13-22(18)38-21)41(36,37)30-15-3-5-16(6-4-15)40(34,35)31-26-29-9-10-39-26/h3-13,30,33H,2H2,1H3,(H,29,31)
Release date: 2024-09-04
Crystal structure of human tankyrase 2 in complex with 1-methyl-7-(4- methylphenyl)-5-oxo-5,6-dihydro-1,6-naphthyridin-1-ium (PDB entry 4UX4)
Macromolecule: TANKYRASE-2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.4.2.30
Sequence length: 240 residues
Sequence: MHHHHHHSSGVDLGTENLYFQSMLNTSGSGTILIDLSPDDKEFQSVEEEMQSTVREHRDGGHAGGIFNRYNILKIQKVCNKKLWERYTHRRKEVSEENHNHANERMLFHGSPFVNAIIHKGFDERHAYIGGMFGAGIYFAENSSKSNQYVYGIGGGTGCPVHKDRSCYICHRQLLFCRVTLGKSFLQFSAMKMAHSPPGHHSVTGRPSVNGLALAEYVIYRGEQAYPEYLITYQIMRPEG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.16229
R free: 0.19837
Average B factor: 29.114
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.2 M LISO4, 0.1 M TRIS HCL, 22% PEG3350, PH 8.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K
Matthews coefficient: 2.4
Solvent content (%): 49
Ligand: (1S)-1-methyl-7-(4-methylphenyl)-5-oxo-1,5-dihydro-1,6-naphthyridin-1-ium (E9L)
Ligand formula: C16 H15 N2 O
Ligand molecular weight: 251.303
Ligand SMILES: Cc1ccc(cc1)C2=NC(=O)C3=CC=C[NH+](C3=C2)C
Ligand InChI: InChI=1S/C16H14N2O/c1-11-5-7-12(8-6-11)14-10-15-13(16(19)17-14)4-3-9-18(15)2/h3-10H,1-2H3/p+1
Release date: 2015-06-10
Structure of Pin1 PPIase domain bound with all-trans retinoic acid (PDB entry 4TNS)
Macromolecule: Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 5.2.1.8
Sequence length: 151 residues
Sequence: MGSSHHHHHHSSGLVPRGSHMLEVLFQGPGSGGKNGQGEPARVRCSHLLVKHSQSRRPSSWRQEQITRTQEEALELINGYIQKIKSGEEDFESLASQFSDCSSAKARGDLGAFSRGQMQKPFEDASFALRTGEMSGPVFTDSGIHIILRTE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.33
R work: 0.16917
R free: 0.18694
Average B factor: 14.818
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 297
Crystal growth procedure: 0.2 M ammonium sulfate, 0.1 M HEPES pH7-8.5 and 0.9 M-1.4 M sodium citrate
Matthews coefficient: 1.63
Solvent content (%): 24.58
Ligand: RETINOIC ACID (REA)
Ligand formula: C20 H28 O2
Ligand molecular weight: 300.435
Ligand SMILES: CC1=C(C(CCC1)(C)C)C=CC(=CC=CC(=CC(=O)O)C)C
Ligand InChI: InChI=1S/C20H28O2/c1-15(8-6-9-16(2)14-19(21)22)11-12-18-17(3)10-7-13-20(18,4)5/h6,8-9,11-12,14H,7,10,13H2,1-5H3,(H,21,22)/b9-6+,12-11+,15-8+,16-14+
Release date: 2015-04-08
PKAB3 in complex with pyrrolidine inhibitor 47a (PDB entry 4Z83)
Macromolecule: cAMP-dependent protein kinase catalytic subunit alpha
Type: Protein, polypeptide(L)
Source organism: Bos taurus
EC number: 2.7.11.11
Sequence length: 350 residues
Sequence: GNAAAAKKGSEQESVKEFLAKAKEDFLKKWENPAQNTAHLDQFERIKTLGTGSFGRVMLVKHMETGNHYAMKILDKQKVVKLKQIEHTLNEKRILQAVNFPFLVKLEFSFKDNSNLYMVMEYAPGGEMFSHLRRIGRFSEPHARFYAAQIVLTFEYLHSLDLIYRDLKPENLMIDQQGYIKVTDFGFAKRVKGRTWTLCGTPEYLAPEIILSKGYNKAVDWWALGVLIYEMAAGYPPFFADQPIQIYEKIVSGKVRFPSHFSSDLKDLLRNLLQVDLTKRFGNLKNGVNDIKNHKWFATTDWIAIYQRKVEAPFIPKFKGPGDTSNFDDYEEEEIRVSINEKCGKEFSEF
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.1798
R free: 0.2175
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 277
Crystal growth procedure: The droplets, containing 16 mg/ml PKAB3, 25 mM Bis-Tris-HCl, pH 7.0, 150 mM KCl, 1.5mM octanoyl-N-methylglucamide and 0.8 mM PKI peptide, were equilibrated against 12-26 % (v/v) methanol.
