satarupa22/MacromolecularLigandDB huggingface dataset:
MerTK kinase domain with type 1.5 inhibitor containing a di-methyl pyrazole group (PDB entry 7OLS)
Macromolecule: Tyrosine-protein kinase Mer
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 298 residues
Sequence: GSHMEELQNKLEDVVIDRNLLILGRILGEGEFGSVMEGNLKQEDGTSLKVAVKTMKLDNSSQREIEEFLSEAACMKDFSHPNVIRLLGVCIEMSSQGIPKPMVILPFMKYGDLHTYLLYSRLETGPRHIPLQTLLRFMVDIALGMEYLSNRNFLHRDLAARNCMLRDDMTVCVADFGLSKKIYSGDYYRQGRIAKMPVKWIAIESLADRVYTSKSDVWAFGVTMWEIATRGMTPYPGVQNHEMYDYLLHGHRLKQPEDCLDELYEIMYSCWRTDPLDRPTFSVLRLQLERLLESLPDV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.89
R work: 0.2187
R free: 0.2819
Average B factor: 47.483
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M Tris pH 8.5, 4.3 M NaCl
Matthews coefficient: 2.27
Solvent content (%): 45.9
Ligand: 5-[4-(1,5-dimethylpyrazol-4-yl)-2-methyl-phenyl]-~{N}-(imidazo[1,2-a]pyridin-6-ylmethyl)-~{N}-methyl-1,3,4-oxadiazol-2-amine (VJZ)
Ligand formula: C23 H23 N7 O
Ligand molecular weight: 413.475
Ligand SMILES: Cc1cc(ccc1c2nnc(o2)N(C)Cc3ccc4nccn4c3)c5cnn(c5C)C
Ligand InChI: InChI=1S/C23H23N7O/c1-15-11-18(20-12-25-29(4)16(20)2)6-7-19(15)22-26-27-23(31-22)28(3)13-17-5-8-21-24-9-10-30(21)14-17/h5-12,14H,13H2,1-4H3
Release date: 2021-09-15
Crystal structure of the alpha gamma mutant (gamma-K151A) of human IDH3 in complex with Mg(2+), citrate and ADP (PDB entry 5GRF)
Macromolecule: Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.1.1.41
Sequence length: 339 residues
Sequence: TGGVQTVTLIPGDGIGPEISAAVMKIFDAAKAPIQWEERNVTAIQGPGGKWMIPSEAKESMDKNKMGLKGPLKTPIAAGHPSMNLLLRKTFDLYANVRPCVSIEGYKTPYTDVNIVTIRENTEGEYSGIEHVIVDGVVQSIKLITEGASKRIAEFAFEYARNNHRSNVTAVHKANIMRMSDGLFLQKCREVAESCKDIKFNEMYLDTVCLNMVQDPSQFDVLVMPNLYGDILSDLCAGLIGGLGVTPSGNIGANGVAIFESVHGTAPDIAGKDMANPTALLLSAVMMLRHMGLFDHAARIEAACFATIKDGKSLTKDLGGNAKCSDFTEEICRRVKDLD
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.5
R work: 0.2069
R free: 0.2475
Average B factor: 68.322
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8
Crystallization temperature (K): 293
Crystal growth procedure: 0.2 M sodium citrate, pH 8.0, 20% (w/v) PEG 3350
Matthews coefficient: 3.6
Solvent content (%): 65.8
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: 2017-02-15
Complex structure of CDK2/Cyclin E1 and a potent, selective macrocyclic inhibitor (PDB entry 8H6P)
Macromolecule: Cyclin-dependent kinase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.22
Sequence length: 298 residues
Sequence: PMENFQKVEKIGEGTYGVVYKARNKLTGEVVALKKIRLDTETEGVPSTAIREISLLKELNHPNIVKLLDVIHTENKLYLVFEFLHQDLKKFMDASALTGIPLPLIKSYLFQLLQGLAFCHSHRVLHRDLKPQNLLINTEGAIKLADFGLARAFGVPVRTYTHEVVTLWYRAPEILLGCKYYSTAVDIWSLGCIFAEMVTRRALFPGDSEIDQLFRIFRTLGTPDEVVWPGVTSMPDYKPSFPKWARQDFSKVVPPLDEDGRSLLSQMLHYDPNKRISAKAALAHPFFQDVTKPVPHLR
