satarupa22/MacromolecularLigandDB huggingface dataset:
Co-crystal structure of KRIT1 with a 1-hydroxy 2-naphthaldehyde derivative (6-(furan-2-yl)-2-hydroxy-1-naphthaldehyde) (PDB entry 8T7V)
Macromolecule: Ras-related protein Rap-1b
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.5.2
Sequence length: 167 residues
Sequence: MREYKLVVLGSGGVGKSALTVQFVQGIFVEKYDPTIEDSYRKQVEVDAQQCMLEILDTAGTEQFTAMRDLYMKNGQGFALVYSITAQSTFNDLQDLREQILRVKDTDDVPMILVGNKCDLEDERVVGKEQGQNLARQWNNCAFLESSAKSKINVNEIFYDLVRQINR
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.25
R work: 0.2021
R free: 0.2502
Average B factor: 50.75
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 293
Crystal growth procedure: 20% PEG 3350, 100mM Tris, pH 8.5, 100mM KCl
Matthews coefficient: 2.34
Solvent content (%): 47.41
Ligand: (7M)-7-(furan-2-yl)-2-hydroxynaphthalene-1-carbaldehyde (ZTA)
Ligand formula: C15 H10 O3
Ligand molecular weight: 238.238
Ligand SMILES: c1cc(oc1)c2ccc3ccc(c(c3c2)C=O)O
Ligand InChI: InChI=1S/C15H10O3/c16-9-13-12-8-11(15-2-1-7-18-15)4-3-10(12)5-6-14(13)17/h1-9,17H
Release date: 2023-12-06
Compound 18 (PDB entry 5ENK)
Macromolecule: Beta-secretase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.23.46
Sequence length: 455 residues
Sequence: MASMTGGQQMGRGSAGVLPAHGTQHGIRLPLRSGLGGAPLGLRLPRETDEEPEEPGRRGSFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHPFLHRYYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTVRANIAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTHVPNLFSLQLCGAGFPLNQSEVLASVGGSMIIGGIDHSLYTGSLWYTPIRREWYYEVIIVRVEINGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVKSIKAASSTEKFPDGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRITILPQQYLRPVEDVATSQDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSACHVHDEFRTAAVEGPFVTLDMEDCGYNIPQTDEST
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.11
R work: 0.23257
R free: 0.25365
Average B factor: 27.315
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 295
Crystal growth procedure: 10% PEG MME 5K, 9% PEG 8K, 0.2 M NH4I, 0.2 M Na-citrate pH 6.4
Matthews coefficient: 2.55
Solvent content (%): 51.82
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: 2016-07-06
Crystal Structure of an Asymmetric Dimer of FGF Receptor 3 Kinases Trapped in A-loop Tyrosine Transphosphorylation Reaction (PDB entry 6PNX)
Macromolecule: Fibroblast growth factor receptor 3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 324 residues
Sequence: MGSSHHHHHHSQDPTLANVSELELPADPKWELSRARLTLGKPLGEGAFGQVVMAEAIGIDKDRAAKPVTVAVKMLKDDATDKDLSDLVSEMEMMKMIGKHKNIINLLGACTQGGPLYVLVEYAAKGNLREFLRARRPPGLDYSFDTSKPPEEQLTFKDLVSCAYQVARGMEYLASQKCIHRDLAARNVLVTEDNVMKIADFGLARDVHNLDYYKKTTNGRLPVKWMAPEALFDEVYTHQSDVWSFGVLLWEIFTLGGSPYPGIPVEELFKLLKEGHRMDKPANCTHDLYMIMRECWHAAPSQRPTFKQLVEDLDRVLTVTSTDE
Oligomeric state: Homo 2-mer
Stoichiometry: A2
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.199
R work: 0.1928
R free: 0.2299
Average B factor: 74.7675
