satarupa22/MacromolecularLigandDB huggingface dataset:
Bromodomain of EP300 liganded with BMS-536924 (PDB entry 7UGI)
Macromolecule: Histone acetyltransferase p300
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1.48
Sequence length: 116 residues
Sequence: SMIFKPEELRQALMPTLEALYRQDPESLPFRQPVDPQLLGIPDYFDIVKSPMDLSTIKRKLDTGQYQEPWQYVDDIWLMFNNAWLYNRKTSRVYKYCSKLSEVFEQEIDPVMQSLG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2
R work: 0.2158
R free: 0.2744
Average B factor: 40.3292
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7
Crystallization temperature (K): 292
Crystal growth procedure: 0.05M Potassium phosphate monobasic 20% w/v Polyethylene glycol 8,000
Matthews coefficient: 2.64
Solvent content (%): 53.45
Ligand: (3M)-4-{[(2S)-2-(3-chlorophenyl)-2-hydroxyethyl]amino}-3-[4-methyl-6-(morpholin-4-yl)-1H-benzimidazol-2-yl]pyridin-2(1H)-one (N6I)
Ligand formula: C25 H26 Cl N5 O3
Ligand molecular weight: 479.959
Ligand SMILES: Cc1cc(cc2c1nc([nH]2)C3=C(C=CNC3=O)NCC(c4cccc(c4)Cl)O)N5CCOCC5
Ligand InChI: InChI=1S/C25H26ClN5O3/c1-15-11-18(31-7-9-34-10-8-31)13-20-23(15)30-24(29-20)22-19(5-6-27-25(22)33)28-14-21(32)16-3-2-4-17(26)12-16/h2-6,11-13,21,32H,7-10,14H2,1H3,(H,29,30)(H2,27,28,33)/t21-/m1/s1
Release date: 2023-04-12
INPP5D PanDDA analysis group deposition -- Crystal Structure of the phosphatase and C2 domains of SHIP1 in complex with Z1310876699 (PDB entry 5RWN)
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): 1.38
R work: 0.1734
R free: 0.1984
Average B factor: 17.689
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: 2.11
Solvent content (%): 41.6
Ligand: 2-fluoro-N-[2-(pyridin-4-yl)ethyl]benzamide (U0V)
Ligand formula: C14 H13 F N2 O
Ligand molecular weight: 244.264
Ligand SMILES: c1ccc(c(c1)C(=O)NCCc2ccncc2)F
Ligand InChI: InChI=1S/C14H13FN2O/c15-13-4-2-1-3-12(13)14(18)17-10-7-11-5-8-16-9-6-11/h1-6,8-9H,7,10H2,(H,17,18)
Release date: 2020-11-11
Crystal Structure of human cyclic GMP-AMP synthase in complex with 5-(4-fluorophenyl)-2-methylpyrazole-3-carboxylic acid (PDB entry 7FTI)
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): 2.0
R work: 0.227
R free: 0.272
Average B factor: 63.06
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: 2.57
Solvent content (%): 52.11
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
ARHGEF2 PanDDA analysis group deposition -- ARHGEF2 and RhoA in complex with PCM-0102102-001 (PDB entry 7G99)
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): 1.78
R work: 0.2063
R free: 0.2366
Average B factor: 48.76
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: 2.48
Solvent content (%): 50.5
