satarupa22/MacromolecularLigandDB huggingface dataset:
Crystal structure of human Casein Kinase I delta in complex with 4-(2,5-Dimethoxyphenyl)-N-(4-(5-(4-fluorphenyl)-2-(methylthio)-1H-imidazol-4-yl)-pyridin-2-yl)-1-methyl-1H-pyrrole-2-carboxamide (PDB entry 5MQV)
Macromolecule: Casein kinase I isoform delta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 314 residues
Sequence: MGSSHHHHHHSSGLVPRGSHMELRVGNRYRLGRKIGSGSFGDIYLGTDIAAGEEVAIKLECVKTKHPQLHIESKIYKMMQGGVGIPTIRWCGAEGDYNVMVMELLGPSLEDLFNFCSRKFSLKTVLLLADQMISRIEYIHSKNFIHRDVKPDNFLMGLGKKGNLVYIIDFGLAKKYRDARTHQHIPYRENKNLTGTARYASINTHLGIEQSRRDDLESLGYVLMYFNLGSLPWQGLKAATKRQKYERISEKKMSTPIEVLCKGYPSEFATYLNFCRSLRFDDKPDYSYLRQLFRNLFHRQGFSYDYVFDWNMLK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.154
R work: 0.1731
R free: 0.1917
Average B factor: 57.0082
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 0.1 M Hepes pH 7.0, 0.7 M NaH2PO4, 0.7 M KH2PO4
Matthews coefficient: 4.09
Solvent content (%): 69.94
Ligand: 4-(2,5-Dimethoxyphenyl)-N-(4-(5-(4-fluorphenyl)-2-(methylthio)-1H-imidazol-4-yl)-pyridin-2-yl)-1-methyl-1H-pyrrole-2-carboxamide (D5Q)
Ligand formula: C29 H26 F N5 O3 S
Ligand molecular weight: 543.612
Ligand SMILES: Cn1cc(cc1C(=O)Nc2cc(ccn2)c3c(nc([nH]3)SC)c4ccc(cc4)F)c5cc(ccc5OC)OC
Ligand InChI: InChI=1S/C29H26FN5O3S/c1-35-16-19(22-15-21(37-2)9-10-24(22)38-3)13-23(35)28(36)32-25-14-18(11-12-31-25)27-26(33-29(34-27)39-4)17-5-7-20(30)8-6-17/h5-16H,1-4H3,(H,33,34)(H,31,32,36)
Release date: 2017-04-05
Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor NPD-3098 (PDB entry 6FTA)
Macromolecule: cAMP-specific 3',5'-cyclic phosphodiesterase 4D
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.4.53
Sequence length: 364 residues
Sequence: GSHMIPRFGVKTEQEDVLAKELEDVNKWGLHVFRIAELSGNRPLTVIMHTIFQERDLLKTFKIPVDTLITYLMTLEDHYHADVAYHNNIHAADVVQSTHVLLSTPALEAVFTDLEILAAIFASAIHDVDHPGVSNQFLINTNSELALMYNDSSVLENHHLAVGFKLLQEENCDIFQNLTKKQRQSLRKMVIDIVLATDMSKHMNLLADLKTMVETKKVTSSGVLLLDNYSDRIQVLQNMVHCADLSNPTKPLQLYRQWTDRIMEEFFRQGDRERERGMEISPMCDKHNASVEKSQVGFIDYIVHPLWETWADLVHPDAQDILDTLEDNREWYQSTIPQSPSPAPDDPEEGRQGQTEKFQFELTL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.34
R work: 0.18122
R free: 0.24012
Average B factor: 52.888
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: 24% PEG 3350, 30% Ethylene Glycol, 0.1 M HEPES pH 7.5
Matthews coefficient: 2.65
Solvent content (%): 53.57
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: 2019-03-20