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 292
Crystal growth procedure: 0.1 M Hepes, pH 7.5, and 1.8 M (NH4)2SO4
Matthews coefficient: 2.57
Solvent content (%): 56.68
Ligand: PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER (ACP)
Ligand formula: C11 H18 N5 O12 P3
Ligand molecular weight: 505.208
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(CP(=O)(O)O)O)O)O)N
Ligand InChI: InChI=1S/C11H18N5O12P3/c12-9-6-10(14-2-13-9)16(3-15-6)11-8(18)7(17)5(27-11)1-26-31(24,25)28-30(22,23)4-29(19,20)21/h2-3,5,7-8,11,17-18H,1,4H2,(H,22,23)(H,24,25)(H2,12,13,14)(H2,19,20,21)/t5-,7-,8-,11-/m1/s1
Release date: 2020-01-22
Crystal Structure of Human DNA Polymerase Eta Inserting dTMPNPP Opposite O6-Methyl-2'-deoxyguanosine (PDB entry 5L1J)
Macromolecule: DNA polymerase eta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 435 residues
Sequence: GPHMATGQDRVVALVDMDCFFVQVEQRQNPHLRNKPCAVVQYKSWKGGGIIAVSYEARAFGVTRSMWADDAKKLCPDLLLAQVRESRGKANLTKYREASVEVMEIMSRFAVIERASIDEAYVDLTSAVQERLQKLQGQPISADLLPSTYIEGLPQGPTTAEETVQKEGMRKQGLFQWLDSLQIDNLTSPDLQLTVGAVIVEEMRAAIERETGFQCSAGISHNKVLAKLACGLNKPNRQTLVSHGSVPQLFSQMPIRKIRSLGGKLGASVIEILGIEYMGELTQFTESQLQSHFGEKNGSWLYAMCRGIEHDPVKPRQLPKTIGCSKNFPGKTALATREQVQWWLLQLAQELEERLTKDRNDNDRVATQLVVSIRVQGDKRLSSLRRCCALTRYDAHKMSHDAFTVIKNCNTSGIQTEWSPPLTMLFLCATKFSAS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.94
R work: 0.15857
R free: 0.20166
Average B factor: 33.677
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 291
Crystal growth procedure: 0.1 M MES pH 5.5, 5mM Magnesium chloride, 16% PEG 2000 MME
Matthews coefficient: 2.11
Solvent content (%): 41.77
Ligand: MAGNESIUM ION (MG)
Ligand formula: Mg
Ligand molecular weight: 24.305
Ligand SMILES: [Mg+2]
Ligand InChI: InChI=1S/Mg/q+2
Release date: 2016-10-05
Dibenzooxepinone inhibitor 12b in complex with p38 MAPK (PDB entry 5MTX)
Macromolecule: Mitogen-activated protein kinase 14
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.24
Sequence length: 360 residues
Sequence: MSQERPTFYRQELNKTIWEVPERYQNLSPVGSGAYGSVCAAFDTKTGLRVAVKKLSRPFQSIIHAKRTYRELRLLKHMKHENVIGLLDVFTPARSLEEFNDVYLVTHLMGADLNNIVKCQKLTDDHVQFLIYQILRGLKYIHSADIIHRDLKPSNLAVNEDCELKILDFGLARHTDDEMTGYVATRWYRAPEIMLNWMHYNQTVDIWSVGCIMAELLTGRTLFPGTDHIDQLKLILRLVGTPGAELLKKISSESARNYIQSLTQMPKMNFANVFIGANPLAVDLLEKMLVLDSDKRITAAQALAHAYFAQYHDPDDEPVADPYDQSFESRDLLIDEWKSLTYDEVISFVPPPLDQEEMES
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.18773
R free: 0.23332
Average B factor: 34.787
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293.15
Crystal growth procedure: 100 mM MES pH 5.6-6.3
20-30 % PEG4000
25 mM BOG
Matthews coefficient: 2.14
Solvent content (%): 42.57
Ligand: octyl beta-D-glucopyranoside (BOG)
Ligand formula: C14 H28 O6
Ligand molecular weight: 292.369
Ligand SMILES: CCCCCCCCOC1C(C(C(C(O1)CO)O)O)O
Ligand InChI: InChI=1S/C14H28O6/c1-2-3-4-5-6-7-8-19-14-13(18)12(17)11(16)10(9-15)20-14/h10-18H,2-9H2,1H3/t10-,11-,12+,13-,14-/m1/s1
Release date: 2017-09-06
Cryogenic apo Human Hsp90a-NTD (PDB entry 7S8Y)