Matthews coefficient: 2.33
Solvent content (%): 47.28
Ligand: 7-{(3S,4R)-4-[(5-bromothiophen-2-yl)carbonyl]pyrrolidin-3-yl}quinazolin-4(3H)-one (4L7)
Ligand formula: C17 H14 Br N3 O2 S
Ligand molecular weight: 404.281
Ligand SMILES: c1cc2c(cc1C3CNCC3C(=O)c4ccc(s4)Br)N=CNC2=O
Ligand InChI: InChI=1S/C17H14BrN3O2S/c18-15-4-3-14(24-15)16(22)12-7-19-6-11(12)9-1-2-10-13(5-9)20-8-21-17(10)23/h1-5,8,11-12,19H,6-7H2,(H,20,21,23)/t11-,12+/m1/s1
Release date: 2015-12-02
Structure of the RIG-I Singleton-Merten syndrome variant C268F (PDB entry 6GPG)
Macromolecule: RNA (5'-R(*CP*GP*AP*CP*GP*CP*UP*AP*GP*CP*GP*UP*CP*G)-3')
Type: RNA, polyribonucleotide
Source organism: synthetic construct
Sequence length: 14 residues
Sequence: CGACGCUAGCGUCG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.894
R work: 0.2096
R free: 0.2597
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M MOPS pH 7.5, 17.5 % (w/v) PEG 3350, 0.25 M NaSCN, 3 % (v/v) 2,2,2 trifluoroethanol
Matthews coefficient: 2.68
Solvent content (%): 54.16
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: 2018-08-08
Kallikrein-related peptidase 8 calcium complex (PDB entry 5MS3)
Macromolecule: Kallikrein-8
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.118
Sequence length: 228 residues
Sequence: VLGGHECQPHSQPWQAALFQGQQLLCGGVLVGGNWVLTAAHCKKPKYTVRLGDHSLQNKDGPEQEIPVVQSIPHPCYNSSDVEDHNHDLMLLQLRDQASLGSKVKPISLADHCTQPGQKCTVSGWGTVTSPRENFPDTLNCAEVKIFPQKKCEDAYPGQITDGMVCAGSSKGADTCQGDSGGPLVCDGALQGITSWGSDPCGRSDKPGVYTNICRYLDWIKKIIGSKG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.3
R work: 0.2213
R free: 0.2656
Average B factor: 29.3418
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.6
Crystallization temperature (K): 291
Crystal growth procedure: 35% (v/v) tert-Butanol, 0.1 M tri-Na citrate/citric acid
Matthews coefficient: 2.01
Solvent content (%): 38.92
Ligand: CALCIUM ION (CA)
Ligand formula: Ca
Ligand molecular weight: 40.078
Ligand SMILES: [Ca+2]
Ligand InChI: InChI=1S/Ca/q+2
Release date: 2018-01-17
Co- Carbonic Anhydrase II pH 11.0 0 atm CO2 (PDB entry 6LV3)
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: 0.1229
R free: 0.1489
Average B factor: 13.94
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 11
Crystallization temperature (K): 293
Crystal growth procedure: 1.3 M sodium citrate, 50 mM Tris-HCl
Matthews coefficient: 2.08
Solvent content (%): 40.98
Ligand: COBALT (II) ION (CO)
Ligand formula: Co
Ligand molecular weight: 58.933
Ligand SMILES: [Co+2]
Ligand InChI: InChI=1S/Co/q+2
Release date: 2020-08-19
Crystal structure of BACE complex with BMC016 (PDB entry 5QCO)