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.44
R work: 0.2211
R free: 0.2924
Average B factor: 78.41
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 291.15
Crystal growth procedure: 0.2 M sodium citrate pH 6.5, 10% PEG3350
Matthews coefficient: 3
Solvent content (%): 59.09
Ligand: (7S,10R)-11-oxa-2,4,5,13,17,23-hexaazatetracyclo[17.3.1.1~3,6~.1~7,10~]pentacosa-1(23),3(25),5,19,21-pentaene-12,18-dione (WZU)
Ligand formula: C18 H22 N6 O3
Ligand molecular weight: 370.406
Ligand SMILES: c1cc2nc(c1)Nc3cc([nH]n3)C4CCC(C4)OC(=O)NCCCNC2=O
Ligand InChI: InChI=1S/C18H22N6O3/c25-17-13-3-1-4-15(21-13)22-16-10-14(23-24-16)11-5-6-12(9-11)27-18(26)20-8-2-7-19-17/h1,3-4,10-12H,2,5-9H2,(H,19,25)(H,20,26)(H2,21,22,23,24)/t11-,12+/m0/s1
Release date: 2023-02-22
Apo Human Calcium/Calmodulin-dependent kinase type 1D (PDB entry 6QP5)
Macromolecule: Calcium/calmodulin-dependent protein kinase type 1D
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.17
Sequence length: 322 residues
Sequence: SMSSWKKQAEDIKKIFEFKETLGTGAFSEVVLAEEKATGKLFAVKCIPKKALKGKESSIENEIAVLRKIKHENIVALEDIYESPNHLYLVMQLVSGGELFDRIVEKGFYTEKDASTLIRQVLDAVYYLHRMGIVHRDLKPENLLYYSQDEESKIMISDFGLSKMEGKGDVMSTACGTPGYVAPEVLAQKPYSKAVDCWSIGVIAYILLCGYPPFYDENDSKLFEQILKAEYEFDSPYWDDISDSAKDFIRNLMEKDPNKRYTCEQAARHPWIAGDTALNKNIHESVSAQIRKNFAKSKWRQAFNATAVVRHMRKLHLGSSLD
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.9
R work: 0.1919
R free: 0.2272
Average B factor: 35.1966
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 30% PEG4000 -- 0.2M lithium sulfate -- 0.1M tris pH 8.5
Matthews coefficient: 2.14
Solvent content (%): 42.57
Ligand: SULFATE ION (SO4)
Ligand formula: O4 S
Ligand molecular weight: 96.063
Ligand SMILES: [O-]S(=O)(=O)[O-]
Ligand InChI: InChI=1S/H2O4S/c1-5(2,3)4/h(H2,1,2,3,4)/p-2
Release date: 2020-03-04
Apo Structure of WT Lipoprotein Lipase in Complex with GPIHBP1 Mutant N78D N82D produced in GnTI-deficient HEK293-F cells (PDB entry 6OAU)
Macromolecule: Lipoprotein lipase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.1.34
Sequence length: 448 residues
Sequence: ADQRRDFIDIESKFALRTPEDTAEDTCHLIPGVAESVATCHFNHSSKTFMVIHGWTVTGMYESWVPKLVAALYKREPDSNVIVVDWLSRAQEHYPVSAGYTKLVGQDVARFINWMEEEFNYPLDNVHLLGYSLGAHAAGIAGSLTNKKVNRITGLDPAGPNFEYAEAPSRLSPDDADFVDVLHTFTRGSPGRSIGIQKPVGHVDIYPNGGTFQPGCNIGEAIRVIAERGLGDVDQLVKCSHERSIHLFIDSLLNEENPSKAYRCSSKEAFEKGLCLSCRKNRCNNLGYEINKVRAKRSSKMYLKTRSQMPYKVFHYQVKIHFSGTESETHTNQAFEISLYGTVAESENIPFTLPEVSTNKTYSFLIYTEVDIGELLMLKLKWKSDSYFSWSDWWSSPGFAIQKIRVKAGETQKKVIFCSREKVSHLQKGKAPAVFVKCHDKSLNKKSG
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.48
R work: 0.213
R free: 0.246
Average B factor: 52
