satarupa22/MacromolecularLigandDB huggingface dataset:
TrkA ECD complex with designed miniprotein ligand (PDB entry 7N3T)
Macromolecule: High affinity nerve growth factor receptor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 359 residues
Sequence: SCPDACCPHGSSGLRCTRDGALDSLHHLPGAENLTELYIENQQHLQHLELRDLRGLGELRNLTIVKSGLRFVAPDAFHFTPRLSRLNLSFNALESLSWKTVQGLSLQELVLSGNPLHCSCALRWLQRWEEEGLGGVPEQKLQCHGQGPLAHMPNASCGVPTLKVQVPNASVDVGDDVLLRCQVEGRGLEQAGWILTELEQSATVMKSGGLPSLGLTLANVTSDLNRKNLTCWAENDVGRAEVSVQVNVSFPASVQLHTAVEMHHWCIPFSVDGQPAPSLRWLFNGSVLNETSFIFTEFLEPAANETVRHGCLRLNQPTHVNNGNYTLLAANPFGQASASIMAAFMDNPAAAHHHHHHHH
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.84
R work: 0.2143
R free: 0.2425
Average B factor: 42.37
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.2
Crystallization temperature (K): 295
Crystal growth procedure: 0.4 M ammonium sulfate, 0.1 M bis-tris pH 6.2, 16% PEG 3350.
Matthews coefficient: 3.25
Solvent content (%): 62.2
Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose (NAG)
Ligand formula: C8 H15 N O6
Ligand molecular weight: 221.208
Ligand SMILES: CC(=O)NC1C(C(C(OC1O)CO)O)O
Ligand InChI: InChI=1S/C8H15NO6/c1-3(11)9-5-7(13)6(12)4(2-10)15-8(5)14/h4-8,10,12-14H,2H2,1H3,(H,9,11)/t4-,5-,6-,7-,8-/m1/s1
Release date: 2022-04-20
Co-Crystal Structure of Akt1 in Complex with Covalent-Allosteric Akt Inhibitor 3 (PDB entry 7NH4)
Macromolecule: RAC-alpha serine/threonine-protein kinase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 446 residues
Sequence: GSDVAIVKEGWLHKRGEYIKTWRPRYFLLKNDGTFIGYKERPQDVDQREAPLNNFSVAQCQLMKTERPRPNTFIIRCLQWTTVIERTFHVETPEEREEWTTAIQTVADGLKKQAAAEMDFRSGSPSDNSGAEEMEVSLAKPKHRVTMNEFEYLKLLGKGTFGKVILVKEKATGRYYAMKILKKEVIVAKDEVAHTLTENRVLQNSRHPFLTALKYSFQTHDRLCFVMEYANGGELFFHLSRERVFSEDRARFYGAEIVSALDYLHSEKNVVYRDLKLENLMLDKDGHIKITDFGLCKEGIKDGATMKTFCGTPEYLAPEVLEDNDYGRAVDWWGLGVVMYEMMCGRLPFYNQDHEKLFELILMEEIRFPRTLGPEAKSLLSGLLKKDPKQRLGGGSEDAKEIMQHRFFAGIVWQHVYEKKLSPPFKPQVTSETDTRYFDEEFTAQM
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.3
R work: 0.2228
R free: 0.2457
Average B factor: 81.99
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 1.25 mM Na-acetate, 3.75 mM Na-citrate, 12% v/v PEG 2000 MME, pH 6.5, 3 mg/mL Akt1 (in 25 mM TRIS, 100 mM NaCl, 10% v/v Glycerol, 5 mM DTT, pH 7.5), 1 uL reservoir + 1 uL protein solution
Matthews coefficient: 2.21
Solvent content (%): 44.35
Ligand: ~{N}-[3-[1-[[4-[5-(hydroxymethyl)-3-phenyl-pyridin-2-yl]phenyl]methyl]piperidin-4-yl]-2-oxidanylidene-1~{H}-benzimidazol-5-yl]propanamide (UCE)
Ligand formula: C34 H35 N5 O3
Ligand molecular weight: 561.673
Ligand SMILES: CCC(=O)Nc1ccc2c(c1)N(C(=O)N2)C3CCN(CC3)Cc4ccc(cc4)c5c(cc(cn5)CO)c6ccccc6
Ligand InChI: InChI=1S/C34H35N5O3/c1-2-32(41)36-27-12-13-30-31(19-27)39(34(42)37-30)28-14-16-38(17-15-28)21-23-8-10-26(11-9-23)33-29(18-24(22-40)20-35-33)25-6-4-3-5-7-25/h3-13,18-20,28,40H,2,14-17,21-22H2,1H3,(H,36,41)(H,37,42)
Release date: 2021-09-08
Crystal structure of hMTH1 N33G in complex with LW14 in the presence of acetate (PDB entry 6GLP)
Macromolecule: 7,8-dihydro-8-oxoguanine triphosphatase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.1.55