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 reduced legumain in complex with cystatin E/M (PDB entry 4N6O)
Macromolecule: legumain
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.22.34
Sequence length: 278 residues
Sequence: GGKHWVVIVAGSNGWYNYRHQADACHAYQIIHRNGIPDEQIVVMMYDDIAYSEDNPTPGIVINRPNGTDVYQGVPKDYTGEDVTPQNFLAVLRGDAEAVKGIGSGKVLKSGPQDHVFIYFTNHGSTGILVFPNEDLHVKDLNETIHYMYKHKMYRKMVFYIEACESGSMMNHLPDNINVYATTAANPRESSYACYYDEKRSTYLGDWYSVNWMEDSDVEDLTKETLHKQYHLVKSHTQTSHVMQYGNKTISTMKVMQFQGMKRKASSPVPLPPVTHLD
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.2087
R free: 0.2307
Average B factor: 24.407
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 277
Crystal growth procedure: 25 % PEG 4000, 
100 mM MES pH 6.5, 
200 mM potassium iodide, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Matthews coefficient: 2.4
Solvent content (%): 48.85
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: 2015-02-11
Crystal Structure of human cyclic GMP-AMP synthase in complex with 6-(2-chloro-5-fluoro-4-methylphenyl)-1H-benzimidazole-4-carboxylic acid (PDB entry 7FTQ)
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): 2.08
R work: 0.213
R free: 0.253
Average B factor: 72.73
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: 2.12
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: 2024-02-21
Cdk2(WT) covalent adduct with D28 at C177 (PDB entry 5OO0)
Macromolecule: Cyclin-dependent kinase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.22
Sequence length: 303 residues
Sequence: GPLGSMENFQKVEKIGEGTYGVVYKARNKLTGEVVALKKIRLDTETEGVPSTAIREISLLKELNHPNIVKLLDVIHTENKLYLVFEFLHQDLKKFMDASALTGIPLPLIKSYLFQLLQGLAFCHSHRVLHRDLKPQNLLINTEGAIKLADFGLARAFGVPVRTYTHEVVTLWYRAPEILLGCKYYSTAVDIWSLGCIFAEMVTRRALFPGDSEIDQLFRIFRTLGTPDEVVWPGVTSMPDYKPSFPKWARQDFSKVVPPLDEDGRSLLSQMLHYDPNKRISAKAALAHPFFQDVTKPVPHLRL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.6
R work: 0.17158
R free: 0.20035
Average B factor: 22.29
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 294
Crystal growth procedure: 15% w/v Jeffamine ED-2003, 50 mM HEPES, 50 mM sodium/potassium phosphate
Matthews coefficient: 1.99
Solvent content (%): 38.3
Ligand: methyl 4-propanoyl-2,3-dihydroquinoxaline-1-carboxylate (9YZ)
Ligand formula: C13 H16 N2 O3
Ligand molecular weight: 248.278
Ligand SMILES: CCC(=O)N1CCN(c2c1cccc2)C(=O)OC
Ligand InChI: InChI=1S/C13H16N2O3/c1-3-12(16)14-8-9-15(13(17)18-2)11-7-5-4-6-10(11)14/h4-7H,3,8-9H2,1-2H3
Release date: 2018-03-14
Crystal structure of CK2a1 H115Y with hematein (PDB entry 6L22)
Macromolecule: Casein kinase II subunit alpha
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 340 residues