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 298
Crystal growth procedure: 0.2M Sodium Malonate, 20% PEG3350, 4% 2-propanol
Matthews coefficient: 2.55
Solvent content (%): 51.77
Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose (NAG)
Ligand formula: C8 H15 N O6
Ligand molecular weight: 221.208
Ligand SMILES: CC(=O)NC1C(C(C(OC1O)CO)O)O
Ligand InChI: InChI=1S/C8H15NO6/c1-3(11)9-5-7(13)6(12)4(2-10)15-8(5)14/h4-8,10,12-14H,2H2,1H3,(H,9,11)/t4-,5-,6-,7-,8-/m1/s1
Release date: 2019-05-08
CDK8/Cyclin C in complex with N-(4-chlorobenzyl)isoquinolin-4-amine (PDB entry 6T41)
Macromolecule: Cyclin-dependent kinase 8
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.22
Sequence length: 407 residues
Sequence: DDKMDYDFKVKLSSERERVEDLFEYEGCKVGRGTYGHVYKAKRKDGKDDKDYALKQIEGTGISMSACREIALLRELKHPNVISLQKVFLSHADRKVWLLFDYAEHDLWHIIKFHRASKANKKPVQLPRGMVKSLLYQILDGIHYLHANWVLHRDLKPANILVMGEGPERGRVKIADMGFARLFNSPLKPLADLDPVVVTFWYRAPELLLGARHYTKAIDIWAIGCIFAELLTSEPIFHCRQEDIKTSNPYHHDQLDRIFNVMGFPADKDWEDIKKMPEHSTLMKDFRRNTYTNCSLIKYMEKHKVKPDSKAFHLLQKLLTMDPIKRITSEQAMQDPYFLEDPLPTSDVFAGCQIPYPKREFLTEEEPDDKGDKKNQQQQQGNNHTNGTGHPGNQDSSHTQGPPLKKV
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.45
R work: 0.1827
R free: 0.2558
Average B factor: 50.5402
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 20%(w/v) PEG-3350 and 0.2 M sodium formate
Matthews coefficient: 2.67
Solvent content (%): 53.96
Ligand: ~{N}-[(4-chlorophenyl)methyl]quinazolin-4-amine (MFE)
Ligand formula: C15 H12 Cl N3
Ligand molecular weight: 269.729
Ligand SMILES: c1ccc2c(c1)c(ncn2)NCc3ccc(cc3)Cl
Ligand InChI: InChI=1S/C15H12ClN3/c16-12-7-5-11(6-8-12)9-17-15-13-3-1-2-4-14(13)18-10-19-15/h1-8,10H,9H2,(H,17,18,19)
Release date: 2020-01-01
Crystal structure of the methylated wild-type AKR1B10 holoenzyme (PDB entry 4XZM)
Macromolecule: Aldo-keto reductase family 1 member B10
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.1.1
Sequence length: 316 residues
Sequence: MATFVELSTKAKMPIVGLGTWKSPLGKVKEAVKVAIDAGYRHIDCAYVYQNEHEVGEAIQEKIQEKAVKREDLFIVSKLWPTFFERPLVRKAFEKTLKDLKLSYLDVYLIHWPQGFKSGDDLFPKDDKGNAIGGKATFLDAWEAMEELVDEGLVKALGVSNFSHFQIEKLLNKPGLKYKPVTNQVECHPYLTQEKLIQYCHSKGITVTAYSPLGSPDRPWAKPEDPSLLEDPKIKEIAAKHKKTAAQVLIRFHIQRNVIVIPKSVTPARIVENIQVFDFKLSDEEMATILSFNRNWRACNVLQSSHLEDYPFNAEY
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.75
R work: 0.203
R free: 0.2499
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 9
Crystallization temperature (K): 293
Crystal growth procedure: 30% PEG 6000, 100 mM sodium cacodylate
Matthews coefficient: 2.49
Solvent content (%): 50.62
Ligand: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE (NAP)
Ligand formula: C21 H28 N7 O17 P3
Ligand molecular weight: 743.405