Sequence length: 182 residues
Sequence: MKHHHHHHPMSDYDIPTTENLYFQGAMGASRLYTLVLVLQPQRVLLGMKKRGFGAGRWGGFGGKVQEGETIEDGARRELQEESGLTVDALHKVGQIVFEFVGEPELMDVHVFCTDSIQGTPVESDEMRPCWFQLDQIPFKDMWPDDSYWFPLLLQKKKFHGYFKFQGQDTILDYTLREVDTV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.5
R work: 0.1688
R free: 0.1985
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 4.5
Crystallization temperature (K): 293
Crystal growth procedure: crystallized in: 23-27% PEG3350, 0.2 M LiSO4, 0.1 M sodium acetate pH 4.5

soaked in: 27% PEG3350, 0.2 M LiSO4, 0.1 M sodium acetate pH 4.5, 20% DMSO, 10 mM compound
Ligand: 1~{H}-imidazo[4,5-b]pyridin-2-amine (BU8)
Ligand formula: C6 H6 N4
Ligand molecular weight: 134.139
Ligand SMILES: c1cc2c(nc1)nc([nH]2)N
Ligand InChI: InChI=1S/C6H6N4/c7-6-9-4-2-1-3-8-5(4)10-6/h1-3H,(H3,7,8,9,10)
Release date: 2019-02-20
Crystal structure of bovine DNMT1 BAH1 domain in complex with H4K20me3 (PDB entry 7LMK)
Macromolecule: DNA (cytosine-5)-methyltransferase 1
Type: Protein, polypeptide(L)
Source organism: Bos taurus
EC number: 2.1.1.37
Sequence length: 158 residues
Sequence: SKNRISWVGDAVKTDGKKSYYKKVCIDSETLEVGDCVSVIPDDSSKPLYLARVTALWEDSSNGQMFHAHWFCAGTDTVLGATSDPLELFLVDECEDMQLSYIHSKVQVIYKAPSGAGSATYFYQLWYDQDYARFESPPKTQPTEDNKYKFCASCARLA
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.647
R work: 0.2058
R free: 0.2583
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 13% PEG1500, 20 mM DTT and 200 mM L-proline, 0.1 M HEPES (pH 7.5)
Matthews coefficient: 2.45
Solvent content (%): 49.87
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: 2021-02-17
Human PARP14 (ARTD8), catalytic fragment in complex with RBN012042 (PDB entry 7L9Y)
Macromolecule: Protein mono-ADP-ribosyltransferase PARP14
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.4.2
Sequence length: 194 residues
Sequence: SNADMKQQNFCVVELLPSDPEYNTVASKFNQTCSHFRIEKIERIQNPDLWNSYQAKKKTMDAKNGQTMNEKQLFHGTDAGSVPHVNRNGFNRSYAGKNAVAYGKGTYFAVNANYSANDTYSRPDANGRKHVYYVRVLTGIYTHGNHSLIVPPSKNPQNPTDLYDTVTDNVHHPSLFVAFYDYQAYPEYLITFRK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.25
R work: 0.266
R free: 0.2984
Average B factor: 44.291
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7
Crystallization temperature (K): 291
Crystal growth procedure: 0.1 M HEPES pH 7.0, 26% v/v Jeffamine ED-2001
Matthews coefficient: 2.73
Solvent content (%): 54.94
Ligand: 7-(cyclopentylamino)-5-fluoro-2-{[(piperidin-4-yl)sulfanyl]methyl}quinazolin-4(3H)-one (XRM)
Ligand formula: C19 H25 F N4 O S
Ligand molecular weight: 376.491
Ligand SMILES: c1c(cc(c2c1N=C(NC2=O)CSC3CCNCC3)F)NC4CCCC4
Ligand InChI: InChI=1S/C19H25FN4OS/c20-15-9-13(22-12-3-1-2-4-12)10-16-18(15)19(25)24-17(23-16)11-26-14-5-7-21-8-6-14/h9-10,12,14,21-22H,1-8,11H2,(H,23,24,25)
Release date: 2021-04-21
Discovery of ASTX029, a clinical candidate which modulates the phosphorylation and catalytic activity of ERK1/2 (PDB entry 7NQW)
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): 1.775
R work: 0.1649
R free: 0.2064
Average B factor: 30.483