Sequence: GPLGSMSGPVPSRARVYTDVNTHRPREYWDYESHVVEWGNQDDYQLVRKLGRGKYSEVFEAINITNNEKVVVKILKPVKKKKIKREIKILENLRGGPNIITLADIVKDPVSRTPALVFEYVNNTDFKQLYQTLTDYDIRFYMYEILKALDYCHSMGIMHRDVKPHNVMIDHEHRKLRLIDWGLAEFYHPGQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRKEPFFHGHDNYDQLVRIAKVLGTEDLYDYIDKYNIELDPRFNDILGRHSRKRWERFVHSENQHLVSPEALDFLDKLLRYDHQSRLTAREAMEHPYFYTVVKDQARMG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.12318084151
R work: 0.180247346967
R free: 0.242924126409
Average B factor: 23.5842533527
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 25% Ethylene Glycol
Matthews coefficient: 1.95
Solvent content (%): 36.9
Ligand: (6aR)-3,4,6a,10-tetrakis(oxidanyl)-6,7-dihydroindeno[2,1-c]chromen-9-one (E3U)
Ligand formula: C16 H12 O6
Ligand molecular weight: 300.263
Ligand SMILES: c1cc(c(c2c1C3=C4C=C(C(=O)C=C4CC3(CO2)O)O)O)O
Ligand InChI: InChI=1S/C16H12O6/c17-10-2-1-8-13-9-4-12(19)11(18)3-7(9)5-16(13,21)6-22-15(8)14(10)20/h1-4,17,19-21H,5-6H2/t16-/m0/s1
Release date: 2020-02-26
Crystal Structure of EGFR-T790M/C797S in Complex with WZ4002 (PDB entry 7ZYN)
Macromolecule: Epidermal growth factor receptor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 333 residues
Sequence: GSHMASGEAPNQALLRILKETEFKKIKVLGSGAFGTVYKGLWIPEGEKVKIPVAIKELREATSPKANKEILDEAYVMASVDNPHVCRLLGICLTSTVQLIMQLMPFGSLLDYVREHKDNIGSQYLLNWCVQIAKGMNYLEDRRLVHRDLAARNVLVKTPQHVKITDFGLAKLLGAAAAEYHAEGGKVPIKWMALESILHRIYTHQSDVWSYGVTVWELMTFGSKPYDGIPASEISSILEKGERLPQPPICTIDVYMIMVKCWMIDADSRPKFRELIIEFSKMARDPQRYLVIQGDERMHLPSPTDSNFYRALMDEEDMDDVVDADEYLIPQQG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.3
R work: 0.1913
R free: 0.2232
Average B factor: 67.02
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 1.5 K-Na-tartrate, 100 mM Na-MES (pH 6.0),
3.9 mg/mL EGFR-WT (in 100 mM NaCl, 25 mM Tris-HCl, 10 % glycerol, 1 mM TCEP) pH 8.0) 1 ul reservoir + 1 ul solution
Matthews coefficient: 3.34
Solvent content (%): 63.18
Ligand: N-{3-[(5-chloro-2-{[2-methoxy-4-(4-methylpiperazin-1-yl)phenyl]amino}pyrimidin-4-yl)oxy]phenyl}prop-2-enamide (0UN)
Ligand formula: C25 H27 Cl N6 O3
Ligand molecular weight: 494.973
Ligand SMILES: CN1CCN(CC1)c2ccc(c(c2)OC)Nc3ncc(c(n3)Oc4cccc(c4)NC(=O)C=C)Cl
Ligand InChI: InChI=1S/C25H27ClN6O3/c1-4-23(33)28-17-6-5-7-19(14-17)35-24-20(26)16-27-25(30-24)29-21-9-8-18(15-22(21)34-3)32-12-10-31(2)11-13-32/h4-9,14-16H,1,10-13H2,2-3H3,(H,28,33)(H,27,29,30)
Release date: 2023-05-03
Crystal structure of human katanin AAA ATPase domain complex with ATPgammaS (PDB entry 5ZQM)
Macromolecule: Katanin p60 ATPase-containing subunit A1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.4.3
