satarupa22/MacromolecularLigandDB huggingface dataset:
Crystal structure of human Caspase-1 with 2-((2-naphthoyl)-L-valyl)-4-hydroxy-N-((3S)-2-hydroxy-5-oxotetrahydrofuran-3-yl)-2-azabicyclo[2.2.2]octane-3-carboxamide (Compound 1) (PDB entry 5MMV)
Macromolecule: Caspase-1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.22.36
Sequence length: 179 residues
Sequence: MNPAMPTSSGSEGNVKLCSLEEAQRIWKQKSAEIYPIMDKSSRTRLALIICNEEFDSIPRRTGAEVDITGMTMLLQNLGYSVDVKKNLTASDMTTELEAFAHRPEHKTSDSTFLVFMSHGIREGICGKKHSEQVPDILQLNAIFNMLNTKNCPSLKDKPKVIIIQACRGDSPGVVWFKD
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.15
R work: 0.197
R free: 0.249
Average B factor: 50.54
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 277
Crystal growth procedure: 0.1 M HEPES (pH 7.4), 2 M (NH4)2SO4, and 25 mM DTT
Matthews coefficient: 2.26
Solvent content (%): 45.56
Ligand: (3~{S})-3-[[(3~{S})-2-[(2~{S})-3-methyl-2-(naphthalen-2-ylcarbonylamino)butanoyl]-4-oxidanyl-2-azabicyclo[2.2.2]octan-3-yl]carbonylamino]-4-oxidanyl-butanoic acid (WE0)
Ligand formula: C28 H35 N3 O7
Ligand molecular weight: 525.593
Ligand SMILES: CC(C)C(C(=O)N1C2CCC(C1C(=O)NC(CC(=O)O)CO)(CC2)O)NC(=O)c3ccc4ccccc4c3
Ligand InChI: InChI=1S/C28H35N3O7/c1-16(2)23(30-25(35)19-8-7-17-5-3-4-6-18(17)13-19)27(37)31-21-9-11-28(38,12-10-21)24(31)26(36)29-20(15-32)14-22(33)34/h3-8,13,16,20-21,23-24,32,38H,9-12,14-15H2,1-2H3,(H,29,36)(H,30,35)(H,33,34)/t20-,21-,23-,24+,28-/m0/s1
Release date: 2017-12-20
Human ERK2 in complex with an irreversible inhibitor (PDB entry 4ZZM)
Macromolecule: MITOGEN-ACTIVATED PROTEIN KINASE 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.24
Sequence length: 350 residues
Sequence: PEMVRGQVFDVGPRYTNLSYIGEGAYGMVCSAYDNLNKVRVAIKKISPFEHQTYCQRTLREIKILLRFRHENIIGINDIIRAPTIEQMKDVYIVQDLMETDLYKLLKTQHLSNDHICYFLYQILRGLKYIHSANVLHRDLKPSNLLLNTTCDLKICDFGLARVADPDHDHTGFLTEYVATRWYRAPEIMLNSKGYTKSIDIWSVGCILAEMLSNRPIFPGKHYLDQLNHILGILGSPSQEDLNCIINLKARNYLLSLPHKNKVPWNRLFPNADSKALDLLDKMLTFNPHKRIEVEQALAHPYLEQYYDPSDEPIAEAPFKFDMELDDLPKEKLKELIFEETARFQPGYRS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.89
R work: 0.2073
R free: 0.2544
Average B factor: 35.19
Matthews coefficient: 2.41
Solvent content (%): 48.94
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: 2015-05-27
Crystal structure of human soluble Adenylyl Cyclase with the inhibitor bithionol (PDB entry 5D0R)
Macromolecule: Adenylate cyclase type 10
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.6.1.1
Sequence length: 475 residues
Sequence: MNTPKEEFQDWPIVRIAAHLPDLIVYGHFSPERPFMDYFDGVLMFVDISGFTAMTEKFSSAMYMDRGAEQLVEILNYHISAIVEKVLIFGGDILKFAGDALLALWRVERKQLKNIITVVIKCSLEIHGLFETQEWEEGLDIRVKIGLAAGHISMLVFGDETHSHFLVIGQAVDDVRLAQNMAQMNDVILSPNCWQLCDRSMIEIESVPDQRAVKVNFLKPPPNFNFDEFFTKCTTFMHYYPSGEHKNLLRLACTLKPDPELEMSLQKYVMESILKQIDNKQLQGYLSELRPVTIVFVNLMFEDQDKAEEIGPAIQDAYMHITSVLKIFQGQINKVFMFDKGCSFLCVFGFPGEKVPDELTHALECAMDIFDFCSQVHKIQTVSIGVASGIVFCGIVGHTVRHEYTVIGQKVNLAARMMMYYPGIVTCDSVTYNGSNLPAYFFKELPKKVMKGVADSGPLYQYWGRTEKVHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.24
R work: 0.1773
R free: 0.2437
Average B factor: 35.966
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6
Crystallization temperature (K): 277