Structure of J-PKAc chimera complexed with Aplithianine A (PDB entry 8FE2)
Macromolecule: DnaJ homolog subfamily B member 1, cAMP-dependent protein kinase catalytic subunit alpha
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.11
Sequence length: 405 residues
Sequence: GKDYYQTLGLARGASDEEIKRAYRRQALRYHPDKNKEPGAEEKFKEIAEAYDVLSDPRKREIFDRYGEEVKEFLAKAKEDFLKKWESPAQNTAHLDQFERIKTLGTGSFGRVMLVKHKETGNHYAMKILDKQKVVKLKQIEHTLNEKRILQAVNFPFLVKLEFSFKDNSNLYMVMEYVPGGEMFSHLRRIGRFSEPHARFYAAQIVLTFEYLHSLDLIYRDLKPENLLIDQQGYIQVTDFGFAKRVKGRTWTLCGTPEYLAPEIILSKGYNKAVDWWALGVLIYEMAAGYPPFFADQPIQIYEKIVSGKVRFPSHFSSDLKDLLRNLLQVDLTKRFGNLKNGVNDIKNHKWFATTDWIAIYQRKVEAPFIPKFKGPGDTSNFDDYEEEEIRVSINEKCGKEFSEF
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.34
R work: 0.1964
R free: 0.2508
Average B factor: 58.26
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277.15
Crystal growth procedure: 200 mM Lithium sulfate, 100 mM HEPES 7.5,  20%  PEG 3350
Matthews coefficient: 2.68
Solvent content (%): 54.16
Ligand: 6-[(6M)-6-(1-methyl-1H-imidazol-5-yl)-2,3-dihydro-4H-1,4-thiazin-4-yl]-9H-purine (XTI)
Ligand formula: C13 H13 N7 S
Ligand molecular weight: 299.354
Ligand SMILES: Cn1cncc1C2=CN(CCS2)c3c4c([nH]cn4)ncn3
Ligand InChI: InChI=1S/C13H13N7S/c1-19-8-14-4-9(19)10-5-20(2-3-21-10)13-11-12(16-6-15-11)17-7-18-13/h4-8H,2-3H2,1H3,(H,15,16,17,18)
Release date: 2023-10-18
Structure of human galactokinase 1 bound with 2-(4-chlorophenyl)-N-(pyrimidin-2-yl)acetamide (PDB entry 6ZGZ)
Macromolecule: Galactokinase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.1.6
Sequence length: 399 residues
Sequence: MAHHHHHHAALRQPQVAELLAEARRAFREEFGAEPELAVSAPGRVNLIGEHTDYNQGLVLPMALELMTVLVGSPRKDGLVSLLTTSEGADEPQRLQFPLPTAQRSLEPGTPRWANYVKGVIQYYPAAPLPGFSAVVVSSVPLGGGLSSSASLEVATYTFLQQLCPDSGTIAARAQVCQQAEHSFAGMPCGIMDQFISLMGQKGHALLIDCRSLETSLVPLSDPKLAVLITNSNVRHSLASSEYPVRRRQCEEVARALGAASLREVQLEELEAARDLVSKEGFRRARHVVGEIRRTAQAAAALRRGDYRAFGRLMVESHRSLRDDYEVSCPELDQLVEAALAVPGVYGSRMTGGGFGGCTVTLLEASAAPHAMRHIQEHYGGTATFYLSQAADGAKVLCL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.3
R work: 0.2142
R free: 0.2563
Average B factor: 43.168
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M MOPS/sodium HEPES pH 7.0-7.5, 40-50 % Morpheus Precipitant Mix 4 (50% mix = 12.5% MPD, 12.5% PEG1000, 12.5% PEG3350), 0.1 M Morpheus Carboxylic acids mix (0.02M each of - sodium formate, ammonium acetate, sodium citrate tribasic dehydrate, sodium potassium tartrate tetrahydrate and sodium oxamate).