Sequence length: 309 residues
Sequence: AADSTGYDKDLVEALERDIISQNPNVRWDDIADLVEAKKLLKEAVVLPMWMPEFFKGIRRPWKGVLMVGPPGTGKTLLAKAVATECKTTFFNVSSSTLTSKYRGESEKLVRLLFEMARFYSPATIFIDEIDSICSRRGTSEEHEASRRVKAELLVQMDGVGGTSENDDPSKMVMVLAATNFPWDIDEALRRRLEKRIYIPLPSAKGREELLRISLRELELADDVDLASIAENMEGYSGADITNVCRDASLMAMRRRIEGLTPEEIRNLSKEEMHMPTTMEDFEMALKKVSKSVSAADIERYEKWIFEFG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.9
R work: 0.24735
R free: 0.28514
Average B factor: 74.619
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 298
Crystal growth procedure: 0.4 M Calcium acetate 
20% (v/v) PEG 3,350
Matthews coefficient: 2.88
Solvent content (%): 57.35
Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER (AGS)
Ligand formula: C10 H16 N5 O12 P3 S
Ligand molecular weight: 523.247
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=S)(O)O)O)O)N
Ligand InChI: InChI=1S/C10H16N5O12P3S/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(25-10)1-24-28(18,19)26-29(20,21)27-30(22,23)31/h2-4,6-7,10,16-17H,1H2,(H,18,19)(H,20,21)(H2,11,12,13)(H2,22,23,31)/t4-,6-,7-,10-/m1/s1
Release date: 2019-02-27
JAK2 JH1 in complex with SY5-103 (PDB entry 6VNM)
Macromolecule: Tyrosine-protein kinase JAK2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 308 residues
Sequence: HHHHHHHHENLYFQGDPTQFEERHLKFLQQLGKGNFGSVEMCRYDPLQDNTGEVVAVKKLQHSTEEHLRDFEREIEILKSLQHDNIVKYKGVCYSAGRRNLKLIMEYLPYGSLRDYLQKHKERIDHIKLLQYTSQICKGMEYLGTKRYIHRDLATRNILVENENRVKIGDFGLTKVLPQDKEYYKVKEPGESPIFWYAPESLTESKFSVASDVWSFGVVLYELFTYIEKSKSPPAEFMRMIGNDKQGQMIVFHLIELLKNNGRLPRPDGCPDEIYMIMTECWNNNVNQRPSFRDLALRVDQIRDNMAG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.2
R work: 0.1983
R free: 0.2385
Average B factor: 56.1698
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 291
Crystal growth procedure: 0.1 M Bis-Tris pH 5.5, 0.2 M NaCl, 25% PEG 3350
Matthews coefficient: 3.08
Solvent content (%): 60.11
Ligand: 4-[1-(but-3-en-1-yl)-1H-pyrazol-4-yl]-N-[4-(piperidin-4-yl)phenyl]-7H-pyrrolo[2,3-d]pyrimidin-2-amine (R5Y)
Ligand formula: C24 H27 N7
Ligand molecular weight: 413.518
Ligand SMILES: C=CCCn1cc(cn1)c2c3cc[nH]c3nc(n2)Nc4ccc(cc4)C5CCNCC5
Ligand InChI: InChI=1S/C24H27N7/c1-2-3-14-31-16-19(15-27-31)22-21-10-13-26-23(21)30-24(29-22)28-20-6-4-17(5-7-20)18-8-11-25-12-9-18/h2,4-7,10,13,15-16,18,25H,1,3,8-9,11-12,14H2,(H2,26,28,29,30)
Release date: 2021-02-17
ULK1 Unc-51 like autophagy activating kinase in complex with inhibitor BTC (PDB entry 6MNH)
Macromolecule: Serine/threonine-protein kinase ULK1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 287 residues
