satarupa22/MacromolecularLigandDB huggingface dataset:
Ortho-Carborane di-propyl-sulfonamide in complex with CA IX mimic (PDB entry 6YO7)
Macromolecule: Carbonic anhydrase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 260 residues
Sequence: MSHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHSFQVTFDDSQDKAVLKGGPLDGTYRLLQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDVGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTEGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLAECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.17
R work: 0.1597
R free: 0.1848
Average B factor: 16.799
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.8
Crystallization temperature (K): 291
Crystal growth procedure: 1.6 M sodium citrate, 50 mM Tris-H2SO4
Matthews coefficient: 2.04
Solvent content (%): 39.77
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: 2020-08-19
Crystal Structure of human phosphodiesterase 10 in complex with 4-(azetidine-1-carbonyl)-2-methyl-N-[2-(2-methyl-5-phenyl-1,2,4-triazol-3-yl)ethyl]pyrazole-3-carboxamide (PDB entry 5SE8)
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): 1.99
R work: 0.173
R free: 0.217
Average B factor: 35.55
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: 2.66
Solvent content (%): 53.7
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
JAK2 in complex with 4-(2-amino-8-{[(2S)-1-hydroxypropan-2-yl]amino}quinazolin-6-yl)-5-ethyl-2-fluorophenol (PDB entry 7Q7L)
Macromolecule: Tyrosine-protein kinase JAK2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 316 residues
Sequence: MHHHHHHDYKDDDDKENLYFQGRDPTQFEERHLKFLQQLGKGNFGSVEMCRYDPLQDNTGEVVAVKKLQHSTEEHLRDFEREIEILKSLQHDNIVKYKGVCYSAGRRNLKLIMEYLPYGSLRDYLQKHKERIDHIKLLQYTSQICKGMEYLGTKRYIHRDLATRNILVENENRVKIGDFGLTKVLPQDKEYYKVKEPGESPIFWYAPESLTESKFSVASDVWSFGVVLYELFTYIEKSKSPPAEFMRMIGNDKQGQSIVTHLIELLKNNGRLPRPDGCPDEIYMIMTECWNNNVNQRPSFRDLALRVDQIRDNMAG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.97
R work: 0.1705
R free: 0.1956
Average B factor: 42.36
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 1.46-1.60 M trisodium citrate (untitrated)
Matthews coefficient: 2.12
Solvent content (%): 42.01
Ligand: 4-[2-azanyl-8-[[(2~{S})-1-oxidanylpropan-2-yl]amino]quinazolin-6-yl]-5-ethyl-2-fluoranyl-phenol (9I2)
Ligand formula: C19 H21 F N4 O2
Ligand molecular weight: 356.394
Ligand SMILES: CCc1cc(c(cc1c2cc3cnc(nc3c(c2)NC(C)CO)N)F)O
Ligand InChI: InChI=1S/C19H21FN4O2/c1-3-11-6-17(26)15(20)7-14(11)12-4-13-8-22-19(21)24-18(13)16(5-12)23-10(2)9-25/h4-8,10,23,25-26H,3,9H2,1-2H3,(H2,21,22,24)/t10-/m0/s1
Release date: 2022-02-02
Human Sirt5 in complex with stalled peptidylimidate intermediate of inhibitory compound 29 (PDB entry 6EQS)