Matthews coefficient: 2.88
Solvent content (%): 57.32
Ligand: beta-D-galactopyranose (GAL)
Ligand formula: C6 H12 O6
Ligand molecular weight: 180.156
Ligand SMILES: C(C1C(C(C(C(O1)O)O)O)O)O
Ligand InChI: InChI=1S/C6H12O6/c7-1-2-3(8)4(9)5(10)6(11)12-2/h2-11H,1H2/t2-,3+,4+,5-,6-/m1/s1
Release date: 2020-07-29
Erk2 signalling protein (PDB entry 6GJB)
Macromolecule: Mitogen-activated protein kinase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.24
Sequence length: 368 residues
Sequence: MAHHHHHHMAAAAAAGAGPEMVRGQVFDVGPRYTNLSYIGEGAYGMVCSAYDNVNKVRVAIKKISPFEHQTYCQRTLREIKILLRFRHENIIGINDIIRAPTIEQMKDVYIVQDLMETDLYKLLKTQHLSNDHICYFLYQILRGLKYIHSANVLHRDLKPSNLLLNTTCDLKICDFGLARVADPDHDHTGFLTEYVATRWYRAPEIMLNSKGYTKSIDIWSVGCILAEMLSNRPIFPGKHYLDQLNHILGILGSPSQEDLNCIINLKARNYLLSLPHKNKVPWNRLFPNADSKALDLLDKMLTFNPHKRIEVEQALAHPYLEQYYDPSDEPIAEAPFKFDMELDDLPKEKLKELIFEETARFQPGYRS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.82
R work: 0.164
R free: 0.206
Average B factor: 41.752
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.3
Crystallization temperature (K): 293
Crystal growth procedure: 0.2M ammonium sulphate, 34% MPEG2000, 0.1MHepes, pH7.3, 0.02M mercaptoethanol
Matthews coefficient: 2.29
Solvent content (%): 46.4
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: 2019-01-02
Structure of the KIV type 2 (KIV-2) domain of lipoprotein (a) (PDB entry 6RX7)
Macromolecule: Apolipoprotein(a)
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21
Sequence length: 111 residues
Sequence: MGHHHHHHENLYFQGAPTEQRPGVQECYHGNGQSYRGTYSTTVTGRTCQAWSSMTPHSHSRTPEYYPNAGLIMNYCRNPDAVAAPYCYTRDPGVRWEYCNLTQCSDAEGTA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.63
R work: 0.232
R free: 0.269
Average B factor: 22.8234
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6
Crystallization temperature (K): 294.15
Crystal growth procedure: PEG400 1% (v/v)
Ammonium sulfate 2 M
HEPES 0.1 M
Matthews coefficient: 2.46
Solvent content (%): 50.06
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: 2020-07-08
Crystal structure of WRN helicase domain in complex with 3 (PDB entry 8PFL)
Macromolecule: Bifunctional 3'-5' exonuclease/ATP-dependent helicase WRN
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1
Sequence length: 431 residues
Sequence: GPNEGEEDDDKDFLWPAPNEEQVTCLKMYFGHSSFKPVQWKVIHSVLEEARDNVAVMATGYGKSLCFQYPPVYVGKIGLVISPLISLMEDQVLQLKMSNIPACFLGSAQSANVLTDIKLGKYRIVYVTPEYCSGNMGLLQQLEADIGITLIAVDEAHCISEWGHDFRDSFRKLGSLKTALPMVPIVALTATASSSIREDIVRCLNLRNPQITCTGFDRPNLYLEVRRKTGNILQDLQPFLVKTSSHWEFEGPTIIYCPSRKMTQQVTGELAKLNLSCGTYHAGMSFSTAKDIHHRFVRDEIQCVIATIAFGMGINKADIRQVIHYGAPKDMESYYQEIGRAGRDGLQSSCHVLWAPADINLNRHLLTEIRNAKFRLYKLKMMAKMEKYLHSSRCRRQIILSHFEDKQVQKASLGIMGTEKCCDNCRSALDH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.1968
R free: 0.2255
Average B factor: 35.67
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 30% Jeffamine ED-2001