Sequence: SLGGTETVGKFEFSRKDLIGHGAFAVVFKGRHREKHDLEVAVKCINKKNLAKSQTLLGKEIKILKELKHENIVALYDFQEMANSVYLVMEYCNGGDLADYLHAMRTLSEDTIRLFLQQIAGAMRLLHSKGIIHRDLKPQNILLSNPAGRRANPNSIRVKIADFGFARYLQSNMMAATLCGSPMYMAPEVIMAQHYDGKADLWSIGTIVYQCLTGKAPFQAASPQDLRLFYEKNKTLVPTIPRETSAPLRQLLLALLQRNHKDRMDFDEFFHHPFLDASPSVRKSPPV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.73
R work: 0.1883
R free: 0.2278
Average B factor: 22.273
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 281
Crystal growth procedure: 31% PEG 4K, 200mM calcium chloride, 100mM bis tris propane pH 8.5
Matthews coefficient: 2.04
Solvent content (%): 39.78
Ligand: N-[(2R)-3-methylbutan-2-yl]-1H-benzotriazole-6-carboxamide (JVD)
Ligand formula: C12 H16 N4 O
Ligand molecular weight: 232.282
Ligand SMILES: CC(C)C(C)NC(=O)c1ccc2c(c1)[nH]nn2
Ligand InChI: InChI=1S/C12H16N4O/c1-7(2)8(3)13-12(17)9-4-5-10-11(6-9)15-16-14-10/h4-8H,1-3H3,(H,13,17)(H,14,15,16)/t8-/m1/s1
Release date: 2019-03-27
Human soluble adenylyl cyclase in complex with the inhibitor TDI10229 (PDB entry 7OVD)
Macromolecule: Adenylate cyclase type 10
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.6.1.1
Sequence length: 475 residues
Sequence: MNTPKEEFQDWPIVRIAAHLPDLIVYGHFSPERPFMDYFDGVLMFVDISGFTAMTEKFSSAMYMDRGAEQLVEILNYHISAIVEKVLIFGGDILKFAGDALLALWRVERKQLKNIITVVIKCSLEIHGLFETQEWEEGLDIRVKIGLAAGHISMLVFGDETHSHFLVIGQAVDDVRLAQNMAQMNDVILSPNCWQLCDRSMIEIESVPDQRAVKVNFLKPPPNFNFDEFFTKCTTFMHYYPSGEHKNLLRLACTLKPDPELEMSLQKYVMESILKQIDNKQLQGYLSELRPVTIVFVNLMFEDQDKAEEIGPAIQDAYMHITSVLKIFQGQINKVFMFDKGCSFLCVFGFPGEKVPDELTHALECAMDIFDFCSQVHKIQTVSIGVASGIVFCGIVGHTVRHEYTVIGQKVNLAARMMMYYPGIVTCDSVTYNGSNLPAYFFKELPKKVMKGVADSGPLYQYWGRTEKVHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.2
R work: 0.1991
R free: 0.2429
Average B factor: 63.23
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 277
Crystal growth procedure: 0.2 M tripotassium citrate, 20%(w/v) PEG 3350
Matthews coefficient: 2.61
Solvent content (%): 52.79
Ligand: 4-chloranyl-6-[1,5-dimethyl-4-(phenylmethyl)pyrazol-3-yl]pyrimidin-2-amine (1S2)
Ligand formula: C16 H16 Cl N5
Ligand molecular weight: 313.785
Ligand SMILES: Cc1c(c(nn1C)c2cc(nc(n2)N)Cl)Cc3ccccc3
Ligand InChI: InChI=1S/C16H16ClN5/c1-10-12(8-11-6-4-3-5-7-11)15(21-22(10)2)13-9-14(17)20-16(18)19-13/h3-7,9H,8H2,1-2H3,(H2,18,19,20)
Release date: 2021-10-06
Crystal structure of the pre-catalytic ternary extension complex of DNA polymerase lambda with an 8-oxo-dG:dA base-pair (PDB entry 5IIM)
Macromolecule: DNA polymerase lambda
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 334 residues