Ligand SMILES: c1cc(c[n+](c1)C2C(C(C(O2)COP(=O)([O-])OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)OP(=O)(O)O)O)O)O)C(=O)N
Ligand InChI: InChI=1S/C21H28N7O17P3/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(44-46(33,34)35)14(30)11(43-21)6-41-48(38,39)45-47(36,37)40-5-10-13(29)15(31)20(42-10)27-3-1-2-9(4-27)18(23)32/h1-4,7-8,10-11,13-16,20-21,29-31H,5-6H2,(H7-,22,23,24,25,32,33,34,35,36,37,38,39)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
Release date: 2015-11-18
Crystal structure of Zn bound human Focal Adhesion Targeting (FAT) domain of the Focal Adhesion Kinase (PDB entry 7W8I)
Macromolecule: Isoform 5 of Focal adhesion kinase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 164 residues
Sequence: SSPADSYNEGVKPWRLQPQEISPPPTANLDRSNDKVYENVTGLVKAVIEMSSKIQPAPPEEYVPMVKEVGLALRTLLATVDETIPLLPASTHREIEMAQKLLNSDLGELINKMKLAQQYVMTSLQQEYKKQMLTAAHALAVDAKNLLDVIDQARLKMLGQTRPH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.943
R work: 0.2261
R free: 0.2625
Average B factor: 52.812
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.05 M Zinc acetate dihydrate, 20% w/v Polyethylene glycol 3,350
Matthews coefficient: 1.93
Solvent content (%): 36.22
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: 2022-12-21
Allosteric activation of human prekallikrein by apple domain disc rotation (PDB entry 6I44)
Macromolecule: Plasma kallikrein
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.34
Sequence length: 627 residues
Sequence: RSHHHHHHGCLTQLYENAFFRGGDVASMYTPNAQYCQMRCTFHPRCLLFSFLPASSINDMEKRFGCFLKDSVTGTLPKVHRTGAVSGHSLKQCGHQISACHRDIYKGVDMRGVNFNVSKVSSVEECQKRCTNNIRCQFFSYATQTFHKAEYRNNCLLKYSPGGTPTAIKVLSNVESGFSLKPCALSEIGCHMNIFQHLAFSDVDVARVLTPDAFVCRTICTYHPNCLFFTFYTNVWKIESQRNVCLLKTSESGTPSSSTPQENTISGYSLLTCKRTLPEPCHSKIYPGVDFGGEELNVTFVKGVNVCQETCTKMIRCQFFTYSLLPEDCKAEACKCFLRLSMDGSPTRIAYGTQGSSGYSLRLCNTGDNSVCTTKTSTRIVGGTQSSWGEWPWQVSLQVKLTAQRHLCGGSLIGHQWVLTAAHCFDGLPLQDVWRIYSGILQLSDITKDTPFSQIKEIIIHQNYKVSEGNHDIALIKLQAPLQYTEFQKPICLPSKGDTSTIYTNCWVTGWGFSAEAGEIQNILQKVNIPLVTNEECQKRYQDYKITQRMVCAGYKEGGKDACKGDAGGPLVCKHNGMWRLVGITSWGEGCARREQPGVYTKVAEYMDWILEKTQSSDGKAQMQSPA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.36
R work: 0.16745
R free: 0.19591
Average B factor: 18.539
Crystallization method: EVAPORATION
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M carboxylic acid, 0.1M Hepes/mops pH 7.5, 12.5%MPD, 12.5%PEG1000, 12.5%PEG3350
Matthews coefficient: 2.34
Solvent content (%): 47.5
Ligand: BENZAMIDINE (BEN)
Ligand formula: C7 H8 N2
Ligand molecular weight: 120.152
Ligand SMILES: [H]N=C(c1ccccc1)N
Ligand InChI: InChI=1S/C7H8N2/c8-7(9)6-4-2-1-3-5-6/h1-5H,(H3,8,9)
Release date: 2019-03-06