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.25M (NH4)2SO4
33% MPEG 2000
0.02M Mercaptoethanol
0.1M pH=7.2 HEPES/NaOH
Matthews coefficient: 2.32
Solvent content (%): 46.87
Ligand: DIMETHYL SULFOXIDE (DMS)
Ligand formula: C2 H6 O S
Ligand molecular weight: 78.133
Ligand SMILES: CS(=O)C
Ligand InChI: InChI=1S/C2H6OS/c1-4(2)3/h1-2H3
Release date: 2021-10-06
Human APE1 E96Q/D210N mismatch substrate complex (PDB entry 5DFJ)
Macromolecule: DNA-(apurinic or apyrimidinic site) lyase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.99.18
Sequence length: 276 residues
Sequence: ALYEDPPDQKTSPSGKPATLKICSWNVDGLRAWIKKKGLDWVKEEAPDILCLQQTKCSENKLPAELQELPGLSHQYWSAPSDKEGYSGVGLLSRQCPLKVSYGIGDEEHDQEGRVIVAEFDSFVLVTAYVPNAGRGLVRLEYRQRWDEAFRKFLKGLASRKPLVLCGNLNVAHEEIDLRNPKGNKKNAGFTPQERQGFGELLQAVPLADSFRHLYPNTPYAYTFWTYMMNARSKNVGWRLDYFLLSHSLLPALCDSKIRSKALGSDHCPITLYLAL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.85
R work: 0.1593
R free: 0.1998
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5
Crystallization temperature (K): 291
Crystal growth procedure: 10% PEG20000, 100 mM sodium citrate, 200 mM MgCl
Matthews coefficient: 2.61
Solvent content (%): 52.91
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: 2015-10-14
Crystal Structure of compound 4 in complex with KRAS G12V C118S GDP and pVHL:ElonginC:ElonginB (PDB entry 8QW7)
Macromolecule: Elongin-B
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 104 residues
Sequence: MDVFLMIRRHKTTIFTDAKESSTVFELKRIVEGILKRPPDEQRLYKDDQLLDDGKTLGECGFTSQTARPQAPATVGLAFRADDTFEALCIEPFSSPPELPDVMK
Oligomeric state: Hetero 4-mer
Stoichiometry: A1, B1, C1, D1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.36
R work: 0.2459
R free: 0.2726
Average B factor: 59.05
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 277
Crystal growth procedure: 200 mM Lithium sulfate monohydrate, 100 mM BIS-TRIS propane pH 5.5, 25% w/v polyethylene glycol 3350
Matthews coefficient: 2.82
Solvent content (%): 56.4
Ligand: (2S,4R)-1-[(2R)-2-[3-[4-[(3S)-4-[4-[5-[(4S)-2-azanyl-3-cyano-4-methyl-6,7-dihydro-5H-1-benzothiophen-4-yl]-1,2,4-oxadiazol-3-yl]pyrimidin-2-yl]-3-methyl-1,4-diazepan-1-yl]butoxy]-1,2-oxazol-5-yl]-3-methyl-butanoyl]-N-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide (X53)
Ligand formula: C50 H60 N12 O6 S2
Ligand molecular weight: 989.218
Ligand SMILES: Cc1c(scn1)c2ccc(cc2)CNC(=O)C3CC(CN3C(=O)C(c4cc(no4)OCCCCN5CCCN(C(C5)C)c6nccc(n6)c7nc(on7)C8(CCCc9c8c(c(s9)N)C#N)C)C(C)C)O
Ligand InChI: InChI=1S/C50H60N12O6S2/c1-29(2)41(47(65)62-27-34(63)22-37(62)46(64)54-25-32-11-13-33(14-12-32)43-31(4)55-28-69-43)38-23-40(58-67-38)66-21-7-6-18-60-19-9-20-61(30(3)26-60)49-53-17-15-36(56-49)45-57-48(68-59-45)50(5)16-8-10-39-42(50)35(24-51)44(52)70-39/h11-15,17,23,28-30,34,37,41,63H,6-10,16,18-22,25-27,52H2,1-5H3,(H,54,64)/t30-,34+,37-,41+,50-/m0/s1
Release date: 2023-12-06
Gcase in complex with small molecule inhibitor 1 (PDB entry 9FDI)
Macromolecule: Lysosomal acid glucosylceramidase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.2.1.45
Sequence length: 546 residues