Sequence: AQPSSQKATNHNLHITEKLEVLAKAYSVQGDKWRALGYAKAINALKSFHKPVTSYQEACSIPGIGKRMAEKIIEILESGHLRKLDHISESVPVLELFSNIWGAGTKTAQMWYQQGFRSLEDIRSQASLTTQQAIGLKHYSDFLERMPREEATEIEQTVQKAAQAFNSGLLCVACGSYRRGKATCGDVDVLITHPDGRSHRGIFSRLLDSLRQEGFLTDDLVSQEENGQQQKYLGVCRLPGPGRRHRRLDIIVVPYSEFACALLYFTGSAHFNRSMRALAKTKGMSLSEHALSTAVVRNTHGCKVGPGRVLPTPTEKDVFRLLGLPYREPAERDW
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.941
R work: 0.1834
R free: 0.2159
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 278
Crystal growth procedure: 0.2 M ammonium acetate, 0.1 M sodium citrate pH 4.8, and 3-5% PEG 4000
Matthews coefficient: 2.94
Solvent content (%): 58.11
Ligand: 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE (DUP)
Ligand formula: C9 H16 N3 O13 P3
Ligand molecular weight: 467.157
Ligand SMILES: C1C(C(OC1N2C=CC(=O)NC2=O)COP(=O)(NP(=O)(O)OP(=O)(O)O)O)O
Ligand InChI: InChI=1S/C9H16N3O13P3/c13-5-3-8(12-2-1-7(14)10-9(12)15)24-6(5)4-23-26(16,17)11-27(18,19)25-28(20,21)22/h1-2,5-6,8,13H,3-4H2,(H,10,14,15)(H2,20,21,22)(H3,11,16,17,18,19)/t5-,6+,8+/m0/s1
Release date: 2016-09-07
Crystal structure of human MTH1 in complex with compound MI1016 (PDB entry 6JVM)
Macromolecule: 7,8-dihydro-8-oxoguanine triphosphatase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.1.55
Sequence length: 156 residues
Sequence: MGASRLYTLVLVLQPQRVLLGMKKRGFGAGRWNGFGGKVQEGETIEDGARRELQEESGLTVDALHKVGQIVFEFVGEPELMDVHVFCTDSIQGTPVESDEMRPCWFQLDQIPFKDMWPDDSYWFPLLLQKKKFHGYFKFQGQDTILDYTLREVDTV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.098
R work: 0.1963
R free: 0.2569
Average B factor: 30.4818
Crystallization method: EVAPORATION
Crystallization pH: 3.75
Crystallization temperature (K): 298
Crystal growth procedure: 30% PEG 6000, 200 mM Lithium sulphate, 100 mM Sodium acetate pH 3.75
Matthews coefficient: 2.28
Solvent content (%): 45.94
Ligand: N4-cyclopropyl-5-ethyl-6-piperidin-1-yl-pyrimidine-2,4-diamine (CGX)
Ligand formula: C14 H23 N5
Ligand molecular weight: 261.366
Ligand SMILES: CCc1c(nc(nc1N2CCCCC2)N)NC3CC3
Ligand InChI: InChI=1S/C14H23N5/c1-2-11-12(16-10-6-7-10)17-14(15)18-13(11)19-8-4-3-5-9-19/h10H,2-9H2,1H3,(H3,15,16,17,18)
Release date: 2020-10-28
CRYSTAL STRUCTURE OF HUMAN WEE1 KINASE DOMAIN IN COMPLEX WITH RAC-IV-098, a MK1775 analogue (PDB entry 5VD7)
Macromolecule: Wee1-like protein kinase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 289 residues
Sequence: GAGSMKSRYTTEFHELEKIGSGEFGSVFKCVKRLDGCIYAIKRSKKPLAGSVDEQNALREVYAHAVLGQHSHVVRYFSAWAEDDHMLIQNEYCNGGSLADAISENYRIMSYFKEAELKDLLLQVGRGLRYIHSMSLVHMDIKPSNIFISRTSIPNAASEEGDEDDWASNKVMFKIGDLGHVTRISSPQVEEGDSRFLANEVLQENYTHLPKADIFALALTVVCAAGAEPLPRNGDQWHEIRQGRLPRIPQVLSQEFTELLKVMIHPDPERRPSAMALVKHSVLLSASRK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.08
R work: 0.2072
R free: 0.2479
Average B factor: 50.4459