Macromolecule: NAD-dependent protein deacylase sirtuin-5, mitochondrial
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.5.1
Sequence length: 275 residues
Sequence: GIDPFTARPSSSMADFRKFFAKAKHIVIISGAGVSAESGVPTFRGAGGYWRKWQAQDLATPLAFAHNPSRVWEFYHYRREVMGSKEPNAGHRAIAECETRLGKQGRRVVVITQNIDELHRKAGTKNLLEIHGSLFKTRCTSCGVVAENYKSPICPALSGKGAPEPGTQDASIPVEKLPRCEEAGCGGLLRPHVVWFGENLDPAILEEVDRELAHCDLCLVVGTSSVVYPAAMFAPQVAARGVPVAEFNTETTPATNRFRFHFQGPCGTTLPEALA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.32
R work: 0.16025
R free: 0.20856
Average B factor: 21.373
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 293
Crystal growth procedure: 30% PEG3350, 0.2 M NaCl, 0.1 M Bis-Tris pH 5.5, 5% 1,3-butandiol
Matthews coefficient: 2.27
Solvent content (%): 45.9
Ligand: 3-[[(~{Z})-~{C}-[(2~{R},3~{R},4~{S},5~{R})-5-[[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxymethyl]-3,4-bis(oxidanyl)oxolan-2-yl]sulfanyl-~{N}-[(5~{S})-6-[[(2~{S})-3-(1~{H}-indol-3-yl)-1-oxidanylidene-1-(propan-2-ylamino)propan-2-yl]amino]-6-oxidanylidene-5-(phenylmethoxycarbonylamino)hexyl]carbonimidoyl]amino]propanoic acid (BV8)
Ligand formula: C47 H63 N11 O19 P2 S
Ligand molecular weight: 1180.078
Ligand SMILES: CC(C)NC(=O)C(Cc1c[nH]c2c1cccc2)NC(=O)C(CCCCN=C(NCCC(=O)O)SC3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)n5cnc6c5ncnc6N)O)O)O)O)NC(=O)OCc7ccccc7
Ligand InChI: InChI=1S/C47H63N11O19P2S/c1-25(2)55-43(66)31(18-27-19-51-29-13-7-6-12-28(27)29)56-42(65)30(57-47(67)72-20-26-10-4-3-5-11-26)14-8-9-16-49-46(50-17-15-34(59)60)80-45-39(64)37(62)33(76-45)22-74-79(70,71)77-78(68,69)73-21-32-36(61)38(63)44(75-32)58-24-54-35-40(48)52-23-53-41(35)58/h3-7,10-13,19,23-25,30-33,36-39,44-45,51,61-64H,8-9,14-18,20-22H2,1-2H3,(H,49,50)(H,55,66)(H,56,65)(H,57,67)(H,59,60)(H,68,69)(H,70,71)(H2,48,52,53)/t30-,31-,32+,33+,36+,37+,38+,39+,44+,45+/m0/s1
Release date: 2017-11-01
Human PRDM9 allele-A ZnF Domain with Associated Recombination Hotspot DNA Sequence I (PDB entry 5EI9)
Macromolecule: DNA (5'-D(*AP*TP*CP*CP*AP*CP*GP*TP*GP*GP*CP*TP*AP*GP*GP*GP*AP*GP*GP*CP*C)-3')
Type: DNA, polydeoxyribonucleotide
Source organism: Homo sapiens
Sequence length: 21 residues
Sequence: ATCCACGTGGCTAGGGAGGCC
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.921
R work: 0.2144
R free: 0.2373
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6
Crystallization temperature (K): 289
Crystal growth procedure: 0.058 M Bistris Propane, 0.042 M Citric acid, 25% PEG3350
Matthews coefficient: 3.04
Solvent content (%): 59.53
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: 2016-02-17
CRYSTAL STRUCTURE OF MYELOPEROXIDASE SUBFORM C (MPO) COMPLEX WITH Compound-41 A.K.A 7-[1-phenyl-3-({4-phenylbicyclo[2.2.2]octan-1-yl}amino)propyl]-3H-[1,2,3]triazolo[4,5-b]pyridin-5-amine (PDB entry 6WY7)