INPP5D PanDDA analysis group deposition -- Crystal Structure of the phosphatase and C2 domains of SHIP1 in complex with Z2856434898 (PDB entry 5RWO)
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): 1.29
R work: 0.1815
R free: 0.2019
Average B factor: 17.569
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: 2.1
Solvent content (%): 41.47
Ligand: 1-(phenylmethyl)-4-pyrrol-1-yl-piperidine (AXG)
Ligand formula: C16 H20 N2
Ligand molecular weight: 240.343
Ligand SMILES: c1ccc(cc1)CN2CCC(CC2)n3cccc3
Ligand InChI: InChI=1S/C16H20N2/c1-2-6-15(7-3-1)14-17-12-8-16(9-13-17)18-10-4-5-11-18/h1-7,10-11,16H,8-9,12-14H2
Release date: 2020-11-11
CDK8/CyclinC in complex with drug ETP-50775 (PDB entry 6TPA)
Macromolecule: Cyclin-dependent kinase 8
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.22
Sequence length: 405 residues
Sequence: SKMDYDFKVKLSSERERVEDLFEYEGCKVGRGTYGHVYKAKRKDGKDDKDYALKQIEGTGISMSACREIALLRELKHPNVISLQKVFLSHADRKVWLLFDYAEHDLWHIIKFHRASKANKKPVQLPRGMVKSLLYQILDGIHYLHANWVLHRDLKPANILVMGEGPERGRVKIADMGFARLFNSPLKPLADLDPVVVTFWYRAPELLLGARHYTKAIDIWAIGCIFAELLTSEPIFHCRQEDIKTSNPYHHDQLDRIFNVMGFPADKDWEDIKKMPEHSTLMKDFRRNTYTNCSLIKYMEKHKVKPDSKAFHLLQKLLTMDPIKRITSEQAMQDPYFLEDPLPTSDVFAGCQIPYPKREFLTEEEPDDKGDKKNQQQQQGNNHTNGTGHPGNQDSSHTQGPPLKK
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.8
R work: 0.2257
R free: 0.2636
Average B factor: 50.7182
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 298
Crystal growth procedure: 20% PEG 3350, 200mM NaFormate, 3% Butanediol
Matthews coefficient: 3.06
Solvent content (%): 59.81
Ligand: 1-[4-chloranyl-3-(trifluoromethyl)phenyl]-3-(5-oxidanylidene-6-pyridin-4-yl-pyrido[2,3-b][1,5]benzoxazepin-9-yl)urea (NZ8)
Ligand formula: C25 H15 Cl F3 N5 O3
Ligand molecular weight: 525.867
Ligand SMILES: c1cc2c(nc1)Oc3cc(ccc3N(C2=O)c4ccncc4)NC(=O)Nc5ccc(c(c5)C(F)(F)F)Cl
Ligand InChI: InChI=1S/C25H15ClF3N5O3/c26-19-5-3-14(12-18(19)25(27,28)29)32-24(36)33-15-4-6-20-21(13-15)37-22-17(2-1-9-31-22)23(35)34(20)16-7-10-30-11-8-16/h1-13H,(H2,32,33,36)
Release date: 2020-11-18
PanDDA analysis group deposition -- Crystal Structure of human NUDT22 in complex with N13920a (PDB entry 5R5Q)
Macromolecule: Uridine diphosphate glucose pyrophosphatase NUDT22
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.1.45
Sequence length: 304 residues
Sequence: SMDPEVTLLLQCPGGGLPQEQIQAELSPAHDRRPLPGGDEAITAIWETRLKAQPWLFDAPKFRLHSATLAPIGSRGPQLLLRLGLTSYRDFLGTNWSSSAAWLRQQGATDWGDTQAYLADPLGVGAALATADDFLVFLRRSRQVAEAPGLVDVPGGHPEPQALCPGGSPQHQDLAGQLVVHELFSSVLQEICDEVNLPLLTLSQPLLLGIARNETSAGRASAEFYVQCSLTSEQVRKHYLSGGPEAHESTGIFFVETQNVRRLPETEMWAELCPSAKGAIILYNRVQGSPTGAALGSPALLPPL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.71
R work: 0.1825
R free: 0.2221
Average B factor: 26.433
