satarupa22/MacromolecularLigandDB huggingface dataset:
BACE-1 in complex with compound #6 (PDB entry 7MYI)
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): 1.25
R work: 0.1398
R free: 0.1657
Average B factor: 16.304
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 100 mM sodium cacodylate pH 7.4, 12% PEG 8K, 200 mM ammonium sulfate
Matthews coefficient: 2.59
Solvent content (%): 52.46
Ligand: (4aR,7aR)-6-(pyrimidin-2-yl)-7a-(thiophen-2-yl)-4,4a,5,6,7,7a-hexahydropyrrolo[3,4-d][1,3]thiazin-2-amine (ZQS)
Ligand formula: C14 H15 N5 S2
Ligand molecular weight: 317.432
Ligand SMILES: c1cc(sc1)C23CN(CC2CSC(=N3)N)c4ncccn4
Ligand InChI: InChI=1S/C14H15N5S2/c15-12-18-14(11-3-1-6-20-11)9-19(7-10(14)8-21-12)13-16-4-2-5-17-13/h1-6,10H,7-9H2,(H2,15,18)/t10-,14-/m0/s1
Release date: 2021-07-21
Crystal structure of carbonic anhydrase 2 with (3aR,4S,9bS)-4-(2-chloro-4-hydroxyphenyl)-3a,4,5,9b-tetrahydro-3H-cyclopenta[c]quinoline-8-sulfonamide (PDB entry 6SYB)
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: 0.1736
R free: 0.2164
Average B factor: 15.799
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8
Crystallization temperature (K): 296
Crystal growth procedure: 1.5 M sodium citrate, 50 mM Tris pH 8.0
Matthews coefficient: 2.08
Solvent content (%): 40.8
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: 2020-10-07
Crystal structure of human exonuclease 1 Exo1 (WT) in complex with 5' recessed-end DNA (rIX) (PDB entry 5V0B)
Macromolecule: Exonuclease 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1
Sequence length: 358 residues
Sequence: MGIQGLLQFIKEASEPIHVRKYKGQVVAVDTYCWLHKGAIACAEKLAKGEPTDRYVGFCMKFVNMLLSHGIKPILVFDGCTLPSKKEVERSRRERRQANLLKGKQLLREGKVSEARECFTRSINITHAMAHKVIKAARSQGVDCLVAPYEADAQLAYLNKAGIVQAIITEDSDLLAFGCKKVILKMDQFGNGLEIDQARLGMCRQLGDVFTEEKFRYMCILSGCDYLSSLRGIGLAKACKVLRLANNPDIVKVIKKIGHYLKMNITVPEDYINGFIRANNTFLYQLVFDPIKRKLIPLNAYEDDVDPETLSYAGQYVDDSIALQIALGNKDINTFEQIDDYNPDTAMPAHSRENLYFQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.63
R work: 0.207
R free: 0.251
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 290
Crystal growth procedure: 100 mM sodium acetate, pH 7.0, 10 mM potassium chloride, 2-4% PEG4000
Matthews coefficient: 2.63
Solvent content (%): 53.15
Ligand: MANGANESE (II) ION (MN)
Ligand formula: Mn
Ligand molecular weight: 54.938
Ligand SMILES: [Mn+2]
Ligand InChI: InChI=1S/Mn/q+2
Release date: 2017-05-24
Distinct mechanism of MUL1-RING domain simultaneously recruiting E2 enzyme and the substrate p53-TAD domain (PDB entry 6M2C)
Macromolecule: Ubiquitin-conjugating enzyme E2 D2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2.23
Sequence length: 149 residues
Sequence: GSMALKRIHKELNDLARDPPAQCSAGPVGDDMFHWQATIMGPNDSPYQGGVFFLTIHFPTDYPFKPPKVAFTTRIYHPNINSNGSICLDILRSQWSPALTISKVLLSICSLLCDPNPDDPLVPEIARIYKTDREKYNRIAREWTQKYAM
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.702
R work: 0.2116
R free: 0.2583
Average B factor: 41.6533
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6
Crystallization temperature (K): 291
Crystal growth procedure: 4% v/v Tacsimate pH 6.0, 12% w/v Polyethylene glycol 3350
Matthews coefficient: 2.38
Solvent content (%): 48.39
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: 2021-04-07
Human LanCL1 bound to GSH (PDB entry 8D19)
Macromolecule: Glutathione S-transferase LANCL1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.5.1.18
Sequence length: 419 residues