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): 2.089
R work: 0.1585
R free: 0.1854
Average B factor: 24.38
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: 2.37
Solvent content (%): 48.09
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 PRMT5:MEP50 in complex with MTA (PDB entry 8VEO)
Macromolecule: Protein arginine N-methyltransferase 5
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1.320
Sequence length: 645 residues
Sequence: MDYKDDDDKAAMAVGGAGGSRVSSGRDLNCVPEIADTLGAVAKQGFDFLCMPVFHPRFKREFIQEPAKNRPGPQTRSDLLLSGRDWNTLIVGKLSPWIRPDSKVEKIRRNSEAAMLQELNFGAYLGLPAFLLPLNQEDNTNLARVLTNHIHTGHHSSMFWMRVPLVAPEDLRDDIIENAPTTHTEEYSGEEKTWMWWHNFRTLCDYSKRIAVALEIGADLPSNHVIDRWLGEPIKAAILPTSIFLTNKKGFPVLSKMHQRLIFRLLKLEVQFIITGTNHHSEKEFCSYLQYLEYLSQNRPPPNAYELFAKGYEDYLQSPLQPLMDNLESQTYEVFEKDPIKYSQYQQAIYKCLLDRVPEEEKDTNVQVLMVLGAGRGPLVNASLRAAKQADRRIKLYAVEKNPNAVVTLENWQFEEWGSQVTVVSSDMREWVAPEKADIIVSELLGSFADNELSPECLDGAQHFLKDDGVSIPGEYTSFLAPISSSKLYNEVRACREKDRDPEAQFEMPYVVRLHNFHQLSAPQPCFTFSHPNRDPMIDNNRYCTLEFPVEVNTVLHGFAGYFETVLYQDITLSIRPETHSPGMFSWFPILFPIKQPITVREGQTICVRFWRCSNSKKVWYEWAVTAPVCSAIHNPTGRSYTIGL
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.03
R work: 0.2392
R free: 0.2775
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 6
Crystallization temperature (K): 291
Crystal growth procedure: 10% PEG 4000, 0.2M magnesium chloride, 0.1M sodium citrate (pH 6.0)
Matthews coefficient: 2.82
Solvent content (%): 56.39
Ligand: 5'-DEOXY-5'-METHYLTHIOADENOSINE (MTA)
Ligand formula: C11 H15 N5 O3 S
Ligand molecular weight: 297.334
Ligand SMILES: CSCC1C(C(C(O1)n2cnc3c2ncnc3N)O)O
Ligand InChI: InChI=1S/C11H15N5O3S/c1-20-2-5-7(17)8(18)11(19-5)16-4-15-6-9(12)13-3-14-10(6)16/h3-5,7-8,11,17-18H,2H2,1H3,(H2,12,13,14)/t5-,7-,8-,11-/m1/s1
Release date: 2024-04-24
Caspase-3 Mutant - S150E (PDB entry 6BGR)
Macromolecule: Caspase-3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.22.56
Sequence length: 175 residues
Sequence: MENTENSVDSKSIKNLEPKIIHGSESMDSGISLDNSYKMDYPEMGLCIIINNKNFHKSTGMTSRSGTDVDAANLRETFRNLKYEVRNKNDLTREEIVELMRDVSKEDHSKRSSFVCVLLSHGEEGIIFGTNGPVDLKKITNFFRGDRCRELTGKPKLFIIQACRGTELDCGIETD
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.16
R work: 0.1744
R free: 0.2341
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 291
Crystal growth procedure: Crystals were obtained at 18 C by the hanging drop vapor diffusion method using 4 mL drops that contained equal volumes of protein and reservoir solutions over a 0.5 mL solution of 100 mM sodium citrate, pH 4.9-5.2, 8-18 % PEG 6000 (w/v), 10 mM DTT, and 3 mM NaN3. Crystals appeared within 3-5 days and were briefly immersed in a cryogenic solution containing 10% MPD (2-methylpentane-2,4-diol) and 90% reservoir solution.