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.1M HEPES pH 7.5, 0.3M sodium/potassium phosphate, 15% PEG Smear High, 20% ethylene glycol
Matthews coefficient: 2.02
Solvent content (%): 39.15
Ligand: 4-chloranyl-~{N}-methyl-pyridine-2-carboxamide (7MU)
Ligand formula: C7 H7 Cl N2 O
Ligand molecular weight: 170.596
Ligand SMILES: CNC(=O)c1cc(ccn1)Cl
Ligand InChI: InChI=1S/C7H7ClN2O/c1-9-7(11)6-4-5(8)2-3-10-6/h2-4H,1H3,(H,9,11)
Release date: 2020-07-01
HUMANISED MONOMERIC RADA IN COMPLEX WITH FHAA TETRAPEPTIDE (PDB entry 5FOX)
Macromolecule: DNA REPAIR AND RECOMBINATION PROTEIN RADA
Type: Protein, polypeptide(L)
Source organism: Pyrococcus furiosus
EC number: 3.6.4
Sequence length: 231 residues
Sequence: MATIGRISTGSKSLDKLLGGGIETQAITEVFGEFGSGKTQLAHTLAVMVQLPPEEGGLNGSVMWIDTENTFRPERIREIAQNRGLDPDEVLKHIAYARAFNSNHQMLLVQQAEDMIKELLNTDRPVKLLIVDSLTSHFRSEYIGRGALAERQQKLAKHLADLHRLANLYDIAVFVTNQVQANGGHILAHSATLRVYLRKGKGGKRIARLIDAPHLPEGEAVFSITEKGIED
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.3
R work: 0.1566
R free: 0.1819
Average B factor: 15.72
Crystallization pH: 6
Crystal growth procedure: 8% PEG-1000, 100 MM NAK PHOSPHATE, PH 6.2
Matthews coefficient: 2.18
Solvent content (%): 44
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: 2016-03-30
INPP5D PanDDA analysis group deposition -- Crystal Structure of the phosphatase and C2 domains of SHIP1 in complex with Z1722836661 (PDB entry 5RXJ)
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): 1.52
R work: 0.1713
R free: 0.1957
Average B factor: 17.598
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: 2.08
Solvent content (%): 40.92
Ligand: 2-(1H-imidazol-1-yl)ethyl dimethylcarbamate (WK4)
Ligand formula: C8 H13 N3 O2
Ligand molecular weight: 183.208
Ligand SMILES: CN(C)C(=O)OCCn1ccnc1
Ligand InChI: InChI=1S/C8H13N3O2/c1-10(2)8(12)13-6-5-11-4-3-9-7-11/h3-4,7H,5-6H2,1-2H3
Release date: 2020-11-11
EGFR kinase in complex with poziotinib (PDB entry 8F1Y)
Macromolecule: Epidermal growth factor receptor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 331 residues
Sequence: GSTSGEAPNQALLRILKETEFKKIKVLGSGAFGTVYKGLWIPEGEKVKIPVAIKELREATSPKANKEILDEAYVMASVDNPHVCRLLGICLTSTVQLITQLMPFGCLLDYVREHKDNIGSQYLLNWCVQIAKGMNYLEDRRLVHRDLAARNVLVKTPQHVKITDFGLAKLLGAEEKEYHAEGGKVPIKWMALESILHRIYTHQSDVWSYGVTVWELMTFGSKPYDGIPASEISSILEKGERLPQPPICTIDVYMIMVKCWMIDADSRPKFRELIIEFSKMARDPQRYLVIQGDERMHLPSPTDSNFYRALMDEEDMDDVVDADEYLIPQQG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.75
R work: 0.2049
R free: 0.2282
Average B factor: 75.6135
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M MES pH=6.5, 1.1 M Sodium Citrate
Matthews coefficient: 3.42
Solvent content (%): 63.98
Ligand: 1-[4-[4-[[3,4-bis(chloranyl)-2-fluoranyl-phenyl]amino]-7-methoxy-quinazolin-6-yl]oxypiperidin-1-yl]propan-1-one (R2E)