0.1 M Hepes pH 7
Matthews coefficient: 2.42
Solvent content (%): 49.23
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: 2024-04-24
PTPN21 PTP domain C1108S mutant (PDB entry 8GVV)
Macromolecule: Tyrosine-protein phosphatase non-receptor type 21
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 299 residues
Sequence: TRATNDERCKILEQRLEQGMVFTEYERILKKRLVDGECSTARLPENAERNRFQDVLPYDDVRVELVPTKENNTGYINASHIKVSVSGIEWDYIATQGPLQNTCQDFWQMVWEQGIAIIAMVTAEEEGGREKSFRYWPRLGSRHNTVTYGRFKITTRFRTDSGCYATTGLKMKHLLTGQERTVWHLQYTDWPEHGCPEDLKGFLSYLEEIQSVRRHTNSTSDPQSPNPPLLVHSSAGVGRTGVVILSEIMIACLEHNEVLDIPRVLDMLRQQRMMLVQTLCQYTFVYRVLIQFLKSSRLI
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.1904
R free: 0.2273
Average B factor: 31.7186
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7
Crystallization temperature (K): 278
Crystal growth procedure: PEG 3350, 250 mM Sodium iodide
Matthews coefficient: 2.29
Solvent content (%): 46.29
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: 2023-09-20
Structure of the cytosolic domain of lysosome-associated TMEM55B (PDB entry 8OQH)
Macromolecule: Type 1 phosphatidylinositol 4,5-bisphosphate 4-phosphatase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.78
Sequence length: 91 residues
Sequence: GSHMSPDSGSAPMITCRVCQSLINVEGKMHQHVVKCGVCNEATPIKNAPPGKKYVRCPCNSLLIAKVTSQRIACPRPYCKRIINLGPVHPG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.76
R work: 0.1942
R free: 0.224
Average B factor: 38.94
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 288
Crystal growth procedure: 0.1M Tris pH8.5, 0.2M Sodium acetate trihydrate, 30% w/v PEG 4000
Matthews coefficient: 2.02
Solvent content (%): 38.96
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: 2023-11-29
Crystal structure of peptide-substrate-binding domain of human type II collagen prolyl 4-hydroxylase complex with Pro-Pro-Gly-Pro-Ala-Gly-Pro-Pro-Gly. (PDB entry 6EVN)
Macromolecule: Prolyl 4-hydroxylase subunit alpha-2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11.2
Sequence length: 102 residues
Sequence: MHHHHHHMLSVDDCFGMGRSAYNEGDYYHTVLWMEQVLKQLDAGEEATTTKSQVLDYLSYAVFQLGDLHRALELTRRLLSLDPSHERAGGNLRYFEQLLEEE
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.48
R work: 0.1631
R free: 0.1788
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 277
Crystal growth procedure: 2.45 M ammonium sulphate, 10% DMSO, 5 mM PPGPAGPPG, 5% D-galactose, 100 mM MOPS, pH 6.5
Matthews coefficient: 2.67
Solvent content (%): 53.95
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: 2018-09-12
INPP5D PanDDA analysis group deposition -- Crystal Structure of the phosphatase and C2 domains of SHIP1 in complex with Z32014663 (PDB entry 5RXY)
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): 1.4
R work: 0.1686
R free: 0.1933
Average B factor: 17.041
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: 2.09
Solvent content (%): 41.06