Matthews coefficient: 2.16
Solvent content (%): 42.97
Ligand: AZIDE ION (AZI)
Ligand formula: N3
Ligand molecular weight: 42.02
Ligand SMILES: [N-]=[N+]=[N-]
Ligand InChI: InChI=1S/N3/c1-3-2/q-1
Release date: 2018-02-21
Co-crystal structure of CBL-B in complex with N-Aryl isoindolin-1-one inhibitor (PDB entry 8GCY)
Macromolecule: E3 ubiquitin-protein ligase CBL-B
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2.27
Sequence length: 391 residues
Sequence: GQAAADRRTVEKTWALMDAVVRLCQNPKLQLKNSPPYILDILPDTYQHLRLILSKYDDNQKLAQLSENEYFKIYIDSLMKKSKRAIRLFKEGKERMYEEQSQDRRNLTKLSLIFSHMLAEIKAIFPNGQFQGDNFRITKADAAEFWRKFFGDKTIVPWKVFRQCLHEVHQISSGLEAMALKSTIDLTCNDYISVFEFDIFTRLFQPWGSILRNWNFLAVTHPGYMAFLTYDEVKARLQKYSTKPGSYIFRLSCTRLGQWAIGYVTGDGNILQTIPHNKPLFQALIDGSAEGFYLYPDGRSYNPDLTGLCEPTPHDHIKVTQEQFELYCEMGSTFQLCKICAENDKDVKIEPCGHLMCTSCLTAWQESDGQGCPFCRCEIKGTEPIIVDPFD
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.81
R work: 0.19491
R free: 0.22962
Average B factor: 32.702
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 291
Crystal growth procedure: 0.1 M Imidazole, 0.1 M MES monohydrate pH 6.5
0.09 M Sodium nitrate, 0.09 M Sodium phosphate dibasic, 0.09M Ammonium sulfate  

12.5% v/v MPD; 12.5% PEG1000; 12.5% w/v PEG 3350
Matthews coefficient: 2.13
Solvent content (%): 42.25
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: 2023-03-22
Tubulin Glutamylase (PDB entry 4YLR)
Macromolecule: Tubulin polyglutamylase TTLL7
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 6
Sequence length: 487 residues
Sequence: GSFTKKKGTITANVAGTKFEIVRLVIDEMGFMKTPDEDETSNLIWCDSAVQQEKISELQNYQRINHFPGMGEICRKDFLARNMTKMIKSRPLDYTFVPRTWIFPAEYTQFQNYVKELKKKRKQKTFIVKPANGAMGHGISLIRNGDKLPSQDHLIVQEYIEKPFLMEGYKFDLRIYILVTSCDPLKIFLYHDGLVRMGTEKYIPPNESNLTQLYMHLTNYSVNKHNEHFERDETENKGSKRSIKWFTEFLQANQHDVAKFWSDISELVVKTLIVAEPHVLHAYRMCRPGQPPGSESVCFEVLGFDILLDRKLKPWLLQINRAPSFGTDQKIDYDVKRGVLLNALKLLNIRTSDKRRNLAKQKAEAQRRLYGQNSIKRLLPGSSDWEQQRHQLERRKEELKERLAQVRKQISREEHENRHMGNYRRIYPPEDKALLEKYENLLAVAFQTFLSGRAASFQRELNNPLKRMKEEDILDLLEQCEIDDEKL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.55
R work: 0.2221
R free: 0.2685
Average B factor: 66.7442
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 289
Crystal growth procedure: PEG 8000, magnesium acetate
Matthews coefficient: 2.71
Solvent content (%): 54.63
Ligand: ADENOSINE-5'-DIPHOSPHATE (ADP)
Ligand formula: C10 H15 N5 O10 P2
Ligand molecular weight: 427.201
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
Ligand InChI: InChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
Release date: 2015-06-17
Crystal structure of MYST acetyltransferase domain in complex with inhibitor (PDB entry 6BA2)
Macromolecule: Histone acetyltransferase KAT8
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1.48
Sequence length: 295 residues
