satarupa22/MacromolecularLigandDB huggingface dataset:
Human CD73 (ecto 5'-nucleotidase) in complex with compound 35 (PDB entry 7JV8)
Macromolecule: 5'-nucleotidase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.5
Sequence length: 529 residues
Sequence: LASMWELTILHTNDVHSRLEQTSEDSSKCVDASRCMGGVARLFTKVQQIRRAEPNVLLLDAGDQYQGTIWFTVYKGAEVAHFMNALRYDAMALGNHEFDNGVEGLIEPLLKEAKFPILSANIKAKGPLASQISGLYLPYKVLPVGDEVVGIVGYTSKETPFLSNPGTNLVFEDEITALQPEVDKLKTLNVNKIIALGHSGFEMDKLIAQKVRGVDVVVGGHSNTFLYTGNPPSKEVPAGKYPFIVTSDDGRKVPVVQAYAFGKYLGYLKIEFDERGNVISSHGNPILLNSSIPEDPSIKADINKWRIKLDDYSTQELGKTIVYLDGSSQSCRFRECNMGNLICDAMINNNLRHTDEMFWNHVSMCILNGGGIRSPIDERNDGTITWENLAAVLPFGGTFDLVQLKGSTLKKAFEHSVHRYGQSTGEFLQVGGIHVVYDLSRKPGDRVVKLDVLCTKCRVPSYDPLKMDEVYKVILPNFLANGGDGFQMIKDELLRHDSGDQDINVVSTYISKMKVIYPAVEGRIKFSHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.46
R work: 0.2203
R free: 0.279
Average B factor: 45.205
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 4
Crystallization temperature (K): 277.15
Crystal growth procedure: 0.10M SPG (Succinic Acid, Sodium Dihydrogen Phosphate and Glycine) pH=4.00, 19.00 %w/v PEG 1500
Matthews coefficient: 2.4
Solvent content (%): 48.82
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: 2020-09-23
ROCK1 IN COMPLEX WITH LIGAND G4998 (PDB entry 7S25)
Macromolecule: Rho-associated protein kinase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 396 residues
Sequence: FETRFEKMDNLLRDPKSEVNSDCLLDGLDALVYDLDFPALRKNKNIDNFLSRYKDTINKIRDLRMKAEDYEVVKVIGRGAFGEVQLVRHKSTRKVYAMKLLSKFEMIKRSDSAFFWEERDIMAFANSPWVVQLFYAFQDDRYLYMVMEYMPGGDLVNLMSNYDVPEKWARFYTAEVVLALDAIHSMGFIHRDVKPDNMLLDKSGHLKLADFGTCMKMNKEGMVRCDTAVGTPDYISPEVLKSQGGDGYYGRECDWWSVGVFLYEMLVGDTPFYADSLVGTYSKIMNHKNSLTFPDDNDISKEAKNLICAFLTDREVRLGRNGVEEIKRHLFFKNDQWAWETLRDTVAPVVPDLSSDIDTSNFDDLEEDKGEEETFPIPKAFVGNQLPFVGFTYYSN
Oligomeric state: Homo 2-mer
Stoichiometry: A2
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.337
R work: 0.2394
R free: 0.2706
Average B factor: 95.04
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: 15-17% PEG 5K MME, 0.1 M HEPES/NaOH pH 7.5, 5% (v/v) tacsimate pH 7.5
Matthews coefficient: 2.85
Solvent content (%): 56.92
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: 2022-10-05
Crystal Structure of human phosphodiesterase 10 in complex with 6-cyclopropyl-N-[2-[2-(dimethylamino)ethyl]-5-pyridin-2-ylpyrazol-3-yl]-3-(pyrimidin-5-ylamino)pyridine-2-carboxamide (PDB entry 5SF4)
Macromolecule: cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.4.17
Sequence length: 343 residues
Sequence: GSSICTSEEWQGLMQFTLPVRLCKEIELFHFDIGPFENMWPGIFVYMVHRSCGTSCFELEKLCRFIMSVKKNYRRVPYHNWKHAVTVAHCMYAILQNNHTLFTDLERKGLLIACLCHDLDHRGFSNSYLQKFDHPLAALYSTSTMEQHHFSQTVSILQLEGHNIFSTLSSSEYEQVLEIIRKAIIATDLALYFGNRKQLEEMYQTGSLNLNNQSHRDRVIGLMMTACDLCSVTKLWPVTKLTANDIYAEFWAEGDEMKKLGIQPIPMMDRDKKDEVPQGQLGFYNAVAIPCYTTLTQILPPTEPLLKACRDNLSQWEKVIRGEETATWISSPSVAQKAAASED