Macromolecule: Heat shock protein HSP 90-alpha
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.4.10
Sequence length: 237 residues
Sequence: HMPEETQTQDQPMEEEEVETFAFQAEIAQLMSLIINTFYSNKEIFLRELISNSSDALDKIRYESLTDPSKLDSGKELHINLIPNKQDRTLTIVDTGIGMTKADLINNLGTIAKSGTKAFMEALQAGADISMIGQFGVGFYSAYLVAEKVTVITKHNDDEQYAWESSAGGSFTVRTDTGEPMGRGTKVILHLKEDQTEYLEERRIKEIVKKHSQFIGYPITLFVEKERDKEVSDDEAE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.59
R work: 0.1645
R free: 0.1913
Average B factor: 28.28
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 100 mM HEPES, pH 7 and 1.6 M sodium citrate dihydrate
Matthews coefficient: 2.68
Solvent content (%): 54.1
Release date: 2022-08-03
Crystal structure of human alkaline ceramidase 3 (ACER3) at 2.7 Angstrom resolution (PDB entry 6G7O)
Macromolecule: Alkaline ceramidase 3,Soluble cytochrome b562
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.5.1
Sequence length: 350 residues
Sequence: FAPAADREGYWGPTTSTLDWCEENYSVTWYIAEFWNTVSNLIMIIPPMFGAVQSVRDGLEKRYIASYLALTVVGMGSWCFHMTLKYEMQLLDELPMIYSCCIFVYCMFECFKIKNSVNYHLLFTLVLFSLIVTTVYLKVKEPIFHQVMYGMLVFTLVLRSIYIVTWVYPWLRGLGYTSLGIFLLGFLFWNIDNIFCESLRNFRKKVPPIIGITTQFHAWWHILTGLGSYLHILFSLYTRTLYLRADLEDNWETLNDNLKVIEKADNAAQVKDALTKMRAAALDAQKATPPKLEDKSPDSPEMKDFRHGFDILVGQIDDALKLANEGKVKEAQAAAEQLKTTRNAYIQKYL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.7
R work: 0.248
R free: 0.27
Average B factor: 74.44
Crystallization method: LIPIDIC CUBIC PHASE
Crystallization pH: 7.5
Crystallization temperature (K): 293.15
Crystal growth procedure: 75mM MgSO4, 34-40% PEG400, 5% DMSO
Matthews coefficient: 3.33
Solvent content (%): 63.08
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: 2019-01-02
Crystal structure of EED in complex with H3K27Me3 peptide and 3-(benzo[d][1,3]dioxol-4-ylmethyl)piperidine-1-carboximidamide (PDB entry 5U5T)
Macromolecule: Polycomb protein EED
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 367 residues
Sequence: GKKCKYSFKCVNSLKEDHNQPLFGVQFNWHSKEGDPLVFATVGSNRVTLYECHSQGEIRLLQSYVDADADENFYTCAWTYDSNTSHPLLAVAGSRGIIRIINPITMQCIKHYVGHGNAINELKFHPRDPNLLLSVSKDHALRLWNIQTDTLVAIFGGVEGHRDEVLSADYDLLGEKIMSCGMDHSLKLWRINSKRMMNAIKESYDYNPNKTNRPFISQKIHFPDFSTRDIHRNYVDCVRWLGDLILSKSCENAIVCWKPGKMEDDIDKIKPSESNVTILGRFDYSQCDIWYMRFSMDFWQKMLALGNQVGKLYVWDLEVEDPHKAKCTTLTHHKCGAAIRQTSFSRDSSILIAVCDDASIWRWDRLR
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.6
R work: 0.168
R free: 0.2
Average B factor: 28.38
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 291
Crystal growth procedure: Using a PEG/salt combination as a precipitant. Briefly, EED was incubated with 10 mM B-nicotinamide adenine dinucleotide hydrate, 2 mM of a tightly binding proprietary compound, and 0.5 mM of a synthesized peptide which comprises the helix on EZH2 which interacts with EED. The crystals were grown using the vapor diffusion method. One uL of the protein mixture was combined with 1 uL of a precipitant comprised of 20% (w/v) PEG3350, 