Ligand: N,N,2,3-tetramethylbenzamide (WNV)
Ligand formula: C11 H15 N O
Ligand molecular weight: 177.243
Ligand SMILES: Cc1cccc(c1C)C(=O)N(C)C
Ligand InChI: InChI=1S/C11H15NO/c1-8-6-5-7-10(9(8)2)11(13)12(3)4/h5-7H,1-4H3
Release date: 2020-11-11
Structure of a human VH antibody domain binding to the cleft of hen egg lysozyme (PDB entry 4U3X)
Macromolecule: Human VH domain antibody
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 121 residues
Sequence: EVQLLESGGGLVQPGGSLRLSCAASGFRFDAEDMGWVRQAPGKGLEWVSSIYGPSGSTYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCAKYTSPPQNHGFDYWGQGTLVTVSS
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.26
R work: 0.1893
R free: 0.24839
Average B factor: 14.923
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 298
Crystal growth procedure: 300 mM sodium citrate, 16% PEG 3350
Matthews coefficient: 2.32
Solvent content (%): 46.94
Ligand: 1,2-ETHANEDIOL (EDO)
Ligand formula: C2 H6 O2
Ligand molecular weight: 62.068
Ligand SMILES: C(CO)O
Ligand InChI: InChI=1S/C2H6O2/c3-1-2-4/h3-4H,1-2H2
Release date: 2015-03-11
PKG II's Carboxyl Terminal Cyclic Nucleotide Binding Domain (CNB-B) in a complex with cGMP (PDB entry 5BV6)
Macromolecule: cGMP-dependent protein kinase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.12
Sequence length: 152 residues
Sequence: GSTAQARDEQYRNFLRSVSLLKNLPEDKLTKIIDCLEVEYYDKGDYIIREGEEGSTFFILAKGKVKVTQSTEGHDQPQLIKTLQKGEYFGEKALISDDVRSANIIAEENDVACLVIDRETFNQTVGTFEELQKYLEGYVANLNRDDEKRHAK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.94
R work: 0.1772
R free: 0.2109
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 4.6
Crystallization temperature (K): 277
Crystal growth procedure: 20 mM CaCl2, 100 mM NaOAc, 30% MPD
Matthews coefficient: 2.02
Solvent content (%): 39.24
Ligand: GUANOSINE-3',5'-MONOPHOSPHATE (35G)
Ligand formula: C10 H12 N5 O7 P
Ligand molecular weight: 345.205
Ligand SMILES: c1nc2c(n1C3C(C4C(O3)COP(=O)(O4)O)O)N=C(NC2=O)N
Ligand InChI: InChI=1S/C10H12N5O7P/c11-10-13-7-4(8(17)14-10)12-2-15(7)9-5(16)6-3(21-9)1-20-23(18,19)22-6/h2-3,5-6,9,16H,1H2,(H,18,19)(H3,11,13,14,17)/t3-,5-,6-,9-/m1/s1
Release date: 2016-01-20
An unusual natural product primary sulfonamide: synthesis, carbonic anhydrase inhibition and protein x-ray structure of Psammaplin C (PDB entry 5G01)
Macromolecule: CARBONIC ANHYDRASE 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 260 residues
Sequence: MSHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHSFKVNFDDSQDKAVLKGGPLDGTYRLTQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDASKASQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTKGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLNETVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.4
R work: 0.1281
R free: 0.16534
Average B factor: 16.176