Macromolecule: Beta-secretase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.23.46
Sequence length: 402 residues
Sequence: GPDEEPEEPGRRGSFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHPFLHRYYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTVRANIAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTHVPNLFSLQLCGAGFPLNQSEVLASVGGSMIIGGIDHSLYTGSLWYTPIRREWYYEVIIVRVEINGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVKSIKAASSTEKFPDGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRITILPQQYLRPVEDVATSQDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSACHVHDEFRTAAVEGPFVTLDMEDCGYNI
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.7
R work: 0.169
R free: 0.217
Average B factor: 76.65
Crystallization method: hanging drop
Crystallization temperature (K): 292
Crystal growth procedure: CRYSTALS WERE GROWN AT 19C BY VAPOUR DIFFUSION IN HANGING DROPS FROM 1.0M AMMONIUM SULFATE. PROTEIN STOCK WAS BACE
MUT46B BATCH XIV 6.3MG/ML IN 10MM TRIS-HCL PH 7.4, 25MM NACL, WITH A 7-FOLD EXCESS OF BMC016 ADDED FROM A 50MM STOCK
SOLUTION IN DMSO (2.0% DMSO IN DROP). CRYO- PROTECTANT WAS 1.2M AMMONIUM SULFATE, 25%(V/V)GLYCEROL, 2.0% DMSO, 1MM
BMC016.
Matthews coefficient: 3.01
Solvent content (%): 59.11
Ligand: (4S)-19-acetyl-4-[(1R)-1-hydroxy-2-({1-[3-(propan-2-yl)phenyl]cyclopropyl}amino)ethyl]-11-oxa-3,16-diazatricyclo[15.3.1.1~6,10~]docosa-1(21),6(22),7,9,17,19-hexaen-2-one (E4A)
Ligand formula: C35 H43 N3 O4
Ligand molecular weight: 569.734
Ligand SMILES: CC(C)c1cccc(c1)C2(CC2)NCC(C3Cc4cccc(c4)OCCCCNc5cc(cc(c5)C(=O)C)C(=O)N3)O
Ligand InChI: InChI=1S/C35H43N3O4/c1-23(2)26-9-7-10-29(19-26)35(12-13-35)37-22-33(40)32-17-25-8-6-11-31(16-25)42-15-5-4-14-36-30-20-27(24(3)39)18-28(21-30)34(41)38-32/h6-11,16,18-21,23,32-33,36-37,40H,4-5,12-15,17,22H2,1-3H3,(H,38,41)/t32-,33+/m0/s1
Release date: 2020-06-03
Factor XIa in Complex with Compound 2d (PDB entry 7V10)
Macromolecule: Coagulation factor XIa light chain
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.27
Sequence length: 238 residues
Sequence: IVGGTASVRGEWPWQVTLHTTSPTQRHLCGGSIIGNQWILTAAHCFYGVESPKILRVYSGILNQSEIKEDTSFFGVQEIIIHDQYKMAESGYDIALLKLETTVNYTDSQRPISLPSKGDRNVIYTDCWVTGWGYRKLRDKIQNTLQKAKIPLVTNEECQKRYRGHKITHKMICAGYREGGKDACKGDSGGPLSCKHNEVWHLVGITSWGEGCAQRERPGVYTNVVEYVDWILEKTQAV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.798
R work: 0.1902
R free: 0.23
Average B factor: 21.9915
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5
Crystallization temperature (K): 293
Crystal growth procedure: 24% PEG 4000, 100mM Na Citrate pH 5.0
Matthews coefficient: 2.22
Solvent content (%): 44.52
Ligand: CITRIC ACID (CIT)
Ligand formula: C6 H8 O7