Sequence: MGSSHHHHHHSSGLVPRGSHMAQRAFPNPYADYNKSLAEGYFDAAGRLTPEFSQRLTNKIRELLQQMERGLKSADPRDGTGYTGWAGIAVLYLHLYDVFGDPAYLQLAHGYVKQSLNCLTKRSITFLCGDAGPLAVAAVLYHKMNNEKQAEDCITRLIHLNKIDPHAPNEMLYGRIGYIYALLFVNKNFGVEKIPQSHIQQICETILTSGENLARKRNFTAKSPLMYEWYQEYYVGAAHGLAGIYYYLMQPSLQVSQGKLHSLVKPSVDYVCQLKFPSGNYPPCIGDNRDLLVHWCHGAPGVIYMLIQAYKVFREEKYLCDAYQCADVIWQYGLLKKGYGLCHGSAGNAYAFLTLYNLTQDMKYLYRACKFAEWCLEYGEHGCRTPDTPFSLFEGMAGTIYFLADLLVPTKARFPAFEL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.52
R work: 0.17214
R free: 0.19231
Average B factor: 21.88
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 282.15
Crystal growth procedure: 0.7-0.75 M succinic acid pH 7.0, 0.1 M bis-tris propane pH 7.0
Matthews coefficient: 2.53
Solvent content (%): 51.35
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: 2023-01-25
CRYSTAL STRUCTURE OF MYELOPEROXIDASE SUBFORM C (MPO) COMPLEX WITH Compound-12 (AKA; 7-benzyl-1H-[1,2,3]triazolo[4,5-b]pyrid (PDB entry 6WYD)
Macromolecule: Myeloperoxidase light chain
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.11.2.2
Sequence length: 105 residues
Sequence: CPEQDKYRTITGMCNNRRSPTLGASNRAFVRWLPAEYEDGFSLPYGWTPGVKRNGFPVALARAVSNEIVRFPTDQLTPDQERSLMFMQWGQLLDHDLDFTPEPAA
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.55
R work: 0.1935
R free: 0.2539
Average B factor: 50.55
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 296
Crystal growth procedure: 0.1M Hepes pH 7.5, 150mM NaCl, 20-25%(V/V)PEG3350.Crystals were cryoprotected by supplementing the mother liquor with 15% (v/v) ethylene glycol and harvested by flash-cooling in liquid nitrogen
Matthews coefficient: 2.39
Solvent content (%): 48.64
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: 2020-10-14
Crystal structure of CK2a1 with hematein (PDB entry 6L1Z)
Macromolecule: Casein Kinase 2 subunit alpha
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 340 residues
Sequence: GPLGSMSGPVPSRARVYTDVNTHRPREYWDYESHVVEWGNQDDYQLVRKLGRGKYSEVFEAINITNNEKVVVKILKPVKKKKIKREIKILENLRGGPNIITLADIVKDPVSRTPALVFEHVNNTDFKQLYQTLTDYDIRFYMYEILKALDYCHSMGIMHRDVKPHNVMIDHEHRKLRLIDWGLAEFYHPGQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRKEPFFHGHDNYDQLVRIAKVLGTEDLYDYIDKYNIELDPRFNDILGRHSRKRWERFVHSENQHLVSPEALDFLDKLLRYDHQSRLTAREAMEHPYFYTVVKDQARMG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.90820949507
R work: 0.194197591942
R free: 0.21629499244
Average B factor: 29.6611674599
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277
Crystal growth procedure: Ethylene Glycol
Matthews coefficient: 2
Solvent content (%): 38.61
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
Human carbonic anhydrase II in complex with pioglitazone (PDB entry 7M26)
Macromolecule: Carbonic anhydrase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 258 residues
Sequence: HHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHAFNVEFDDSQDKAVLKGGPLDGTYRLIQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDFGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTKGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLLECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.3
R work: 0.1187
R free: 0.1454
Average B factor: 13.912
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.3
Crystallization temperature (K): 293
Crystal growth procedure: Protein concentration was 4 mg/mL; equal volumes (250 nL) of protein plus reservoir were added to the plate; the reservoir was 1.5 M tri-potassium citrate, 0.1 M tris buffer at pH 8.3.