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystal growth procedure: 200 NL PLUS 200 NL OF PROTEIN AT 5 MGS/ML AND RESERVOIR IN SITTING DROP PLATES. RESERVOIR WAS 2.6 TO 2.8 M AMMONIUM SULFATE WITH 100 MM TRIS PH 8.5
Matthews coefficient: 2.1
Solvent content (%): 41.5
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: 2016-05-25
Bromodomain of CBP liganded with iCBP4 (PDB entry 8FXA)
Macromolecule: CREB-binding protein
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1.48
Sequence length: 116 residues
Sequence: KKIFKPEELRQALMPTLEALYRQDPESLPFRQPVDPQLLGIPDYFDIVKNPMDLSTIKRKLDTGQYQEPWQYVDDVWLMFNNAWLYNRKTSRVYKFCSKLAEVFEQEIDPVMQSLG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.65
R work: 0.1458
R free: 0.1801
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 291
Crystal growth procedure: 0.2 M Magnesium chloride hexahydrate, 0.1 M BIS-TRIS pH 5.5, 25% w/v Polyethylene glycol 3350
Matthews coefficient: 2.25
Solvent content (%): 45.41
Ligand: 1,2-ETHANEDIOL (EDO)
Ligand formula: C2 H6 O2
Ligand molecular weight: 62.068
Ligand SMILES: C(CO)O
Ligand InChI: InChI=1S/C2H6O2/c3-1-2-4/h3-4H,1-2H2
Release date: 2024-02-07
Application of Off-Rate Screening in the Identification of Novel Pan-Isoform Inhibitors of Pyruvate Dehydrogenase Kinase (PDB entry 5M4N)
Macromolecule: [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.2
Sequence length: 408 residues
Sequence: MRWVWALLKNASLAGSAPKYIEHFSKFSPSPLSMKQFLDFGSSNACEKTSFTFLRQELPVRLANIMKEINLLPDRVLSTPSVQLVQSWYVQSLLDIMEFLDKDPEDHRTLSQFTDALVTIRNRHNDVVPTMAQGVLEYKDTYGDDPVSNQNIQYFLDRFYLSRISIRMLINQHTLIFDGSTNPAHPKHIGSIDPNCNVSEVVKDAYDMAKLLCDKYYMASPDLEIQEINAANSKQPIHMVYVPSHLYHMLFELFKNAMRATVESHESSLILPPIKVMVALGEEDLSIKMSDRGGGVPLRKIERLFSYMYSTAPTPQPGTGGTPLAGFGYGLPISRLYAKYFQGDLQLFSMEGFGTDAVIYLKALSTDSVERLPVYNKSAWRHYQTIQEAGDWCVPSTEPKNTSTYRVS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.6
R work: 0.20269
R free: 0.25958
Average B factor: 76.632
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 5.8
Crystallization temperature (K): 277
Crystal growth procedure: 0.1 M SODIUM ACETATE PH 5.8
0.125 M MAGNESIUM CHLORIDE
6% ISOPROPANOL
Matthews coefficient: 3.11
Solvent content (%): 60.5
Ligand: [2,4-bis(oxidanyl)phenyl]-[(2~{S})-2-methyl-6-(3-methylquinolin-2-yl)-3,4-dihydro-2~{H}-quinolin-1-yl]methanone (7FV)
Ligand formula: C27 H24 N2 O3
Ligand molecular weight: 424.491
Ligand SMILES: Cc1cc2ccccc2nc1c3ccc4c(c3)CCC(N4C(=O)c5ccc(cc5O)O)C
Ligand InChI: InChI=1S/C27H24N2O3/c1-16-13-18-5-3-4-6-23(18)28-26(16)20-9-12-24-19(14-20)8-7-17(2)29(24)27(32)22-11-10-21(30)15-25(22)31/h3-6,9-15,17,30-31H,7-8H2,1-2H3/t17-/m0/s1
Release date: 2017-02-22
IRAK4 bound to benzoxazole compound (PDB entry 6N8G)
Macromolecule: Interleukin-1 receptor-associated kinase 4
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 297 residues