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.25
R work: 0.1847
R free: 0.2345
Average B factor: 40.878
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 295
Crystal growth procedure: 5-20 mg/mL protein in 25mM HEPES/NaOH pH7.5, 150mM NaCl, 50mM BME mixed 1:1 with reservoir 0.1M HEPES/NaOH pH7.5, 30% PEG550MME, 50mM MgCl2
Matthews coefficient: 2.59
Solvent content (%): 52.52
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: 2022-10-12
Crystal structure of a TCR in complex with HLA-A*11:01 bound to KRAS peptide (VVVGAGGVGK) (PDB entry 7OW5)
Macromolecule: MHC class I antigen
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 276 residues
Sequence: GSHSMRYFYTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEYWDQETRNVKAQSQTDRVDLGTLRGYYNQSEDGSHTIQIMYGCDVGPDGRFLRGYRQDAYDGKDYIALNEDLRSWTAADMAAQITKRKWEAAHAAEQQRAYLEGRCVEWLRRYLENGKETLQRTDPPKTHMTHHPISDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDGTFQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRWEP
Oligomeric state: Hetero 5-mer
Stoichiometry: A1, B1, C1, D1, E1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.58
R work: 0.20595
R free: 0.27356
Average B factor: 88.001
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.2 M Ammonium citrate tribasic pH 7.0, 20% w/v PEG 3350
Matthews coefficient: 3.36
Solvent content (%): 63.35
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: 2022-07-20
FKBP12 in complex with the BMP potentiator compound 6 at 1.03A resolution (PDB entry 6YF2)
Macromolecule: Peptidyl-prolyl cis-trans isomerase FKBP1A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 5.2.1.8
Sequence length: 109 residues
Sequence: GPGVQVETISPGDGRTFPKRGQTCVVHYTGMLEDGKKFDSSRDRNKPFKFMLGKQEVIRGWEEGVAQMSVGQRAKLTISPDYAYGATGHPGIIPPHATLVFDVELLKLE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.03
R work: 0.1409
R free: 0.1488
Average B factor: 10.47
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 298
Crystal growth procedure: 1.9 M AmSO4, 0.15 M CdCl2
Matthews coefficient: 1.88
Solvent content (%): 34.44
Ligand: (1~{R},9~{S},12~{S},13~{R},14~{S},17~{R},18~{E},21~{S},23~{S},24~{R},25~{S},27~{R})-23,25-dimethoxy-12-[(~{E})-1-[(1~{R},3~{R},4~{R})-3-methoxy-4-oxidanyl-cyclohexyl]prop-1-en-2-yl]-13,19,21,27-tetramethyl-1,14-bis(oxidanyl)-17-(2-oxidanylidenepropyl)-11,28-dioxa-4-azatricyclo[22.3.1.0^{4,9}]octacos-18-ene-2,3,10,16-tetrone (OP5)
Ligand formula: C44 H69 N O13
Ligand molecular weight: 820.018
Ligand SMILES: CC1CC(C2C(CC(C(O2)(C(=O)C(=O)N3CCCCC3C(=O)OC(C(C(CC(=O)C(C=C(C1)C)CC(=O)C)O)C)C(=CC4CCC(C(C4)OC)O)C)O)C)OC)OC