0.2 M potassium iodide, and 0.1M Tris-HCl, pH 8.5, on a cover slip which was  suspended over a reservoir comprised of 0.5 mL of precipitant at 18 Celsius and sealed. The crystals grew in 4-6 days at 18 Celsius and then harvested and soaked in defined drops consisting of 30 uL of precipitant and 2 mM of compound for 24 h. Crystals were cryopreserved for data collection using a cryosolution consisting of 30% PEG 400 (v/v), 20% (w/v) PEG 3350, 0.2 M potassium iodide, and 0.1M Tris-HCl, pH 8.5
Matthews coefficient: 2.25
Solvent content (%): 45.42
Ligand: (3R)-3-[(2H-1,3-benzodioxol-4-yl)methyl]piperidine-1-carboximidamide (7W7)
Ligand formula: C14 H19 N3 O2
Ligand molecular weight: 261.32
Ligand SMILES: c1cc(c2c(c1)OCO2)CC3CCCN(C3)C(=N)N
Ligand InChI: InChI=1S/C14H19N3O2/c15-14(16)17-6-2-3-10(8-17)7-11-4-1-5-12-13(11)19-9-18-12/h1,4-5,10H,2-3,6-9H2,(H3,15,16)/t10-/m1/s1
Release date: 2017-01-11
INPP5D PanDDA analysis group deposition -- Crystal Structure of the phosphatase and C2 domains of SHIP1 in complex with Z2856434816 (PDB entry 5RW6)
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): 1.32
R work: 0.1759
R free: 0.1999
Average B factor: 17.767
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 (%): 41.79
Ligand: 1-(pyridin-4-yl)-N-[(thiophen-2-yl)methyl]methanamine (WLS)
Ligand formula: C11 H12 N2 S
Ligand molecular weight: 204.291
Ligand SMILES: c1cc(sc1)CNCc2ccncc2
Ligand InChI: InChI=1S/C11H12N2S/c1-2-11(14-7-1)9-13-8-10-3-5-12-6-4-10/h1-7,13H,8-9H2
Release date: 2020-11-11
Nucleotide-binding domain 1 of the human cystic fibrosis transmembrane conductance regulator (CFTR) with ATP (PDB entry 5TF7)
Macromolecule: Cystic fibrosis transmembrane conductance regulator
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.3.49
Sequence length: 229 residues
Sequence: SLTTTEVVMENVTAFWEEGGTPVLKDINFKIERGQLLAVAGSTGAGKTSLLMMIMGELEPSEGKIKHSGRISFCSQFSWIMPGTIKENIIFGVSYDEYRYRSVIKACQLEEDISKFAEKDNIVLGEGGITLSGGQRARISLARAVYKDADLYLLDSPFGYLDVLTEKEIFESCVCKLMANKTRILVTSKMEHLKKADKILILHEGSSYFYGTFSELQNLQPDFSSKLMG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.931
R work: 0.1569
R free: 0.1995
Crystallization method: MICROBATCH
Crystallization pH: 7.5
Crystallization temperature (K): 279
Crystal growth procedure: 40% (v/v) PEG 400, 100 mM NH4Cl, and 100 mM MES, pH 6
Matthews coefficient: 2.38
Solvent content (%): 48.3
Ligand: MAGNESIUM ION (MG)
Ligand formula: Mg
Ligand molecular weight: 24.305
Ligand SMILES: [Mg+2]
Ligand InChI: InChI=1S/Mg/q+2
Release date: 2018-05-09
DNA Polymerase Mu, 8-oxodGTP:At Product State Ternary Complex, 10 mM Mn2+ (960min) (PDB entry 7KT6)
Macromolecule: DNA-directed DNA/RNA polymerase mu
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 356 residues
Sequence: GSAAAPLSPAWMPAYACQRPTPLTHHNTGLSEALEILAEAAGFEGSEGRLLTFCRAASVLKALPSPVTTLSQLQGLPHFGEHSSRVVQELLEHGVCEEVERVRRSERYQTMKLFTQIFGVGVKTADRWYREGLRTLDDLREQPQKLTQQQKAGLQHHQDLSTPVLRSDVDALQQVVEEAVGQALPGATVTLTGGFRRGKLQGHDVDFLITHPKEGQEAGLLPRVMCRLQDQGLILYHQHQHSCCESPTRLAQQSHMDAFERSFCIFRLPQPGSWKAVRVDLVVAPVSQFPFALLGWTGSKLFQRELRRFSRKEKGLWLNSHGLFDPEQKTFFQAASEEDIFRHLGLEYLPPEQRNA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.87