Matthews coefficient: 2.11
Solvent content (%): 41.67
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: 2022-02-02
Crystal structure of IRE1a in complex with G-6904 (PDB entry 6XDB)
Macromolecule: Serine/threonine-protein kinase/endoribonuclease IRE1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 434 residues
Sequence: GSSPSLEQDDGDEETSVVIVGKISFCPKDVLGHGAEGTIVYRGMFDNRDVAVKRILPECFSFADREVQLLRESDEHPNVIRYFCTEKDRQFQYIAIELCAATLQEYVEQKDFAHLGLEPITLLQQTTSGLAHLHSLNIVHRNLKPHNILISMPNAHGKIKAMISDFGLCKKLAVGRHSFSRRSGVPGTEGWIAPEMLSEDCKENPTYTVDIFSAGCVFYYVISEGSHPFGKSLQRQANILLGACSLDCLHPEKHEDVIARELIEKMIAMDPQKRPSAKHVLKHPFFWSLEKQLQFFQDVSDRIEKESLDGPIVKQLERGGRAVVKMDWRENITVPLQTDLRKFRTYKGGSVRDLLRAMRNKKHHYRELPAEVRETLGSLPDDFVCYFTSRFPHLLAHTYRAMELCSHERLFQPYYFHEPPEPQPPVTPDALGNS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.45
R work: 0.193
R free: 0.2274
Average B factor: 79.0287
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 0.1 M Hepes pH 7.5, 42% PEG200, 1 M Lithium chloride, 3% w/v 6-Aminohexanoic acid
Matthews coefficient: 2.97
Solvent content (%): 58.52
Ligand: 4-amino-N-(6-chloro-2-fluoro-3-{[(2-fluorophenyl)sulfonyl]amino}phenyl)-6-(1,3-dimethyl-1H-pyrazol-4-yl)quinazoline-8-carboxamide (N8S)
Ligand formula: C26 H20 Cl F2 N7 O3 S
Ligand molecular weight: 583.997
Ligand SMILES: Cc1c(cn(n1)C)c2cc3c(c(c2)C(=O)Nc4c(ccc(c4F)NS(=O)(=O)c5ccccc5F)Cl)ncnc3N
Ligand InChI: InChI=1S/C26H20ClF2N7O3S/c1-13-17(11-36(2)34-13)14-9-15-23(31-12-32-25(15)30)16(10-14)26(37)33-24-18(27)7-8-20(22(24)29)35-40(38,39)21-6-4-3-5-19(21)28/h3-12,35H,1-2H3,(H,33,37)(H2,30,31,32)
Release date: 2021-04-21
Crystal structure of human Ube2T E54R mutant (PDB entry 6R75)
Macromolecule: Ubiquitin-conjugating enzyme E2 T
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2.23
Sequence length: 201 residues
Sequence: GPGSMQRASRLKRELHMLATEPPPGITCWQDKDQMDDLRAQILGGANTPYEKGVFKLRVIIPERYPFEPPQIRFLTPIYHPNIDSAGRICLDVLKLPPKGAWRPSLNIATVLTSIQLLMSEPNPDDPLMADISSEFKYNKPAFLKNARQWTEKHARQKQKADEEEMLDNLPEAGDSRVHNSTQKRKASQLVGIEKKFHPDV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2
R work: 0.2252
R free: 0.2644
Average B factor: 24.326
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 0.1 M Tris-HCl pH 8.5, 20% v/v glycerol ethoxylate, 3% v/v poly(ethylene imine)
Matthews coefficient: 2.21
Solvent content (%): 44.35
Release date: 2019-10-16
Crystal structure of KRAS-G12D bound to GDP with switch 1 open conformation (PDB entry 7F0W)
Macromolecule: Isoform 2B of GTPase KRas
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.5.2