Ligand InChI: InChI=1S/C44H69NO13/c1-24-16-25(2)18-37(55-8)40-38(56-9)20-27(4)44(53,58-40)41(50)42(51)45-15-11-10-12-32(45)43(52)57-39(26(3)19-30-13-14-33(47)36(22-30)54-7)29(6)34(48)23-35(49)31(17-24)21-28(5)46/h17,19,25,27,29-34,36-40,47-48,53H,10-16,18,20-23H2,1-9H3/b24-17+,26-19+/t25-,27+,29+,30-,31-,32-,33+,34-,36+,37-,38-,39+,40+,44+/m0/s1
Release date: 2021-03-10
The structure of cyclin-dependent kinase 5 (CDK5) in complex with p25 and Compound 13 (PDB entry 7VDR)
Macromolecule: Cyclin-dependent-like kinase 5
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 292 residues
Sequence: SQKYEKLEKIGEGTYGTVFKAKNRETHEIVALKRVRLDDDDEGVPSSALREICLLKELKHKNIVRLHDVLHSDKKLTLVFEFCDQDLKKYFDSCNGDLDPEIVKSFLFQLLKGLGFCHSRNVLHRDLKPQNLLINRNGELKLADFGLARAFGIPVRCYSAEVVTLWYRPPDVLFGAKLYSTSIDMWSAGCIFAELANAGRPLFPGNDVDDQLKRIFRLLGTPTEEQWPSMTKLPDYKPYPMYPATTSLVNVVPKLNATGRDLLQNLLKCNPVQRISAEEALQHPYFSDFCPP
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.55
R work: 0.2188
R free: 0.2558
Average B factor: 78.045
Crystallization method: EVAPORATION
Crystallization pH: 5.5
Crystallization temperature (K): 291
Crystal growth procedure: 0.1M MES pH 5.5, 0.3M MgCl2, 20% PEG3350
Matthews coefficient: 2.74
Solvent content (%): 55.12
Ligand: (1R)-1-[7-[(2-fluoranyl-4-pyrazol-1-yl-phenyl)amino]-1,6-naphthyridin-2-yl]-1-(1-methylpiperidin-4-yl)ethanol (63I)
Ligand formula: C25 H27 F N6 O
Ligand molecular weight: 446.52
Ligand SMILES: CC(c1ccc2cnc(cc2n1)Nc3ccc(cc3F)n4cccn4)(C5CCN(CC5)C)O
Ligand InChI: InChI=1S/C25H27FN6O/c1-25(33,18-8-12-31(2)13-9-18)23-7-4-17-16-27-24(15-22(17)29-23)30-21-6-5-19(14-20(21)26)32-11-3-10-28-32/h3-7,10-11,14-16,18,33H,8-9,12-13H2,1-2H3,(H,27,30)/t25-/m1/s1
Release date: 2022-03-09
Crystal structure of SmyD3 in complex with covalent inhibitor 5 (PDB entry 6IJL)
Macromolecule: Histone-lysine N-methyltransferase SMYD3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1.43
Sequence length: 428 residues
Sequence: MEPLKVEKFATANRGNGLRAVTPLRPGELLFRSDPLAYTVCKGSRGVVCDRCLLGKEKLMRCSQCRVAKYCSAKCQKKAWPDHKRECKCLKSCKPRYPPDSVRLLGRVVFKLMDGAPSESEKLYSFYDLESNINKLTEDRKEGLRQLVMTFQHFMREEIQDASQLPPAFDLFEAFAKVICNSFTICNAEMQEVGVGLYPSISLLNHSCDPNCSIVFNGPHLLLRAVRDIEVGEELTICYLDMLMTSEERRKQLRDQYCFECDCFRCQTQDKDADMLTGDEQVWKEVQESLKKIEELKAHWKWEQVLAMCQAIISSNSERLPDINIYQLKVLDCAMDACINLGLLEEALFYGTRTMEPYRIFFPGSHPVRGVQVMKVGKLQLHQGMFPQAMKNLRLAFDIMRVTHGREHSLIEDLILLLEECDANIRAS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.351
R work: 0.2809
R free: 0.316
Average B factor: 27.8926
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.2M Magnesium acetate, 17% PEG 3350
Matthews coefficient: 2.24
Solvent content (%): 45.08
Ligand: propyl (2~{R})-4-[2-[4-(1-azanylcyclopropyl)phenyl]quinolin-7-yl]carbonyl-2-methyl-piperazine-1-carboxylate (A8U)
Ligand formula: C28 H32 N4 O3
Ligand molecular weight: 472.579
Ligand SMILES: CCCOC(=O)N1CCN(CC1C)C(=O)c2ccc3ccc(nc3c2)c4ccc(cc4)C5(CC5)N