Ligand formula: C23 H23 Cl2 F N4 O3
Ligand molecular weight: 493.358
Ligand SMILES: CCC(=O)N1CCC(CC1)Oc2cc3c(cc2OC)ncnc3Nc4ccc(c(c4F)Cl)Cl
Ligand InChI: InChI=1S/C23H23Cl2FN4O3/c1-3-20(31)30-8-6-13(7-9-30)33-19-10-14-17(11-18(19)32-2)27-12-28-23(14)29-16-5-4-15(24)21(25)22(16)26/h4-5,10-13H,3,6-9H2,1-2H3,(H,27,28,29)
Release date: 2023-11-08
Crystal structure of human BACE-1 bound to Compound 24B (PDB entry 4WY1)
Macromolecule: Beta-secretase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.23.46
Sequence length: 404 residues
Sequence: GSFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHPFLHRYYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTVRANIAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTHVPNLFSLQLCGAGFPLNQSEVLASVGGSMIIGGIDHSLYTGSLWYTPIRREWYYEVIIVRVEINGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVKSIKAASSTEKFPDGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRITILPQQYLRPVEDVATSQDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSACHVHDEFRTAAVEGPFVTLDMEDCGYNIPQTDESRSHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.98
R work: 0.1672
R free: 0.2199
Average B factor: 35.93
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 298
Crystal growth procedure: 30% PEG 200;0.1 M sodium acetate, pH 5.2-5.4; protein buffer is NaBorate, pH 8.5
Matthews coefficient: 2.16
Solvent content (%): 43.1
Ligand: (4aR,8aS)-8a-(2,4-difluorophenyl)-4,4a,5,6,8,8a-hexahydropyrano[3,4-d][1,3]thiazin-2-amine (3VO)
Ligand formula: C13 H14 F2 N2 O S
Ligand molecular weight: 284.325
Ligand SMILES: c1cc(c(cc1F)F)C23COCCC2CSC(=N3)N
Ligand InChI: InChI=1S/C13H14F2N2OS/c14-9-1-2-10(11(15)5-9)13-7-18-4-3-8(13)6-19-12(16)17-13/h1-2,5,8H,3-4,6-7H2,(H2,16,17)/t8-,13-/m0/s1
Release date: 2015-03-04
TPX2 residues 7-20 fused to Aurora A residues 116-389 in complex with AMP-PNP (PDB entry 6VPG)
Macromolecule: TPX2 fragment - Aurora A kinase domain fusion
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 292 residues
Sequence: GAHMSYSYDAPSDFINFSSKQKNEESKKRQWALEDFEIGRPLGKGKFGNVYLAREKQSKFILALKVLFKAQLEKAGVEHQLRREVEIQSHLRHPNILRLYGYFHDATRVYLILEYAPLGTVYRELQKLSKFDEQRTATYITELANALSYCHSKRVIHRDIKPENLLLGSAGELKIADFGWSVHAPSSRRTTLCGTLDYLPPEMIEGRMHDEKVDLWSLGVLCYEFLVGKPPFEANTYQETYKRISRVEFTFPDFVTEGARDLISRLLKHNPSQRPMLREVLEHPWITANSSK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.64
R work: 0.1991
R free: 0.2453
Crystallization method: EVAPORATION
Crystallization pH: 7
Crystallization temperature (K): 298
Crystal growth procedure: 0.1 M HEPES pH 7, 0.9 M KCl, 1.08 M ammonium sulfate, 12% glycerol
Matthews coefficient: 2.93
Solvent content (%): 58.08
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: 2020-08-05