Sequence length: 169 residues
Sequence: STEYKLVVVGADGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKCDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQGVDDAFYTLVREIRKHKEK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.39
R work: 0.1708
R free: 0.1896
Average B factor: 23.36
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.8
Crystallization temperature (K): 298
Crystal growth procedure: 1.0 M sodium citrate, 0.1M Tris pH 7.0, 0.2M NaCl
Matthews coefficient: 2.57
Solvent content (%): 52.09
Ligand: GUANOSINE-5'-DIPHOSPHATE (GDP)
Ligand formula: C10 H15 N5 O11 P2
Ligand molecular weight: 443.201
Ligand SMILES: c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
Ligand InChI: InChI=1S/C10H15N5O11P2/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(25-9)1-24-28(22,23)26-27(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1
Release date: 2021-06-23
Crystal structure of human Pim-1 kinase in complex with a consensuspeptide and fragment like molekule N-quinolin-5-ylpyridine-3-carboxamide (PDB entry 5MZL)
Macromolecule: Serine/threonine-protein kinase pim-1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 313 residues
Sequence: MLLSKINSLAHLRAAPCNDLHATKLAPGKEKEPLESQYQVGPLLGSGGFGSVYSGIRVSDNLPVAIKHVEKDRISDWGELPNGTRVPMEVVLLKKVSSGFSGVIRLLDWFERPDSFVLILERPEPVQDLFDFITERGALQEELARSFFWQVLEAVRHCHNCGVLHRDIKDENILIDLNRGELKLIDFGSGALLKDTVYTDFDGTRVYSPPEWIRYHRYHGRSAAVWSLGILLYDMVCGDIPFEHDEEIIGGQVFFRQRVSSECQHLIRWCLALRPSDRPTFEEIQNHPWMQDVLLPQETAEIHLHSLSPGPSK
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.955
R work: 0.157
R free: 0.1834
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 277
Crystal growth procedure: HEPES
NaCl
Glycerol
DTT
BIS-TRIS-propane
PEG3350
Ethylene-glycol
DMSO
Matthews coefficient: 3.1
Solvent content (%): 60.29
Ligand: ~{N}-quinolin-5-ylpyridine-3-carboxamide (8ET)
Ligand formula: C15 H11 N3 O
Ligand molecular weight: 249.267
Ligand SMILES: c1cc2c(cccn2)c(c1)NC(=O)c3cccnc3
Ligand InChI: InChI=1S/C15H11N3O/c19-15(11-4-2-8-16-10-11)18-14-7-1-6-13-12(14)5-3-9-17-13/h1-10H,(H,18,19)
Release date: 2018-02-14
Human DNMT1(729-1600) Bound to Zebularine-Containing 12mer dsDNA (PDB entry 6X9I)
Macromolecule: DNA (cytosine-5)-methyltransferase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1.37
Sequence length: 874 residues