Ligand InChI: InChI=1S/C28H32N4O3/c1-3-16-35-27(34)32-15-14-31(18-19(32)2)26(33)22-5-4-21-8-11-24(30-25(21)17-22)20-6-9-23(10-7-20)28(29)12-13-28/h4-11,17,19H,3,12-16,18,29H2,1-2H3/t19-/m1/s1
Release date: 2019-08-14
Crystal structure of human Cathepsin-S with bound ligand (PDB entry 5QBX)
Macromolecule: Cathepsin S
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.22.27
Sequence length: 223 residues
Sequence: ILPDSVDWREKGCVTEVKYQGSCGASWAFSAVGALEAQLKLKTGKLVSLSAQNLVDCSTEKYGNKGCNGGFMTTAFQYIIDNKGIDSDASYPYKAMDQKCQYDSKYRAATCSKYTELPYGREDVLKEAVANKGPVSVGVDARHPSFFLYRSGVYYEPSCTQNVNHGVLVVGYGDLNGKEYWLVKNSWGHNFGEEGYIRMARNKGNHCGIASFPSYPEILQGGG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.1
R work: 0.188
R free: 0.227
Average B factor: 31.49
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 4.5
Crystallization temperature (K): 293
Crystal growth procedure: 100MM SODIUM ACETATE PH 4.5, 200MM AMMONIUM ACETATE, 25% PEG 8000. PROTEIN CONCENTRATION 7 MG/ML, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K
Matthews coefficient: 2.3
Solvent content (%): 46.5
Ligand: (2S)-1-[4-(2-methoxyphenyl)piperidin-1-yl]-3-{3-[3-{[2-(piperidin-1-yl)ethyl]sulfanyl}-4-(trifluoromethyl)phenyl]-4,5,6,7-tetrahydro-1H-pyrazolo[4,3-c]pyridin-1-yl}propan-2-ol (B8V)
Ligand formula: C35 H46 F3 N5 O2 S
Ligand molecular weight: 657.832
Ligand SMILES: COc1ccccc1C2CCN(CC2)CC(Cn3c4c(c(n3)c5ccc(c(c5)SCCN6CCCCC6)C(F)(F)F)CNCC4)O
Ligand InChI: InChI=1S/C35H46F3N5O2S/c1-45-32-8-4-3-7-28(32)25-12-17-42(18-13-25)23-27(44)24-43-31-11-14-39-22-29(31)34(40-43)26-9-10-30(35(36,37)38)33(21-26)46-20-19-41-15-5-2-6-16-41/h3-4,7-10,21,25,27,39,44H,2,5-6,11-20,22-24H2,1H3/t27-/m0/s1
Release date: 2017-12-20
Human Exonuclease 5 crystal structure (T88E) in complex with ssDNA and Mg (PDB entry 7LWA)
Macromolecule: Exonuclease V
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1
Sequence length: 346 residues
Sequence: SNALEDAQESKALVNMPGPSSESLGKDDKPISLQNWKRGLDILSPMERFHLKYLYVTDLAEQNWCELQTAYGKELPGFLAPEKAAVLDTGASIHLARELELHDLVTVPVTTKEDAWAIKFLNILLLIPTLQSEGHIREFPVFGEVEGVLLVGVIDELHYTAKGELELAELKTRRRPMLPLEAQKKKDCFQVSLYKYIFDAMVQGKVTPASLIHHTKLCLEKPLGPSVLRHAQQGGFSVKSLGDLMELVFLSLTLSDLPVIDILKIEYIHQETATVLGTEIVAFKEKEVRAKVQHYMAYWMGHREPQGVDVEEAWKCRTCTYADICEWRKGSGVLSSTLAPQVKKAK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.85
R work: 0.2034
R free: 0.2506
Average B factor: 54.254
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 20% PEG3350 and 0.1 M magnesium formate
Matthews coefficient: 2.39
Solvent content (%): 48.6
Ligand: IRON/SULFUR CLUSTER (SF4)
Ligand formula: Fe4 S4
Ligand molecular weight: 351.64
Ligand SMILES: [S]12[Fe]3[S]4[Fe]1[S]5[Fe]2[S]3[Fe]45
Ligand InChI: InChI=1S/4Fe.4S
Release date: 2021-07-14
Structure of the catalytic domain of tankyrase 1 in complex with olaparib (PDB entry 7KKO)
Macromolecule: Poly [ADP-ribose] polymerase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.4.2