R work: 0.1652
R free: 0.1932
Average B factor: 31.0192
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 85-90mM HEPES pH 7.5, 17-18% PEG4000
Matthews coefficient: 2.5
Solvent content (%): 50.88
Ligand: SODIUM ION ()
Ligand formula: Na
Ligand molecular weight: 22.99
Ligand SMILES: [Na+]
Ligand InChI: InChI=1S/Na/q+1
Release date: 2021-12-15
Crystal structure of the Angiotensin-1 converting enzyme N-domain in complex with amyloid-beta 10-16 (PDB entry 5AM9)
Macromolecule: ANGIOTENSIN-CONVERTING ENZYME
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.2.1
Sequence length: 629 residues
Sequence: LDPGLQPGQFSADEAGAQLFAQSYQSSAEQVLFQSVAASWAHDTNITAENARRQEEAALLSQEFAEAWGQKAKELYEPIWQQFTDPQLRRIIGAVRTLGSANLPLAKRQQYNALLSQMSRIYSTAKVCLPQKTATCWSLDPDLTNILASSRSYAMLLFAWEGWHNAAGIPLKPLYEDFTALSNEAYKQDGFTDTGAYWRSWYNSPTFEDDLEHLYQQLEPLYLNLHAFVRRALHRRYGDRYINLRGPIPAHLLGDMWAQSWENIYDMVVPFPDKPNLDVTSTMLQQGWQATHMFRVAEEFFTSLELSPMPPEFWEGSMLEKPADGREVVCHASAWDFYNRKDFRIKQCTRVTMDQLSTVHHEMGHIQYYLQYKDLPVSLRRGANPGFHEAIGDVLALSVSTPEHLHKIGLLDRVTNDTESDINYLLKMALEKIAFLPFGYLVDQWRWGVFSGRTPPSRYNFDWWYLRTKYQGICPPVTRNETHFDAGAKFHVPNVTPYIRYFVSFVLQFQFHEALCKEAGYEGPLHQCDIYRSTKAGAKLRKVLRAGSSRPWQEVLKDMVGLDALDAQPLLKYFQLVTQWLQEQNQQNGEVLGWPEYQWHPPLPDNYPEGIDLVTDEAEASKFVEEYDL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.19674
R free: 0.22907
Average B factor: 27.347
Crystallization pH: 8.5
Crystal growth procedure: 0.06 M DIVALENT CATIONS, 0.1 M TRIS/BICINE PH 8.5, 30 % PEG550MME/PEG20000
Matthews coefficient: 2.95
Solvent content (%): 58
Ligand: GLUTAMINE (GLN)
Ligand formula: C5 H10 N2 O3
Ligand molecular weight: 146.144
Ligand SMILES: C(CC(=O)N)C(C(=O)O)N
Ligand InChI: InChI=1S/C5H10N2O3/c6-3(5(9)10)1-2-4(7)8/h3H,1-2,6H2,(H2,7,8)(H,9,10)/t3-/m0/s1
Release date: 2016-01-13
PanDDA analysis group deposition of models with modelled events (e.g. bound ligands) -- Crystal Structure of human PARP14 Macrodomain 3 in complex with FMOPL000242a (PDB entry 5QIA)
Macromolecule: Poly [ADP-ribose] polymerase 14
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.4.2.30
Sequence length: 183 residues
Sequence: SMFYGTVSSPDSGVYEMKIGSIIFQVASGDITKEEADVIVNSTSNSFNLKAGVSKAILECAGQNVERECSQQAQQRKNDYIITGGGFLRCKNIIHVIGGNDVKSSVSSVLQECEKKNYSSICLPAIGTGNAKQHPDKVAEAIIDAIEDFVQKGSAQSVKKVKVVIFLPQVLDVFYANMKKREG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.14
R work: 0.1585
R free: 0.1981
Average B factor: 18.296
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.4
Crystallization temperature (K): 277
Crystal growth procedure: 80 mM KBr, 30 % PEG2kMME
Matthews coefficient: 2
Solvent content (%): 38.56
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: 2019-04-10
BACE-1 in complex with compound #18 (PDB entry 7MYR)