Sequence: HMNRISWVGEAVKTDGKKSYYKKVCIDAETLEVGDCVSVIPDDSSKPLYLARVTALWEDSSNGQMFHAHWFCAGTDTVLGATSDPLELFLVDECEDMQLSYIHSKVKVIYKAPSENWAMEGGMDPESLLEGDDGKTYFYQLWYDQDYARFESPPKTQPTEDNKFKFCVSCARLAEMRQKEIPRVLEQLEDLDSRVLYYSATKNGILYRVGDGVYLPPEAFTFNIKLSSPVKRPRKEPVDEDLYPEHYRKYSDYIKGSNLDAPEPYRIGRIKEIFCPKKSNGRPNETDIKIRVNKFYRPENTHKSTPASYHADINLLYWSDEEAVVDFKAVQGRCTVEYGEDLPECVQVYSMGGPNRFYFLEAYNAKSKSFEDPPNHARSPGNKGKGKGKGKGKPKSQACEPSEPEIEIKLPKLRTLDVFSGCGGLSEGFHQAGISDTLWAIEMWDPAAQAFRLNNPGSTVFTEDCNILLKLVMAGETTNSRGQRLPQKGDVEMLCGGPPCQGFSGMNRFNSRTYSKFKNSLVVSFLSYCDYYRPRFFLLENVRNFVSFKRSMVLKLTLRCLVRMGYQCTFGVLQAGQYGVAQTRRRAIILAAAPGEKLPLFPEPLHVFAPRACQLSVVVDDKKFVSNITRLSSGPFRTITVRDTMSDLPEVRNGASALEISYNGEPQSWFQRQLRGAQYQPILRDHICKDMSALVAARMRHIPLAPGSDWRDLPNIEVRLSDGTMARKLRYTHHDRKNGRSSSGALRGVCSCVEAGKACDPAARQFNTLIPWCLPHTGNRHNHWAGLYGRLEWDGFFSTTVTNPEPMGKQGRVLHPEQHRVVSVRECARSQGFPDTYRLFGNILDKHRQVGNAVPPPLAKAIGLEIKLCMLAKA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.2
R work: 0.1939
R free: 0.2252
Average B factor: 70.81
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.1
Crystallization temperature (K): 292
Crystal growth procedure: 14-18% polyethylene glycol (PEG) 3350, 0.1 M citric acid (pH 5.1)
Matthews coefficient: 2.96
Solvent content (%): 58.43
Ligand: S-ADENOSYL-L-HOMOCYSTEINE (SAH)
Ligand formula: C14 H20 N6 O5 S
Ligand molecular weight: 384.411
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)CSCCC(C(=O)O)N)O)O)N
Ligand InChI: InChI=1S/C14H20N6O5S/c15-6(14(23)24)1-2-26-3-7-9(21)10(22)13(25-7)20-5-19-8-11(16)17-4-18-12(8)20/h4-7,9-10,13,21-22H,1-3,15H2,(H,23,24)(H2,16,17,18)/t6-,7+,9+,10+,13+/m0/s1
Release date: 2021-07-07
Bruton's tyrosine kinase in complex with 5-(piperidin-1-yl)-3-{[4-(piperidin-4-yl)phenyl]amino}pyrazine-2-carboxamide (PDB entry 8GC7)
Macromolecule: Tyrosine-protein kinase BTK
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 270 residues
Sequence: GLGYGSWEIDPKDLTFLKELGTGQFGVVKYGKWRGQYDVAIKMIKEGSMSEDEFIEEAKVMMNLSHEKLVQLYGVCTKQRPIFIITEYMANGCLLNYLREMRHRFQTQQLLEMCKDVCEAMEYLESKQFLHRDLAARNCLVNDQGVVKVSDFGLSRYVLDDEYTSSVGSKFPVRWSPPEVLMYSKFSSKSDIWAFGVLMWEIYSLGKMPYERFTNSETAEHIAQGLRLYRPHLASEKVYTIMYSCWHEKADERPTFKILLSNILDVMDEE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.9
R work: 0.192
R free: 0.2269
Average B factor: 12.92
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.06 M Magnesium chloride hexahydrate,
0.06 M Calcium chloride dihydrate, 0.1M Imidazole, 0.1M MES monohydrate, 24% v/v PEG 500 MME, 12 % w/v PEG 20000, pH 6.5
Matthews coefficient: 2.41
Solvent content (%): 48.94
Ligand: 5-(piperidin-1-yl)-3-[4-(piperidin-4-yl)anilino]pyrazine-2-carboxamide (YXJ)
Ligand formula: C21 H28 N6 O
Ligand molecular weight: 380.487
Ligand SMILES: c1cc(ccc1C2CCNCC2)Nc3c(ncc(n3)N4CCCCC4)C(=O)N