Sequence length: 213 residues
Sequence: GSQGTILLDLAPEDKEYQSVEEEMQSTIREHRDGGNAGGIFNRYNVIRIQKVVNKKLRERFCHRQKEVSEENHNHHNERMLFHGSPFINAIIHKGFDERHAYIGGMFGAGIYFAENSSKSNQYVYGIGGGTGCPTHKDRSCYICHRQMLFCRVTLGKSFLQFSTMKMAHAPPGHHSVIGRPSVNGLAYAEYVIYRGEQAYPEYLITYQIMKPE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.56
R work: 0.194
R free: 0.221
Average B factor: 29.77
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 277
Crystal growth procedure: Salt: 0.4 M potassium acetate
Precipitant: 22.0 %w/v PEG 4000
Buffer: 0.1 M MES (pH 6.14)
Matthews coefficient: 2.45
Solvent content (%): 49.81
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: 2021-01-06
Crystal Structure of Thrombin in complex with compound17 (PDB entry 6ZUH)
Macromolecule: Prothrombin
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.5
Sequence length: 36 residues
Sequence: TFGSGEADCGLRPLFEKKSLEDKTERELLESYIDGR
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.7
R work: 0.1781
R free: 0.2178
Average B factor: 26.847
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 283
Crystal growth procedure: 0.02 M phosphate buffer pH 7.5, 
27% PEG 8000, 100 mM NaCl
Matthews coefficient: 2.52
Solvent content (%): 51.16
Ligand: [2-[(3-chlorophenyl)methylamino]-7-methoxy-1,3-benzoxazol-5-yl]-(2,2-dimethylmorpholin-4-yl)methanone (N6H)
Ligand formula: C22 H24 Cl N3 O4
Ligand molecular weight: 429.897
Ligand SMILES: CC1(CN(CCO1)C(=O)c2cc3c(c(c2)OC)oc(n3)NCc4cccc(c4)Cl)C
Ligand InChI: InChI=1S/C22H24ClN3O4/c1-22(2)13-26(7-8-29-22)20(27)15-10-17-19(18(11-15)28-3)30-21(25-17)24-12-14-5-4-6-16(23)9-14/h4-6,9-11H,7-8,12-13H2,1-3H3,(H,24,25)
Release date: 2020-08-26
Human Carbonic Anhydrase II (hCAII) in complex with (R)-N-(3-Indol-1-yl-2-methyl-propyl)-4-sulfamoyl-benzamide (PDB entry 8R1I)
Macromolecule: Carbonic anhydrase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 265 residues
Sequence: GSPEFMSHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHAFNVEFDDSQDKAVLKGGPLDGTYRLIQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDFGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTKGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLLECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.46
R work: 0.168
R free: 0.1917
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 10 mg/mL hCAII with ligand (at 1:1 molar ratio) in 50 mM deuterated TRIS buffer and 2.7-3.0 M ammonium sulfate at pH 7.8-8.0
Matthews coefficient: 2.07
Solvent content (%): 40.53
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: 2023-12-06
Human P300 complexed with a glycine-based inhibitor (PDB entry 7SSK)
Macromolecule: Histone acetyltransferase p300
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1.48
Sequence length: 569 residues