Sequence: MEFSSPSREECPKPLSRVSIMAGSLTGLLLLQAVSWASGARPCIPKSFGYSSVVCVCNATYCDSFDPPTFPALGTFSRYESTRSGRRMELSMGPIQANHTGTGLLLTLQPEQKFQKVKGFGGAMTDAAALNILALSPPAQNLLLKSYFSEEGIGYNIIRVPMASCDFSIRTYTYADTPDDFQLHNFSLPEEDTKLKIPLIHRALQLAQRPVSLLASPWTSPTWLKTNGAVNGKGSLKGQPGDIYHQTWARYFVKFLDAYAEHKLQFWAVTAENEPSAGLLSGYPFQCLGFTPEHQRDFIARDLGPTLANSTHHNVRLLMLDDQRLLLPHWAKVVLTDPEAAKYVHGIAVHWYLDFLAPAKATLGETHRLFPNTMLFASEACVGSKFWEQSVRLGSWDRGMQYSHSIITNLLYHVVGWTDWNLALNPEGGPNWVRNFVDSPIIVDITKDTFYKQPMFYHLGHFSKFIPEGSQRVGLVASQKNDLDAVALMHPDGSAVVVVLNRSSKDVPLTIKDPAVGFLETISPGYSIHTYLWRRQHHHHHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.41
R work: 0.15678
R free: 0.18319
Average B factor: 21.631
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.35M KSCN
28% PEG 3350
Matthews coefficient: 2.16
Solvent content (%): 43.05
Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose (NAG)
Ligand formula: C8 H15 N O6
Ligand molecular weight: 221.208
Ligand SMILES: CC(=O)NC1C(C(C(OC1O)CO)O)O
Ligand InChI: InChI=1S/C8H15NO6/c1-3(11)9-5-7(13)6(12)4(2-10)15-8(5)14/h4-8,10,12-14H,2H2,1H3,(H,9,11)/t4-,5-,6-,7-,8-/m1/s1
Release date: 2024-07-03
Crystal Structure of the Human vaccinia-related kinase 1 bound to (R)-2-phenylaminopteridinone inhibitor (PDB entry 6BP0)
Macromolecule: Serine/threonine-protein kinase VRK1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 364 residues
Sequence: SMRVKAAQAGRQSSAKRHLAEQFAVGEIITDMAAAAWKVGLPIGQGGFGCIYLADMNSSESVGSDAPCVVKVEPSDNGPLFTELKFYQRAAKPEQIQKWIRTRKLKYLGVPKYWGSGLHDKNGKSYRFMIMDRFGSDLQKIYEANAKRFSRKTVLQLSLRILDILEYIHEHEYVHGDIKASNLLLNYKNPDQVYLVDYGLAYRYCPEGVHKAYAADPKRCHDGTIEFTSIDAHNGVAPSRRGDLEILGYCMIQWLTGHLPWEDNLKDPKYVRDSKIRYRENIASLMDKCFPAANAPGEIAKYMETVKLLDYTEKPLYENLRDILLQGLKAIGSKDDGKLDLSVVENGGLKAKTITKKRAAEIEE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.9
R work: 0.1867
R free: 0.22589
Average B factor: 37.609
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 293
Crystal growth procedure: 22% PEG3350; 0.02M Lithium Sulfate; 0.1M Buffer system SBG pH 7.0
Matthews coefficient: 2.58
Solvent content (%): 52.32
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: 2017-12-06
Human Carbonic anhydrase II bound by anthracene-9-sulfonamide (PDB entry 6T5C)
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): 1.22
R work: 0.1228
R free: 0.1532
Average B factor: 14.862
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: Crystallization buffer was 0.1M sodium BICINE, pH 9, 0.2 M ammonium sulfate and 2M sodium malonate pH 7 made from 1M sodium BICINE and 3.4M sodium malonate
Matthews coefficient: 2.08
Solvent content (%): 40.98
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: 2020-10-14
Crystal structure of Human CSNK1A1 with A86 (PDB entry 6GZD)
Macromolecule: Casein kinase I isoform alpha
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 374 residues
Sequence: MGSSHHHHHHSSGVDLWSHPQFEKGTENLYFQGGGGRMASSSGSKAEFIVGGKYKLGRKIGSGSFGDIYLATNITNGEEVAVKLESQKARHPQLHYESKLYKILQGGVGIPHIRWYGQEKDYNVLVMDLLGPSLEDLFNFCSRRFTMKTVLMLADQMISRIEYVHTKNFIHRDIKPDNFLMGIGRHCNKLFLIDFGLAKKYRDNRTRQHIPYREDKNLTGTARYASINAHLGIEQSRRDDMESLGYVLMYFNRTSLPWQGLKAATKKQKYEKISEKKMSTPVEVLCKGFPAEFAMYLNYCRGLRFEEAPDYMYLRQLFRILFRTLNHQYDYTFDWTMLKQKAAQQAASSSGQGQQAQTPTGKQTDKTKSNMKGF