Sequence: MGSSHHHHHHSSGLVPRGSTKVKYVDKIHIGNYEIDAWYFSPFPEDYGKQPKLWLCEYCLKYMKYEKSYRFHLGQCQWRQPPGKEIYRKSNISVHEVDGKDHKIYCQNLCLLAKLFLDHKTLYFDVEPFVFYILTEVDRQGAHIVGYFSKEKESPDGNNVSCIMILPPYQRRGYGRFLIAFSYELSKLESTVGSPEKPLSDLGKLSYRSYWSSVLLENLRDFRGTLSIKDLSQMTSITQNDIISTLQSLNMVKYWKGQHVICVTPKLVEEHLKSAQYKKPPITVDSVCLKWAPPK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.85003821102
R work: 0.193825526814
R free: 0.228016935366
Average B factor: 29.4680609733
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7
Crystallization temperature (K): 293
Crystal growth procedure: 2 M NaCl, 0.1 M Tris pH 7.0, 0.22 M MgCl2
Matthews coefficient: 2.31
Solvent content (%): 46.79
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: 2018-08-01
Crystal structure of STK17b (DRAK2) in complex with UNC-AP-194 probe (PDB entry 6Y6H)
Macromolecule: Serine/threonine-protein kinase 17B
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 327 residues
Sequence: MHHHHHHSSGVDLGTENLYFQSMENFNNFYILTSKELGRGKFAVVRQCISKSTGQEYAAKFLKKRRRGQDCRAEILHEIAVLELAKSCPRVINLHEVYENTSEIILILEYAAGGEIFSLCLPELAEMVSENDVIRLIKQILEGVYYLHQNNIVHLDLKPQNILLSSIYPLGDIKIVDFGMSRKIGHACELREIMGTPEYLAPEILNYDPITTATDMWNIGIIAYMLLTHTSPFVGEDNQETYLNISQVNVDYSEETFSSVSQLATDFIQSLLVKNPEKRPTAEICLSHSWLQQWDFENLFHPEETSSSSQTQDHSVRSSEDKTSKSS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.95
R work: 0.1812
R free: 0.2116
Average B factor: 38.067
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6
Crystallization temperature (K): 277.15
Crystal growth procedure: 13% PEG 3350, 0.1M NaCl, 0.1M bis-tris 6.0
Matthews coefficient: 2.68
Solvent content (%): 54.14
Ligand: 2-[6-(1-benzothiophen-2-yl)thieno[3,2-d]pyrimidin-4-yl]sulfanylethanoic acid (OBW)
Ligand formula: C16 H10 N2 O2 S3
Ligand molecular weight: 358.458
Ligand SMILES: c1ccc2c(c1)cc(s2)c3cc4c(s3)c(ncn4)SCC(=O)O
Ligand InChI: InChI=1S/C16H10N2O2S3/c19-14(20)7-21-16-15-10(17-8-18-16)6-13(23-15)12-5-9-3-1-2-4-11(9)22-12/h1-6,8H,7H2,(H,19,20)
Release date: 2020-03-11
Crystal structure of a GEF domain from the Orientia tsutsugamushi protein OtDUB in complex with Rac1 (PDB entry 6X1G)
Macromolecule: ULP_PROTEASE domain-containing protein
Type: Protein, polypeptide(L)
Source organism: Orientia tsutsugamushi str. Ikeda
Sequence length: 219 residues
Sequence: MERLVKKVTSNLETELKFFKGRLVQELMQIVKNENGRIDHTSKNWQESASVLLNSQEKGAVSLAEVERAVSKMTQKLRDQKVSEEEVVNIESKLKFERASLEAKLFDDNEIKELINKRIKEDALRAIPFLGSDSESFMEKISPFVKLPDDSYSLLKANDKHHPFQNILYSNALKFFADSSDIGYLNDDSLKNLTPENLNAFEQAVAADIDKLMHHHHHH
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.6
R work: 0.181
R free: 0.2182
Average B factor: 45.588
Crystallization method: MICROBATCH
Crystallization pH: 9.5
Crystallization temperature (K): 293
Crystal growth procedure: 25 mM CHES pH 9.5, 25% (w/v) PEG 8000
Matthews coefficient: 2.4
Solvent content (%): 48.8
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: 2020-11-25
Crystal Structure of G305A HDAC8 in complex with M344 (PDB entry 5THV)
Macromolecule: Histone deacetylase 8