Ligand molecular weight: 192.124
Ligand SMILES: C(C(=O)O)C(CC(=O)O)(C(=O)O)O
Ligand InChI: InChI=1S/C6H8O7/c7-3(8)1-6(13,5(11)12)2-4(9)10/h13H,1-2H2,(H,7,8)(H,9,10)(H,11,12)
Release date: 2022-08-03
Crystal Structure of human cyclic GMP-AMP synthase in complex with 5-bromo-N-[[2-fluoro-5-(1-methylpyrazol-4-yl)phenyl]methyl]-2-hydroxybenzamide (PDB entry 7FTS)
Macromolecule: Cyclic GMP-AMP synthase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.86
Sequence length: 362 residues
Sequence: GASKLRAVLEKLKLSRDDISTAAGMVKGVVDHLLLRLKCDSAFRGVGLLNTGSYYEHVKISAPNEFDVMFKLEVPRIQLEEYSNTRAYYFVKFKRNPKENPLSQFLEGEILSASKMLSKFRKIIKEEINDIKDTDVIMKRKRGGSPAVTLLISEKISVDITLALESKSSWPASTQEGLRIQNWLSAKVRKQLRLKPFYLVPKHAKEGNGFQEETWRLSFSHIEKEILNNHGKSKTCCENKEEKCCRKDCLKLMKYLLEQLKERFKDKKHLDKFSSYHVKTAFFHVCTQNPQDSQWDRKDLGLCFDNCVTYFLQCLRTEKLENYFIPEFNLFSSNLIDKRSKEFLTKQIEYERNNEFPVFDEF
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.215
R work: 0.2194
R free: 0.2814
Average B factor: 84.9217
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 293
Crystal growth procedure: 10-12 mg/mL protein in 25 mM Tris/HCl pH7.5, 500mM NaCl, 2mM TCEP, supplemented with 10x molar excess of ligand and, if needed, with 10 mM MgCl2 and 5mM ATP, then mixed 1:1 with reservoir of the Procomplex screen. Several conditions resulted in crystals
Matthews coefficient: 2.62
Solvent content (%): 53.11
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: 2024-02-21
Protein Tyrosine Phosphatase 1B (1-301), F182A mutant, apo state (PDB entry 6OL4)
Macromolecule: Tyrosine-protein phosphatase non-receptor type 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 296 residues
Sequence: EMEKEFEQIDKSGSWAAIYQDIRHEASDFPCRVAKLPKNKNRNRYRDVSPFDHSRIKLHQEDNDYINASLIKMEEAQRSYILTQGPLPNTCGHFWEMVWEQKSRGVVMLNRVMEKGSLKCAQYWPQKEEKEMIFEDTNLKLTLISEDIKSYYTVRQLELENLTTQETREILHFHYTTWPDAGVPESPASFLNFLFKVRESGSLSPEHGPVVVHCSAGIGRSGTFCLADTCLLLMDKRKDPSSVDIKKVLLEMRKFRMGLIQTADQLRFSYLAVIEGAKFIMGDSSVQDQWKELSHE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.15
R work: 0.2156
R free: 0.2574
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7
Crystallization temperature (K): 277
Crystal growth procedure: 0.1M Hepes,  0.2 M magnesium acetate and 15-20% polyethylene glycol 8000
Matthews coefficient: 3.37
Solvent content (%): 63.53
Ligand: GLYCEROL (GOL)
Ligand formula: C3 H8 O3
Ligand molecular weight: 92.094
Ligand SMILES: C(C(CO)O)O
Ligand InChI: InChI=1S/C3H8O3/c4-1-3(6)2-5/h3-6H,1-2H2
Release date: 2020-03-25
Crystal structure of EGFR_TMX in complex with covalently bound fragment 4 (PDB entry 8HV4)
Macromolecule: Epidermal growth factor receptor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 331 residues