Sequence: RFHSFSFYELKNVTNNFDERPISVGGNKMGEGGFGVVYKGYVNNTTVAVKKLAAMVDITTEELKQQFDQEIKVMAKCQHENLVELLGFSSDGDDLCLVYVYMPNGSLLDRLSCLDGTPPLSWHMRCKIAQGAANGINFLHENHHIHRDIKSANILLDEAFTAKISDFGLARASEKFAQTVMTSRIVGTTAYMAPEALRGEITPKSDIYSFGVVLLEIITGLPAVDEHREPQLLLDIKEEIEDEEKTIEDYIDKKMNDADSTSVEAMYSVASQCLHEKKNKRPDIKKVQQLLQEMTAS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2
R work: 0.1743
R free: 0.2198
Average B factor: 49.999
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 296
Crystal growth procedure: 1.6-1.7 M Sodium Malonate,  pH 7.0,  100-150 mM Sodium acetate,  10 mM DTT
Matthews coefficient: 2.72
Solvent content (%): 54.83
Ligand: N-[2-(morpholin-4-yl)-6-(piperidin-1-yl)-1,3-benzoxazol-5-yl]-6-(1H-pyrrolo[2,3-b]pyridin-5-yl)pyridine-2-carboxamide (KFD)
Ligand formula: C29 H29 N7 O3
Ligand molecular weight: 523.586
Ligand SMILES: c1cc(nc(c1)C(=O)Nc2cc3c(cc2N4CCCCC4)oc(n3)N5CCOCC5)c6cc7cc[nH]c7nc6
Ligand InChI: InChI=1S/C29H29N7O3/c37-28(22-6-4-5-21(32-22)20-15-19-7-8-30-27(19)31-18-20)33-23-16-24-26(17-25(23)35-9-2-1-3-10-35)39-29(34-24)36-11-13-38-14-12-36/h4-8,15-18H,1-3,9-14H2,(H,30,31)(H,33,37)
Release date: 2018-12-12
Human PDK1 kinase domain in complex with Valsartan (PDB entry 8DQT)
Macromolecule: 3-phosphoinositide-dependent protein kinase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 311 residues
Sequence: GAMDGTAAEPRPGAGSLQHAQPPPQPRKKRPEDFKFGKILGEGSFSTVVLARELATSREYAIKILEKRHIIKENKVPYVTRERDVMSRLDHPFFVKLYFTFQDDEKLYFGLSYAKNGELLKYIRKIGSFDETCTRFYTAEIVSALEYLHGKGIIHRDLKPENILLNEDMHIQITDFGTAKVLSPESKQARANSFVGTAQYVSPELLTEKSACKSSDLWALGCIIYQLVAGLPPFRAGNEGLIFAKIIKLEYDFPEKFFPKARDLVEKLLVLDATKRLGCEEMEGYGPLKAHPFFESVTWENLHQQTPPKLT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.31
R work: 0.1991
R free: 0.2242
Average B factor: 24.98
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.8
Crystallization temperature (K): 293
Crystal growth procedure: 1.2M sodium citrate, 0.1M Hepes pH 7.8
Matthews coefficient: 2.22
Solvent content (%): 44.61
Ligand: (2~{S})-3-methyl-2-[pentanoyl-[[4-[2-(2~{H}-1,2,3,4-tetrazol-5-yl)phenyl]phenyl]methyl]amino]butanoic acid (U35)
Ligand formula: C24 H29 N5 O3
Ligand molecular weight: 435.519
Ligand SMILES: CCCCC(=O)N(Cc1ccc(cc1)c2ccccc2c3n[nH]nn3)C(C(C)C)C(=O)O
Ligand InChI: InChI=1S/C24H29N5O3/c1-4-5-10-21(30)29(22(16(2)3)24(31)32)15-17-11-13-18(14-12-17)19-8-6-7-9-20(19)23-25-27-28-26-23/h6-9,11-14,16,22H,4-5,10,15H2,1-3H3,(H,31,32)(H,25,26,27,28)/t22-/m0/s1
Release date: 2023-06-21
Crystal structure of 1-hydroxy-5-methylpyridine-2(1H)-thione bound to human carbonic anhydrase II (PDB entry 4Q7V)
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): 1.6
R work: 0.16728
R free: 0.21171
Average B factor: 11.924
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 8
Crystallization temperature (K): 291
Crystal growth procedure: Ammonium sulfate, pH 8.0, VAPOR DIFFUSION, temperature 291K
Matthews coefficient: 2.05
Solvent content (%): 40
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: 2015-03-11