Sequence: GGHHHHHHGIFKPEELRQALMPTLEALYRQDPESLPFRQPVDPQLLGIPDYFDIVKSPMDLSTIKRKLDTGQYQEPWQYVDDIWLMFNNAWLYNRKTSRVYKYCSKLSEVFEQEIDPVMQSLGYCCGRKLEFSPQTLCCYGKQLCTIPRDATYYSYQNRYHFCEKCFNEIQGESVSLGDDPSQPQTTINKEQFSKRKNDTLDPELFVECTECGRKMHQICVLHHEIIWPAGFVCDGCLKKSARTRKENKFSAKRLPSTRLGTFLENRVNDFLRRQNHPESGEVTVRVVHASDKTVEVKPGMKARFVDSGEMAESFPYRTKALFAFEEIDGVDLCFFGMHVQEYGSDCPPPNQRRVYISYLDSVHFFRPKCLRTAVYHEILIGYLEYVKKLGYTTGHIWACPPSEGDDYIFHCHPPDQKIPKPKRLQEWFKKMLDKAVSERIVHDYKDIFKQATEDRLTSAKELPYFEGDFWPNVLEESIKESGGSGQKLYATMEKHKEVFFVIRLIAGPAANSLPPIVDPDPLIPCDLMDGRDAFLTLARDKHLEFSSLRRAQWSTMCMLVELHTQSQD
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.36
R work: 0.1867
R free: 0.235
Average B factor: 42.975
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 6.5
Crystallization temperature (K): 277
Crystal growth procedure: 20% PEG3350, 0.1 M MES pH 6.5
Matthews coefficient: 2.52
Solvent content (%): 51.28
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: 2022-11-09
Crystal structure of an inhibitor-bound Syk (PDB entry 5GHV)
Macromolecule: Tyrosine-protein kinase SYK
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 290 residues
Sequence: EEIRPKEVYLDRKLLTLEDKELGSGNFGTVKKGYYQMKKVVKTVAVKILKNEANDPALKDELLAEANVMQQLDNPYIVRMIGICEAESWMLVMEMAELGPLNKYLQQNRHVKDKNIIELVHQVSMGMKYLEESNFVHRDLAARNVLLVTQHYAKISDFGLSKALRADENYYKAQTHGKWPVKWYAPECINYYKFSSKSDVWSFGVLMWEAFSYGQKPYRGMKGSEVTAMLEKGERMGCPAGCPREMYDLMNLCWTYDVENRPGFAAVELRLRNYYYDVVNLEHHHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.8
R work: 0.217
R free: 0.227
Average B factor: 43.35
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 278
Crystal growth procedure: 10~20%(V/V) PEG3350, 100 MM TRIS-HCL
Matthews coefficient: 2.07
Solvent content (%): 40.64
Ligand: 1-({1-[2-({3,5-dimethyl-4-[2-(pyrrolidin-1-yl)ethoxy]phenyl}amino)pyrimidin-4-yl]-4-methyl-1H-pyrrol-3-yl}methyl)azetidin-3-ol (X5G)
Ligand formula: C27 H36 N6 O2
Ligand molecular weight: 476.614
Ligand SMILES: Cc1cc(cc(c1OCCN2CCCC2)C)Nc3nccc(n3)n4cc(c(c4)CN5CC(C5)O)C
Ligand InChI: InChI=1S/C27H36N6O2/c1-19-12-23(13-20(2)26(19)35-11-10-31-8-4-5-9-31)29-27-28-7-6-25(30-27)33-14-21(3)22(16-33)15-32-17-24(34)18-32/h6-7,12-14,16,24,34H,4-5,8-11,15,17-18H2,1-3H3,(H,28,29,30)
Release date: 2016-07-06
Crystal Structure of human phosphodiesterase 10 in complex with 9-methoxy-3,5-dihydropyrimido[5,4-b]indol-4-one (PDB entry 5SKB)
Macromolecule: cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.4.17
Sequence length: 343 residues
Sequence: GSSICTSEEWQGLMQFTLPVRLCKEIELFHFDIGPFENMWPGIFVYMVHRSCGTSCFELEKLCRFIMSVKKNYRRVPYHNWKHAVTVAHCMYAILQNNHTLFTDLERKGLLIACLCHDLDHRGFSNSYLQKFDHPLAALYSTSTMEQHHFSQTVSILQLEGHNIFSTLSSSEYEQVLEIIRKAIIATDLALYFGNRKQLEEMYQTGSLNLNNQSHRDRVIGLMMTACDLCSVTKLWPVTKLTANDIYAEFWAEGDEMKKLGIQPIPMMDRDKKDEVPQGQLGFYNAVAIPCYTTLTQILPPTEPLLKACRDNLSQWEKVIRGEETATWISSPSVAQKAAASED
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.35