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.9
Crystallization temperature (K): 291
Crystal growth procedure: 5.0 MG/ML WEE1, 25 mM Na/K phosphate, 1 mM DTT, 0.05 M ammonium sulfate, 0.05 M Bis-tris (pH 5.5), 7.5 % PEG 3350, 1 mM RAC-IV-098
Matthews coefficient: 2.18
Solvent content (%): 43.54
Ligand: 6-{[3-fluoro-4-(4-methylpiperazin-1-yl)phenyl]amino}-1-[6-(2-hydroxypropan-2-yl)pyridin-2-yl]-2-(prop-2-en-1-yl)-1,2-dihydro-3H-pyrazolo[3,4-d]pyrimidin-3-one (99V)
Ligand formula: C27 H31 F N8 O2
Ligand molecular weight: 518.586
Ligand SMILES: CC(C)(c1cccc(n1)N2c3c(cnc(n3)Nc4ccc(c(c4)F)N5CCN(CC5)C)C(=O)N2CC=C)O
Ligand InChI: InChI=1S/C27H31FN8O2/c1-5-11-35-25(37)19-17-29-26(32-24(19)36(35)23-8-6-7-22(31-23)27(2,3)38)30-18-9-10-21(20(28)16-18)34-14-12-33(4)13-15-34/h5-10,16-17,38H,1,11-15H2,2-4H3,(H,29,30,32)
Release date: 2018-04-04
Crystal structure of CDK4 in complex with CyclinD1 and P27 (PDB entry 6P8G)
Macromolecule: G1/S-specific cyclin-D1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 249 residues
Sequence: DANLLNDRVLRAMLKAEETCAPSVSYFKCVQKEVLPSMRKIVATWMLEVCEEQKCEEEVFPLAMNYLDRFLSLEPVKKSRLQLLGATCMFVASKMKETIPLTAEKLCIYTDNSIRPEELLQMELLLVNKLKWNLAAMTPHDFIEHFLSKMPEAEENKQIIRKHAQTFVALCATDVKFISNPPSMVAAGSVVAAVQGLNLRSPNNFLSYYRLTRFLSRVIKCDPDCLRACQEQIEALLESSLRQAQQNMD
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.8
R work: 0.2213
R free: 0.2747
Crystallization method: MICROBATCH
Crystallization temperature (K): 295
Crystal growth procedure: 100mM Tris (7.0)
200mM MgCl2
10% PEG 8000
Matthews coefficient: 2.72
Solvent content (%): 54.71
Release date: 2019-12-25
Fragment-based screening of HSP70 sheds light on the functional role of ATP-binding site residues (PDB entry 5AQJ)
Macromolecule: HEAT SHOCK COGNATE 71 KDA PROTEIN
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.3.51
Sequence length: 386 residues
Sequence: GPLGSMSKGPAVGIDLGTTYSCVGVFQHGKVEIIANDQGNRTTPSYVAFTDTERLIGDAAKNQVAMNPTNTVFDAKRLIGRRFDDAVVQSDMKHWPFMVVNDAGRPKVQVEYKGETKSFYPEEVSSMVLTKMKEIAEAYLGKTVTNAVVTVPAYFNDSQRQATKDAGTIAGLNVLRIINEPTAAAIAYGLDKKVGAERNVLIFDLGGGTFDVSILTIEDGIFEVKSTAGDTHLGGEDFDNRMVNHFIAEFKRKHKKDISENKRAVRRLRTACERAKRTLSSSTQASIEIDSLYEGIDFYTSITRARFEELNADLFRGTLDPVEKALRDAKLDKSQIHDIVLVGGSTRIPKIQKLLQDFFNGKELNKSINPDEAVAYGAAVQAAILS
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.96
R work: 0.1903
R free: 0.2212
Average B factor: 55.11
Crystallization pH: 8.5
Crystal growth procedure: 16-26% (W/V) PEG3350, 0.1 M K-NA TARTRATE, 0.1 M TRIS.HCL PH 8.5 AND 25% (V/V) GLYCEROL
Matthews coefficient: 2.46
Solvent content (%): 49.96
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: 2016-10-05