Macromolecule: Beta-secretase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.23.46
Sequence length: 442 residues
Sequence: MAGVLPAHGTQHGIRLPLRSGLGGAPLGLRLPRETDEEPEEPGRRGSFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHPFLHRYYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTVRANIAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTHVPNLFSLQLCGAGFPLNQSEVLASVGGSMIIGGIDHSLYTGSLWYTPIRREWYYEVIIVRVEINGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVKSIKAASSTEKFPDGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRITILPQQYLRPVEDVATSQDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSACHVHDEFRTAAVEGPFVTLDMEDCGYNIPQTDEST
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.72
R work: 0.1703
R free: 0.1958
Average B factor: 17.36
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 100mM sodium cacodylate pH 7.4, 12% PEG 8K, 200mM ammonium sulfate
Matthews coefficient: 2.61
Solvent content (%): 52.86
Ligand: (4aR,7aR)-6-(5-fluoropyrimidin-2-yl)-7a-(1,2-thiazol-5-yl)-4,4a,5,6,7,7a-hexahydropyrrolo[3,4-d][1,3]thiazin-2-amine (ZRD)
Ligand formula: C13 H13 F N6 S2
Ligand molecular weight: 336.411
Ligand SMILES: c1cnsc1C23CN(CC2CSC(=N3)N)c4ncc(cn4)F
Ligand InChI: InChI=1S/C13H13FN6S2/c14-9-3-16-12(17-4-9)20-5-8-6-21-11(15)19-13(8,7-20)10-1-2-18-22-10/h1-4,8H,5-7H2,(H2,15,19)/t8-,13-/m0/s1
Release date: 2021-07-14
Crystal Structure of the Human Vaccinia-related Kinase 1 Bound to an Oxindole Inhibitor (PDB entry 5UKF)
Macromolecule: Serine/threonine-protein kinase VRK1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 363 residues
Sequence: MRVKAAQAGRQSSAKRHLAEQFAVGEIITDMAAAAWKVGLPIGQGGFGCIYLADMNSSESVGSDAPCVVKVEPSDNGPLFTELKFYQRAAKPEQIQKWIRTRKLKYLGVPKYWGSGLHDKNGKSYRFMIMDRFGSDLQKIYEANAKRFSRKTVLQLSLRILDILEYIHEHEYVHGDIKASNLLLNYKNPDQVYLVDYGLAYRYCPEGVHKAYAADPKRCHDGTIEFTSIDAHNGVAPSRRGDLEILGYCMIQWLTGHLPWEDNLKDPKYVRDSKIRYRENIASLMDKCFPAANAPGEIAKYMETVKLLDYTEKPLYENLRDILLQGLKAIGSKDDGKLDLSVVENGGLKAKTITKKRAAEIEE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.4
R work: 0.177
R free: 0.214
Average B factor: 60.07
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 293
Crystal growth procedure: 27.5% PEG 3350; 0.3M AmSO4; 0.1M HEPES pH 7.0
Matthews coefficient: 2.59
Solvent content (%): 52.52
Ligand: 4-{[(Z)-(7-oxo-6,7-dihydro-8H-[1,3]thiazolo[5,4-e]indol-8-ylidene)methyl]amino}benzene-1-sulfonamide (8E1)
Ligand formula: C16 H12 N4 O3 S2
Ligand molecular weight: 372.421
Ligand SMILES: c1cc(ccc1NC=C2c3c(ccc4c3scn4)NC2=O)S(=O)(=O)N
Ligand InChI: InChI=1S/C16H12N4O3S2/c17-25(22,23)10-3-1-9(2-4-10)18-7-11-14-12(20-16(11)21)5-6-13-15(14)24-8-19-13/h1-8,18H,(H,20,21)(H2,17,22,23)/b11-7-
Release date: 2017-03-29
The ATAD2 bromodomain in complex with compound 5 (PDB entry 6EPV)
Macromolecule: ATPase family AAA domain-containing protein 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.1.3
Sequence length: 130 residues
Sequence: SMQEEDTFRELRIFLRNVTHRLAIDKRFRVFTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLRDIDLICSNALEYNPDRDPGDRLIRHRACALRDTAYAIIKEELDEDFEQLCEEIQESR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.793