Sequence: GSGEAPNQALLRILKETEFKKIKVLGSGAFGTVYKGLWIPEGEKVKIPVAIKELREATSPKANKEILDEAYVMASVDNPHVCRLLGICLTSTVQLIMQLMPFGSLLDYVREHKDNIGSQYLLNWCVQIAKGMNYLEDRRLVHRDLAARNVLVKTPQHVKITDFGRAKLLGAAAAEYHAEGGKVPIKWMALESILHRIYTHQSDVWSYGVTVWELMTFGSKPYDGIPASEISSILEKGERLPQPPICTIDVYMIMVKCWMIDADSRPKFRELIIEFSKMARDPQRYLVIQGDERMHLPSPTDSNFYRALMDEEDMDDVVDADEYLIPQQGNS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.2
R work: 0.23692
R free: 0.27492
Average B factor: 42.537
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 292
Crystal growth procedure: 0.1M TRIS pH 8.5, 0.15M Sodium citrate, 25%PEG400
Matthews coefficient: 3.36
Solvent content (%): 63.45
Ligand: ~{N}-pyridin-2-ylprop-2-enamide (MWU)
Ligand formula: C8 H8 N2 O
Ligand molecular weight: 148.162
Ligand SMILES: C=CC(=O)Nc1ccccn1
Ligand InChI: InChI=1S/C8H8N2O/c1-2-8(11)10-7-5-3-4-6-9-7/h2-6H,1H2,(H,9,10,11)
Release date: 2023-12-13
Crystal structure of HCK kinase complexed with a pyrrolo-pyrimidine inhibitor 7-[trans-4-(4-methylpiperazin-1-yl)cyclohexyl]-5-(4-phenoxyphenyl)-7H-pyrrolo[2,3-d]pyrimidin-4-amine (PDB entry 5ZJ6)
Macromolecule: Tyrosine-protein kinase HCK
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 287 residues
Sequence: GSSGSSGMSSKPQKPWEKDAWEIPRESLKLEKKLGAGQFGEVWMATYNKHTKVAVKTMKPGSMSVEAFLAEANVMKTLQHDKLVKLHAVVTKEPIYIITEFMAKGSLLDFLKSDEGSKQPLPKLIDFSAQIAEGMAFIEQRNYIHRDLRAANILVSASLVCKIADFGLARVIEDNEYTAREGAKFPIKWTAPEAINFGSFTIKSDVWSFGILLMEIVTYGRIPYPGMSNPEVIRALERGYRMPRPENCPEELYNIMMRCWKNRPEERPTFEYIQSVLDDFYTATESQ
Oligomeric state: Homo 2-mer
Stoichiometry: A2
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.696
R work: 0.2066
R free: 0.2401
Average B factor: 21.5299
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 288
Crystal growth procedure: 0.1 M Tris-HCl (pH 8.5)
25 % (v/v) PEG 10,000
Matthews coefficient: 2.19
Solvent content (%): 43.75
Ligand: 7-[trans-4-(4-methylpiperazin-1-yl)cyclohexyl]-5-(4-phenoxyphenyl)-7H-pyrrolo[2,3-d]pyrimidin-4-amine (VSE)
Ligand formula: C29 H34 N6 O
Ligand molecular weight: 482.62
Ligand SMILES: CN1CCN(CC1)C2CCC(CC2)n3cc(c4c3ncnc4N)c5ccc(cc5)Oc6ccccc6
Ligand InChI: InChI=1S/C29H34N6O/c1-33-15-17-34(18-16-33)22-9-11-23(12-10-22)35-19-26(27-28(30)31-20-32-29(27)35)21-7-13-25(14-8-21)36-24-5-3-2-4-6-24/h2-8,13-14,19-20,22-23H,9-12,15-18H2,1H3,(H2,30,31,32)/t22-,23-
Release date: 2018-06-06
Human CYP3A4 bound to an inhibitor (PDB entry 6DA8)
Macromolecule: Cytochrome P450 3A4
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.14
Sequence length: 487 residues