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.28
R work: 0.17496
R free: 0.22117
Average B factor: 58.303
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8
Crystallization temperature (K): 277.15
Crystal growth procedure: CSNK1A1 at a concentration of 5.8 mg/ml (50 mM Tris-HCl, 300 mM NaCl, 0.25 mM TCEP, pH 8.0) was pre-incubated with 0.7 mM (4.7-fold molar excess) of Mg2+-ATP (120 mM in UPW) for 1 h. 0.1 uL of the protein solution was then mixed with 0.1 uL of reservoir solution (0.10 M MES/NaOH pH 6.8, 10.0% 2-propanol, 26.0% PEG400) and equilibrated at 4 C over 0.06mL of reservoir solution. Well diffracting crystals appeared within 4 days and grew to full size over 23 days.
Matthews coefficient: 3.02
Solvent content (%): 59.23
Ligand: DIMETHYL SULFOXIDE (DMS)
Ligand formula: C2 H6 O S
Ligand molecular weight: 78.133
Ligand SMILES: CS(=O)C
Ligand InChI: InChI=1S/C2H6OS/c1-4(2)3/h1-2H3
Release date: 2018-08-29
Crystal structure of SVBP-VASH1 complex (PDB entry 6J9H)
Macromolecule: Small vasohibin-binding protein
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 66 residues
Sequence: MDPPARKEKTKVKESVSRVEKAKQKSAQQELKQRQRAEIYALNRVMTELEQQQFDEFCKQMQPPGE
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.31
R work: 0.2477
R free: 0.2709
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 0.1M Na citrate tribasic dihydrate pH 5.5, 16% PEG 8000, 0.01M Cadmium chloride hydrate
Matthews coefficient: 2.96
Solvent content (%): 58.51
Release date: 2019-06-19
Carbonic Anhydrase II Inhibitor RA6 (PDB entry 5NXO)
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): 1.2
R work: 0.1253
R free: 0.1502
Average B factor: 14.15
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.8
Crystallization temperature (K): 291
Crystal growth procedure: 50 mM Tris
1.6 M Natrium Citrate
Matthews coefficient: 2.11
Solvent content (%): 41.74
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: 2018-01-17
Human PPARgamma ligand binding dmain complexed with SB1406 in a covalent bonded form (PDB entry 5DSH)
Macromolecule: Peroxisome proliferator-activated receptor gamma
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 287 residues
Sequence: GSHMAEISSDIDQLNPESADLRALAKHLYDSYIKSFPLTKAKARAILTGKTTDKSPFVIYDMNSLMMGEDKIKFKHITPLQEQSKEVAIRIFQGCQFRSVEAVQEITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQGFMTREFLKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQDNLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLLQVIKKTETDMSLHPLLQEIYKDLY
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.95
R work: 0.20477
R free: 0.25743
Average B factor: 85.374
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 297
Crystal growth procedure: 2.2M sodium malonate pH 7.0
Matthews coefficient: 2.67
Solvent content (%): 54.01
Ligand: N-[3-(benzyloxy)phenyl]-3-nitrobenzamide (6BH)
Ligand formula: C20 H16 N2 O4
Ligand molecular weight: 348.352
Ligand SMILES: c1ccc(cc1)COc2cccc(c2)NC(=O)c3cccc(c3)[N+](=O)[O-]