R work: 0.188
R free: 0.2488
Average B factor: 49.029
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 295
Crystal growth procedure: 5-20 mg/mL protein in 25mM HEPES/NaOH pH7.5, 150mM NaCl, 50mM BME mixed 1:1 with reservoir 0.1M HEPES/NaOH pH7.5, 30% PEG550MME, 50mM MgCl2
Matthews coefficient: 2.62
Solvent content (%): 53.09
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: 2022-10-12
Crystal structure of haspin (GSG2) in complex with bisubstrate inhibitor ARC-3372 (PDB entry 5HTC)
Macromolecule: Serine/threonine-protein kinase haspin
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 357 residues
Sequence: MHHHHHHSSGVDLGTENLYFQSMGECSQKGPVPFSHCLPTEKLQRCEKIGEGVFGEVFQTIADHTPVAIKIIAIEGPDLVNGSHQKTFEEILPEIIISKELSLLSGEVCNRTEGFIGLNSVHCVQGSYPPLLLKAWDHYNSTKGSANDRPDFFKDDQLFIVLEFEFGGIDLEQMRTKLSSLATAKSILHQLTASLAVAEASLRFEHRDLHWGNVLLKKTSLKKLHYTLNGKSSTIPSCGLQVSIIDYTLSRLERDGIVVFCDVSMDEDLFTGDGDYQFDIYRLMKKENNNRWGEYHPYSNVLWLHYLTDKMLKQMTFKTKCNTPAMKQIKRKIQEFHRTMLNFSSATDLLCQHSLFK
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.5
R work: 0.14962
R free: 0.17125
Average B factor: 21.768
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277.15
Crystal growth procedure: 52-60% MPD and 0.1 M SPG pH 6.5-7.0
Matthews coefficient: 2.93
Solvent content (%): 58.06
Ligand: (4S)-2-METHYL-2,4-PENTANEDIOL (MPD)
Ligand formula: C6 H14 O2
Ligand molecular weight: 118.174
Ligand SMILES: CC(CC(C)(C)O)O
Ligand InChI: InChI=1S/C6H14O2/c1-5(7)4-6(2,3)8/h5,7-8H,4H2,1-3H3/t5-/m0/s1
Release date: 2016-03-16
Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor NPD-417 (PDB entry 6IBF)
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): 2.31
R work: 0.20326
R free: 0.26234
Average B factor: 42.327
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: 2.61
Solvent content (%): 52.92
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: 2019-12-18
Crystal structure of human DHODH in complex with inhibitor 1291 (PDB entry 6J3C)
Macromolecule: Dihydroorotate dehydrogenase (quinone), mitochondrial
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.3.5.2
Sequence length: 366 residues
Sequence: ATGDERFYAEHLMPTLQGLLDPESAHRLAVRFTSLGLLPRARFQDSDMLEVRVLGHKFRNPVGIAAGFDKHGEAVDGLYKMGFGFVEIGSVTPKPQEGNPRPRVFRLPEDQAVINRYGFNSHGLSVVEHRLRARQQKQAKLTEDGLPLGVNLGKNKTSVDAAEDYAEGVRVLGPLADYLVVNVSSPNTAGLRSLQGKAELRRLLTKVLQERDGLRRVHRPAVLVKIAPDLTSQDKEDIASVVKELGIDGLIVTNTTVSRPAGLQGALRSETGGLSGKPLRDLSTQTIREMYALTQGRVPIIGVGGVSSGQDALEKIRAGASLVQLYTALTFWGPPVVGKVKRELEALLKEQGFGGVTDAIGADHRR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.851
R work: 0.1689
R free: 0.1951
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: hepes pH4.6, 2M AMMONIUM SULPHATE, 30% Glycerol
Matthews coefficient: 3.66
Solvent content (%): 66.41
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: 2019-08-21