Sequence: MAYLYGTHSHGLFKKLGIPGPTPLPFLGNILSYHKGFCMFDMECHKKYGKVWGFYDGQQPVLAITDPDMIKTVLVKECYSVFTNRRPFGPVGFMKSAISIAEDEEWKRLRSLLSPTFTSGKLKEMVPIIAQYGDVLVRNLRREAETGKPVTLKDVFGAYSMDVITSTSFGVNIDSLNNPQDPFVENTKKLLRFDFLDPFFLSITVFPFLIPILEVLNICVFPREVTNFLRKSVKRMKESRLEDTQKHRVDFLQLMIDSQNSKETESHKALSDLELVAQSIIFIFAGYETTSSVLSFIMYELATHPDVQQKLQEEIDAVLPNKAPPTYDTVLQMEYLDMVVNETLRLFPIAMRLERVCKKDVEINGMFIPKGVVVMIPSYALHRDPKYWTEPEKFLPERFSKKNKDNIDPYIYTPFGSGPRNCIGMRFALMNMKLALIRVLQNFSFKPCKETQIPLKLSLGGLLQPEKPVVLKVESRDGTVSGAHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.802
R work: 0.2156
R free: 0.2911
Crystallization method: MICROBATCH
Crystallization temperature (K): 293
Crystal growth procedure: peg 3500, sodium malonate
Matthews coefficient: 2.19
Solvent content (%): 43.94
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: 2019-04-03
CRYSTAL STRUCTURE OF HUMAN MDM2 IN COMPLEX WITH 12-MER PEPTIDE INHIBITOR M3 (PDB entry 5UMM)
Macromolecule: E3 ubiquitin-protein ligase Mdm2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2.27
Sequence length: 85 residues
Sequence: ETLVRPKPLLLKLLKSVGAQKDTYTMKEVLFYLGQYIMTKRLYDEKQQHIVYCSNDLLGDLFGVPSFSVKEHRKIYTMIYRNLVV
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.65
R work: 0.17795
R free: 0.23112
Average B factor: 32.574
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 298
Crystal growth procedure: 0.1 M sodium cacodylate pH 5.5, 25% PEG (w/v) 4000
Matthews coefficient: 1.84
Solvent content (%): 33.2
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: 2018-01-31
Crystal structure of BACE1 in complex with 2-aminooxazoline-3-azaxanthene compound 12 (PDB entry 5UYU)
Macromolecule: Beta-secretase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.23.46
Sequence length: 411 residues
Sequence: LPRETDEEPEEPGKKGSFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHPFLHRYYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTVRANIAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTHVPNLFSLQLCGAGFPLNQSEVLASVGGSMIIGGIDHSLYTGSLWYTPIRREWYYEVIIVRVEINGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVKSIKAASSTEKFPDGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRITILPQQYLRPVEDVATSQDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSACHVHDEFRTAAVEGPFVTLDMEDCGYNIPQTDES
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.9
R work: 0.2052
R free: 0.228
Average B factor: 29.7
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 6.6
Crystallization temperature (K): 298
Crystal growth procedure: 21% polyethylene glycol 5000 MME, 180 mM sodium citrate (pH 6.6), 200 mM ammonium iodide, 3% (v/v) DMSO
Matthews coefficient: 2.81
Solvent content (%): 56.19
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: 2017-05-17