R work: 0.2101
R free: 0.2174
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 2M ammonium sulfate, 0.1M Bis-Tris pH 5.5
Matthews coefficient: 4.07
Solvent content (%): 69.79
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: 2018-10-31
Crystal Structure of Nup358/RanBP2 Ran-binding domain 2 in complex with Ran-GPPNHP (PDB entry 7MNX)
Macromolecule: GTP-binding nuclear protein Ran
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 217 residues
Sequence: SMAAQGEPQVQFKLVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGPIKFNVWDTAGQEKFGGLRDGYYIQAQCAIIMFDVTSRVTYKNVPNWHRDLVRVCENIPIVLCGNKVDIKDRKVKAKSIVFHRKKNLQYYDISAKSNYNFEKPFLWLARKLIGDPNLEFVAMPALAPPEVVMDPALAAQYEHDLEVAQTTALPDEDDDL
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.4
R work: 0.1918
R free: 0.2301
Average B factor: 75.3795
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 294
Crystal growth procedure: 15% w/v PEG3350, 0.125 M magnesium formate
Matthews coefficient: 2.34
Solvent content (%): 47.54
Ligand: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER (GNP)
Ligand formula: C10 H17 N6 O13 P3
Ligand molecular weight: 522.196
Ligand SMILES: c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(NP(=O)(O)O)O)O)O)N=C(NC2=O)N
Ligand InChI: InChI=1S/C10H17N6O13P3/c11-10-13-7-4(8(19)14-10)12-2-16(7)9-6(18)5(17)3(28-9)1-27-32(25,26)29-31(23,24)15-30(20,21)22/h2-3,5-6,9,17-18H,1H2,(H,25,26)(H3,11,13,14,19)(H4,15,20,21,22,23,24)/t3-,5-,6-,9-/m1/s1
Release date: 2022-06-15
Biochemical, Cellular and Structural Characterization of Novel ERK3 Inhibitors (PDB entry 6YKY)
Macromolecule: Mitogen-activated protein kinase 6
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.24
Sequence length: 319 residues
Sequence: MNIHGFDLGSRYMDLKPLGCGGNGLVFSAVDNDCDKRVAIKKIVLTDPQSVKHALREIKIIRRLDHDNIVKVFEILGPSGSQLTDDVGSLTELNSVYIVQEYMETDLANVLEQGPLLEEHARLFMYQLLRGLKYIHSANVLHRDLKPANLFINTEDLVLKIGDFGLARIMDPHYSHKGHLSEGLVTKWYRSPRLLLSPNNYTKAIDMWAAGCIFAEMLTGKTLFAGAHELEQMQLILESIPVVHEEDRQELLSVIPVYIRNDMTEPHKPLTQLLPGISREAVDFLEQILTFSPMDRLTAEEALSHPYMSIYSFPMDEPI
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.52
R work: 0.198
R free: 0.251
Average B factor: 70
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6
Crystallization temperature (K): 277
Crystal growth procedure: 100 mM Bis-Tris (pH 6), 100 mM Lithium acetate, 18%v/v Sokalan CP42, 3%vv Glycerol
Matthews coefficient: 2.49
Solvent content (%): 50.67
Ligand: 3-(4-methoxyphenyl)-~{N}-[(3~{R})-1-pyridin-4-ylpyrrolidin-3-yl]-[1,2,3]triazolo[4,5-d]pyrimidin-5-amine (OWQ)
Ligand formula: C20 H20 N8 O
Ligand molecular weight: 388.426
Ligand SMILES: COc1ccc(cc1)n2c3c(cnc(n3)NC4CCN(C4)c5ccncc5)nn2
Ligand InChI: InChI=1S/C20H20N8O/c1-29-17-4-2-16(3-5-17)28-19-18(25-26-28)12-22-20(24-19)23-14-8-11-27(13-14)15-6-9-21-10-7-15/h2-7,9-10,12,14H,8,11,13H2,1H3,(H,22,23,24)/t14-/m1/s1
Release date: 2020-09-23