Ligand InChI: InChI=1S/C21H28N6O/c22-20(28)19-21(26-18(14-24-19)27-12-2-1-3-13-27)25-17-6-4-15(5-7-17)16-8-10-23-11-9-16/h4-7,14,16,23H,1-3,8-13H2,(H2,22,28)(H,25,26)
Release date: 2024-01-31
Structure of MAP kinase phosphatase 5 in complex with 3,3-dimethyl-1-((5,6-dihydropyrido[2,3-h]quinazolin-2-yl)thio)butan-2-one, an allosteric inhibitor (PDB entry 7UMV)
Macromolecule: Dual specificity protein phosphatase 10
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.16
Sequence length: 152 residues
Sequence: GSHMAELTPILPFLFLGNEQDAQDLDTMQRLNIGYVINVTTHLPLYHYEKGLFNYKRLPATDSNKQNLRQYFEEAFEFIEEAHQCGKGLLIHCQAGVSRSATIVIAYLMKHTRMTMTDAYKFVKGKRPIISPNLNFMGQLLEFEEDLNNGVT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.1543
R free: 0.172
Average B factor: 33.66
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 100 mM Tris, pH 7.5, 200 mM ammonium acetate, 40% w/v PEG3350
Matthews coefficient: 4.37
Solvent content (%): 71.87
Ligand: 1-{[(10aP)-5,6-dihydropyrido[2,3-h]quinazolin-2-yl]sulfanyl}-3,3-dimethylbutan-2-one (NUU)
Ligand formula: C17 H19 N3 O S
Ligand molecular weight: 313.417
Ligand SMILES: CC(C)(C)C(=O)CSc1ncc2c(n1)-c3cccnc3CC2
Ligand InChI: InChI=1S/C17H19N3OS/c1-17(2,3)14(21)10-22-16-19-9-11-6-7-13-12(15(11)20-16)5-4-8-18-13/h4-5,8-9H,6-7,10H2,1-3H3
Release date: 2022-10-05
CREBBP Bromodomain in complex with Cpd10 (1-(3-(7-(difluoromethyl)-6-(1-methyl-1H-pyrazol-4-yl)-3,4-dihydroquinolin-1(2H)-yl)-1-(tetrahydro-2H-pyran-4-yl)-1,4,6,7-tetrahydro-5H-pyrazolo[4,3-c]pyridin-5-yl)ethan-1-one) (PDB entry 5W0L)
Macromolecule: CREB-binding protein
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1.48
Sequence length: 148 residues
Sequence: MHHHHHHGSLVPRGSMDYKDDDDKENLYFQGSKKIFKPEELRQALMPTLEALYRQDPESLPFRQPVDPQLLGIPDYFDIVKNPMDLSTIKRKLDTGQYQEPWQYVDDVWLMFNNAWLYNRKTSRVYKFCSKLAEVFEQEIDPVMQSLG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.549
R work: 0.1925
R free: 0.2294
Average B factor: 23.0636
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 6.5
Crystallization temperature (K): 277
Crystal growth procedure: 100 mM Bis-Tris pH 5.5, 200-300 mM KSCN, 21-25% PEG 3350
Matthews coefficient: 1.94
Solvent content (%): 36.58
Ligand: 1-{3-[7-(difluoromethyl)-6-(1-methyl-1H-pyrazol-4-yl)-3,4-dihydroquinolin-1(2H)-yl]-1-(oxan-4-yl)-1,4,6,7-tetrahydro-5H-pyrazolo[4,3-c]pyridin-5-yl}ethan-1-one (9UD)
Ligand formula: C27 H32 F2 N6 O2
Ligand molecular weight: 510.579
Ligand SMILES: CC(=O)N1CCc2c(c(nn2C3CCOCC3)N4CCCc5c4cc(c(c5)c6cnn(c6)C)C(F)F)C1