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.5.1.98
Sequence length: 389 residues
Sequence: MEEPEEPADSGQSLVPVYIYSPEYVSMCDSLAKIPKRASMVHSLIEAYALHKQMRIVKPKVASMEEMATFHTDAYLQHLQKVSQEGDDDHPDSIEYGLGYDCPATEGIFDYAAAIGGATITAAQCLIDGMCKVAINWSGGWHHAKKDEASGFCYLNDAVLGILRLRRKFERILYVDLDLHHGDGVEDAFSFTSKVMTVSLHKFSPGFFPGTGDVSDVGLGKGRYYSVNVPIQDGIQDEKYYQICESVLKEVYQAFNPKAVVLQLGADTIAGDPMCSFNMTPVGIGKCLKYILQWQLATLILGGGAYNLANTARCWTYLTGVILGKTLSSEIPDHEFFTAYGPDYVLEITPSCRPDRNEPHRIQQILNYIKGNLKHVVIEGRGSHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.868
R work: 0.1724
R free: 0.2097
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 294
Crystal growth procedure: 200 mM BisTris (pH 6.5), 13% w/v PEG 4000, 4 mM TCEP
Matthews coefficient: 2.37
Solvent content (%): 48.2
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: 2016-12-21
Crystal Structure of HD-PTP phosphatase (PDB entry 5LM2)
Macromolecule: Tyrosine-protein phosphatase non-receptor type 23
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 352 residues
Sequence: PMAAHEASSLYSEEKAKLLREMMAKIEDKNEVLDQFMDSMQLDPETVDNLDAYSHIPPQLMEKCAALSVRPDTVRNLVQSMQVLSGVFTDVEASLKDIRDLLEEDELLEQKFQEAVGQAGAISITSKAELAEVRREWAKYMEVHEKASFTNSELHRAMNLHVGNLRLLSGPLDQVRAALPTPALSPEDKAVLQNLKRILAKVQEMRDQRVSLEQQLRELIQKDDITASLVTTDHSEMKKLFEEQLKKYDQLKVYLEQNLAAQDRVLCALTEANVQYAAVRRVLSDLDQKWNSTLQTLVASYEAYEDLMKKSQEGRDFYADLESKVAALLERTQSTCQAREAARQQLLDRELK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.54
R work: 0.2147
R free: 0.271
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 294
Crystal growth procedure: 0.1 M Bis-Tris pH 6.0, 0.1-0.2 M Na-Formate and 13-15% PEG3350
Matthews coefficient: 2.73
Solvent content (%): 54.86
Release date: 2016-11-30
Cocrystal structure of human CaMKII-alpha (CAMK2A)kinase domain and GluN2B in complex with ADP (PDB entry 7UJS)
Macromolecule: Calcium/calmodulin-dependent protein kinase type II subunit alpha
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.17
Sequence length: 268 residues
Sequence: TRFTEEYQLFEELGKGAFSVVRRCVKVLAGQEYAAKIINTKKLSARDHQKLEREARICRLLKHPNIVRLHDSISEEGHHYLIFDLVTGGELFEDIVAREYYSEADASHCIQQILEAVLHCHQMGVVHRDLKPENLLLASKLKGAAVKLADFGLAIEVEGEQQAWFGFAGTPGYLSPEVLRKDPYGKPVDLWACGVILYILLVGYPPFWDEDQHRLYKQIKAGAYDFPSPEWDTVTPEAKDLINKMLTINPSKRITAAEALKHPWISHR
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.75
R work: 0.1972
R free: 0.2622
Average B factor: 34.825
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.6
Crystallization temperature (K): 277
Crystal growth procedure: 0.1M 1,3-bis(tris(hydroxymethyl)methylamino)propane, 0.1 M Ammonium sulfate, 20% PEG 3350
Matthews coefficient: 2.36
Solvent content (%): 47.83
Ligand: ADENOSINE-5'-DIPHOSPHATE (ADP)
Ligand formula: C10 H15 N5 O10 P2
Ligand molecular weight: 427.201
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
Ligand InChI: InChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
Release date: 2022-04-13