Ligand InChI: InChI=1S/C20H16N2O4/c23-20(16-8-4-10-18(12-16)22(24)25)21-17-9-5-11-19(13-17)26-14-15-6-2-1-3-7-15/h1-13H,14H2,(H,21,23)
Release date: 2016-09-21
Crystal Structure of CK2alpha with Compound 2 bound to second crystal form (PDB entry 6YPG)
Macromolecule: Casein kinase II subunit alpha
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 328 residues
Sequence: SGPVPSRARVYTDVNTHRPSEYWDYESHVVEWGNQDDYQLVRKLGRGKYSEVFEAINITNNEKVVVKILKPVAAAKIKREIKILENLRGGPNIITLADIVKDPVSRTPALVFEHVNNTDFKQLYQTLTDYDIRFYMYEILKALDYCHSMGIMHRDVKPHNVMIDHEHRKLRLIDWGLAEFYHPGQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRKEPFFHGHDNYDQLVRIAKVLGTEDLYDYIDKYNIELDPRFNDILGRHSRKRWERFVHSENQHLVSPEALDFLDKLLRYDHQSRLTAREAMEHPYFYTVVK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.51
R work: 0.2374
R free: 0.243
Average B factor: 28.336
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 298
Crystal growth procedure: 112.5mM Mes, 35% glycerol ethoxylate, 180 mM ammonium acetate
Matthews coefficient: 2.01
Solvent content (%): 38.76
Ligand: 4-[(4-naphthalen-2-yl-1,3-thiazol-2-yl)amino]-2-oxidanyl-benzoic acid (N5Q)
Ligand formula: C20 H14 N2 O3 S
Ligand molecular weight: 362.402
Ligand SMILES: c1ccc2cc(ccc2c1)c3csc(n3)Nc4ccc(c(c4)O)C(=O)O
Ligand InChI: InChI=1S/C20H14N2O3S/c23-18-10-15(7-8-16(18)19(24)25)21-20-22-17(11-26-20)14-6-5-12-3-1-2-4-13(12)9-14/h1-11,23H,(H,21,22)(H,24,25)
Release date: 2020-07-15
Fragment-based discovery of a highly potent, orally bioavailable inhibitor which modulates the phosphorylation and catalytic activity of ERK1/2 (PDB entry 6G9J)
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): 1.98
R work: 0.159
R free: 0.212
Average B factor: 38.051
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.2
Crystallization temperature (K): 293
Crystal growth procedure: 0.3M (NH4)2SO4, 32.0%w/v MPEG 2000, 0.1M HEPES/NaOHpH=7.2, 0.02M Mercaptoethanol
Matthews coefficient: 2.29
Solvent content (%): 46.25
Ligand: 2-[5-[5-chloranyl-2-(oxan-4-ylamino)pyrimidin-4-yl]-3-oxidanylidene-1~{H}-isoindol-2-yl]-~{N}-[(1~{R})-1-phenylethyl]ethanamide (ERK)
Ligand formula: C27 H28 Cl N5 O3
Ligand molecular weight: 505.996
Ligand SMILES: CC(c1ccccc1)NC(=O)CN2Cc3ccc(cc3C2=O)c4c(cnc(n4)NC5CCOCC5)Cl
Ligand InChI: InChI=1S/C27H28ClN5O3/c1-17(18-5-3-2-4-6-18)30-24(34)16-33-15-20-8-7-19(13-22(20)26(33)35)25-23(28)14-29-27(32-25)31-21-9-11-36-12-10-21/h2-8,13-14,17,21H,9-12,15-16H2,1H3,(H,30,34)(H,29,31,32)/t17-/m1/s1
Release date: 2018-05-30
Crystal Structure of Bruton's Tyrosine Kinase in complex with a substituted Cinnoline (PDB entry 4ZLZ)
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): 2
R work: 0.1756
R free: 0.2408
Average B factor: 21.292
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 277
Crystal growth procedure: 10% polyethylene glycol 4000, 20% glycerol, 0.1M imidazole/MES, pH 6.5, 0.12M alcohol mixture
Matthews coefficient: 2.28
Solvent content (%): 46.13
Ligand: IMIDAZOLE (IMD)
Ligand formula: C3 H5 N2
Ligand molecular weight: 69.085
Ligand SMILES: c1c[nH+]c[nH]1
Ligand InChI: InChI=1S/C3H4N2/c1-2-5-3-4-1/h1-3H,(H,4,5)/p+1
Release date: 2015-07-01