Ligand InChI: InChI=1S/C27H32F2N6O2/c1-17(36)33-9-5-24-23(16-33)27(31-35(24)20-6-10-37-11-7-20)34-8-3-4-18-12-21(19-14-30-32(2)15-19)22(26(28)29)13-25(18)34/h12-15,20,26H,3-11,16H2,1-2H3
Release date: 2018-03-07
Crystal structure of human wild type beta-1,4-galactosyltransferase-1 (B4GalT1) in apo-open monomeric form (PDB entry 6FWT)
Macromolecule: Beta-1,4-galactosyltransferase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.4.1
Sequence length: 277 residues
Sequence: TTALSLPACPEESPLLVGPMLIEFNMPVDLELVAKQNPNVKMGGRYAPRDCVSPHKVAIIIPFRNRQEHLKYWLYYLHPVLQRQQLDYGIYVINQAGDTIFNRAKLLNVGFQEALKDYDYTCFVFSDVDLIPMNDHNAYRCFSQPRHISVAMDKFGFSLPYVQYFGGVSALSKQQFLTINGFPNNYWGWGGEDDDIFNRLVFRGMSISRPNAVVGRCRMIRHSRDKKNEPNPQRFDRIAHTKETMLSDGLNSLTYQVLDVQRYPLYTQITVDIGTPS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.845
R work: 0.1659
R free: 0.218
Average B factor: 31.11
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.2 M Potassium Nitrate, 20% (w/v) PEG 3350
Matthews coefficient: 2.09
Solvent content (%): 41.19
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: 2018-10-10
p38a bound with SR348 (PDB entry 6ZWP)
Macromolecule: Mitogen-activated protein kinase 14
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.24
Sequence length: 361 residues
Sequence: GMSQERPTFYRQELNKTIWEVPERYQNLSPVGSGAYGSVCAAFDTKTGHRVAVKKLSRPFQSIIHAKRTYRELRLLKHMKHENVIGLLDVFTPARSLEEFNDVYLVTHLMGADLNNIVKCQKLTDDHVQFLIYQILRGLKYIHSADIIHRDLKPSNLAVNEDCELKILDFGLARHTDDEMTGYVATRWYRAPEIMLNWMHYNQTVDIWSVGCIMAELLTGRTLFPGTDHIDQLKLILRLVGTPGAELLKKISSESARNYIQSLAQMPKMNFANVFIGANPLAVDLLEKMLVLDSDKRITAAQALAHAYFAQYHDPDDEPVADPYDQSFESRDLLIDEWKSLTYDEVISFVPPPLDQEEMES
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.9
R work: 0.213
R free: 0.2511
Average B factor: 46.639
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.8
Crystallization temperature (K): 278
Crystal growth procedure: 15% MMW PegSmear
0.1 M MES
Matthews coefficient: 2.21
Solvent content (%): 44.23
Ligand: 5-azanyl-~{N}-[[4-[[(2~{S})-4-cyclohexyl-1-[(4-fluorophenyl)amino]-1-oxidanylidene-butan-2-yl]carbamoyl]phenyl]methyl]-1-phenyl-pyrazole-4-carboxamide (OE8)
Ligand formula: C34 H37 F N6 O3
Ligand molecular weight: 596.694
Ligand SMILES: c1ccc(cc1)n2c(c(cn2)C(=O)NCc3ccc(cc3)C(=O)NC(CCC4CCCCC4)C(=O)Nc5ccc(cc5)F)N
Ligand InChI: InChI=1S/C34H37FN6O3/c35-26-16-18-27(19-17-26)39-34(44)30(20-13-23-7-3-1-4-8-23)40-32(42)25-14-11-24(12-15-25)21-37-33(43)29-22-38-41(31(29)36)28-9-5-2-6-10-28/h2,5-6,9-12,14-19,22-23,30H,1,3-4,7-8,13,20-21,36H2,(H,37,43)(H,39,44)(H,40,42)/t30-/m0/s1
Release date: 2020-08-12