BRAF in Complex with N-(3-(tert-butyl)phenyl)-4-methyl-3-(6-morpholinopyrimidin-4-yl)benzamide (PDB entry 5VAL)
Macromolecule: Serine/threonine-protein kinase B-raf
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 281 residues
Sequence: GSDSSDDWEIPDGQITVGQRIGSGSFGTVYKGKWHGDVAVKMLNVTAPTPQQLQAFKNEVGVLRKTRHVNILLFMGYSTKPQLAIVTQWCEGSSLYHHLHIIETKFEMIKLIDIARQTAQGMDYLHAKSIIHRDLKSNNIFLHEDLTVKIGDFGLATVKSRWSGSHQFEQLSGSILWMAPEVIRMQDKNPYSFQSDVYAFGIVLYELMTGQLPYSNINNRDQIIFMVGRGYLSPDLSKVRSNCPKAMKRLMAECLKKKRDERPLFPQILASIELLARSLPK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.26
R work: 0.181
R free: 0.217
Average B factor: 38.11
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8.4
Crystallization temperature (K): 291
Crystal growth procedure: 100 mM Tris ph 8.4, 12% PEG8000, and 100mM NaCl
Matthews coefficient: 2.84
Solvent content (%): 56.65
Ligand: N-(3-tert-butylphenyl)-4-methyl-3-[6-(morpholin-4-yl)pyrimidin-4-yl]benzamide (92D)
Ligand formula: C26 H30 N4 O2
Ligand molecular weight: 430.542
Ligand SMILES: Cc1ccc(cc1c2cc(ncn2)N3CCOCC3)C(=O)Nc4cccc(c4)C(C)(C)C
Ligand InChI: InChI=1S/C26H30N4O2/c1-18-8-9-19(25(31)29-21-7-5-6-20(15-21)26(2,3)4)14-22(18)23-16-24(28-17-27-23)30-10-12-32-13-11-30/h5-9,14-17H,10-13H2,1-4H3,(H,29,31)
Release date: 2017-06-28
Crystal Structure of PRMT5:MEP50 in complex with MTA and H4 peptide (PDB entry 5FA5)
Macromolecule: Protein arginine N-methyltransferase 5
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1
Sequence length: 650 residues
Sequence: MDYKDDDDKGRATMAAMAVGGAGGSRVSSGRDLNCVPEIADTLGAVAKQGFDFLCMPVFHPRFKREFIQEPAKNRPGPQTRSDLLLSGRDWNTLIVGKLSPWIRPDSKVEKIRRNSEAAMLQELNFGAYLGLPAFLLPLNQEDNTNLARVLTNHIHTGHHSSMFWMRVPLVAPEDLRDDIIENAPTTHTEEYSGEEKTWMWWHNFRTLCDYSKRIAVALEIGADLPSNHVIDRWLGEPIKAAILPTSIFLTNKKGFPVLSKMHQRLIFRLLKLEVQFIITGTNHHSEKEFCSYLQYLEYLSQNRPPPNAYELFAKGYEDYLQSPLQPLMDNLESQTYEVFEKDPIKYSQYQQAIYKCLLDRVPEEEKDTNVQVLMVLGAGRGPLVNASLRAAKQADRRIKLYAVEKNPNAVVTLENWQFEEWGSQVTVVSSDMREWVAPEKADIIVSELLGSFADNELSPECLDGAQHFLKDDGVSIPGEYTSFLAPISSSKLYNEVRACREKDRDPEAQFEMPYVVRLHNFHQLSAPQPCFTFSHPNRDPMIDNNRYCTLEFPVEVNTVLHGFAGYFETVLYQDITLSIRPETHSPGMFSWFPILFPIKQPITVREGQTICVRFWRCSNSKKVWYEWAVTAPVCSAIHNPTGRSYTIGL
Oligomeric state: Hetero 8-mer
Stoichiometry: A4, B4
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.34
R work: 0.177
R free: 0.2213
Average B factor: 64.79
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 281
Crystal growth procedure: 200 mM ammonium sulfate, 20-28% PEG 3350, 2 mM 5-deoxy-5-(methylthio)adenosine, 1 mM H4 peptide (1-20)
Matthews coefficient: 2.7
Solvent content (%): 54.47
Ligand: 5'-DEOXY-5'-METHYLTHIOADENOSINE (MTA)
Ligand formula: C11 H15 N5 O3 S
Ligand molecular weight: 297.334
Ligand SMILES: CSCC1C(C(C(O1)n2cnc3c2ncnc3N)O)O
Ligand InChI: InChI=1S/C11H15N5O3S/c1-20-2-5-7(17)8(18)11(19-5)16-4-15-6-9(12)13-3-14-10(6)16/h3-5,7-8,11,17-18H,2H2,1H3,(H2,12,13,14)/t5-,7-,8-,11-/m1/s1
Release date: 2016-02-24