Crystal growth procedure: 0.1 M SODIUM ACETATE PH 4.8, 0.2 M TRI-SODIUM-CITRATE, 15% (W/V) PEG 4000, 10% (V/V) GLYCEROL
Matthews coefficient: 2.63
Solvent content (%): 53.25
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: 2016-03-16
Structure of p38 alpha (Mitogen-activated protein kinase 14) complexed with inhibitor 6 (PDB entry 8VXE)
Macromolecule: Mitogen-activated protein kinase 14
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.24
Sequence length: 387 residues
Sequence: MSYYHHHHHHDYDIPTTENLYFQGAMDPSQERPTFYRQELNKTIWEVPERYQNLSPVGSGAYGSVCAAFDTKTGLRVAVKKLSRPFQSIIHAKRTYRELRLLKHMKHENVIGLLDVFTPARSLEEFNDVYLVTHLMGADLNNIVKCQKLTDDHVQFLIYQILRGLKYIHSADIIHRDLKPSNLAVNEDCELKILDFGLARHTDDEMTGYVATRWYRAPEIMLNWMHYNQTVDIWSVGCIMAELLTGRTLFPGTDHIDQLKLILRLVGTPGAELLKKISSESARNYIQSLTQMPKMNFANVFIGANPLAVDLLEKMLVLDSDKRITAAQALAHAYFAQYHDPDDEPVADPYDQSFESRDLLIDEWKSLTYDEVISFVPPPLDQEEMES
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.85
R work: 0.2179
R free: 0.28853
Average B factor: 46.929
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 5
Crystallization temperature (K): 277
Crystal growth procedure: 10% PEG6000, 0.1 MES/NaOH pH 5.0
Matthews coefficient: 2.15
Solvent content (%): 42.72
Ligand: (4M)-4-[3-(4-fluorophenyl)-1-methyl-1H-pyrazol-4-yl]-1H-pyrrolo[2,3-b]pyridine (A1AD9)
Ligand formula: C17 H13 F N4
Ligand molecular weight: 292.31
Ligand SMILES: Cn1cc(c(n1)c2ccc(cc2)F)c3ccnc4c3cc[nH]4
Ligand InChI: InChI=1S/C17H13FN4/c1-22-10-15(13-6-8-19-17-14(13)7-9-20-17)16(21-22)11-2-4-12(18)5-3-11/h2-10H,1H3,(H,19,20)
Release date: 2024-05-08
TGF-BETA RECEPTOR TYPE 1 KINASE DOMAIN (T204D,I211V,Y249F,S280T, Y282F,S287N,A350C,L352F) (PDB entry 5E8U)
Macromolecule: TGF-beta receptor type-1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.30
Sequence length: 307 residues
Sequence: GHMTIARDIVLQESVGKGRFGEVWRGKWRGEEVAVKIFSSREERSWFREAEIFQTVMLRHENILGFIAADNKDNGTWTQLWLVTDFHEHGNLFDYLNRYTVTVEGMIKLALSTASGLAHLHMEIVGTQGKPAIAHRDLKSKNILVKKNGTCCICDFGLAVRHDSATDTIDIAPNHRVGTKRYMAPEVLDDSINMKHFESFKRADIYAMGLVFWEIARRCSIGGIHEDYQLPYYDLVPSDPSVEEMRKVVCEQKLRPNIPNRWQSCEALRVMAKIMRECWYANGAARLTALRIKKTLSQLSQQEGIKM
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.03
R work: 0.1793
R free: 0.2228
Average B factor: 31.27
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.6
Crystallization temperature (K): 277
Crystal growth procedure: 23%(w/v) PEG3350, 3%(v/v) glcyerol
Matthews coefficient: 2.04
Solvent content (%): 39.69
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: 2016-05-11
Structure of the enzyme-product complex resulting from TDG action on a GfC mismatch (PDB entry 4Z7B)
Macromolecule: G/T mismatch-specific thymine DNA glycosylase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.2.2.29
Sequence length: 204 residues
Sequence: GSHMASFNGVSEAELLTKTLPDILTFNLDIVIIGINPGLMAAYKGHHYPGPGNHFWKCLFMSGLSEVQLNHMDDHTLPGKYGIGFTNMVERTTPGSKDLSSKEFREGGRILVQKLQKYQPRIAVFNGKCIYEIFSKEVFGVKVKNLEFGLQPHKIPDTETLCYVMPSSSARCAQFPRAQDKVHYYIKLKDLRDQLKGIERNMDV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.02
R work: 0.1871
R free: 0.2325
Average B factor: 57.23
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6
Crystallization temperature (K): 298
Crystal growth procedure: 30% PEG 4000, 0.2M ammonium acetate, 0.1M sodium acetate
Matthews coefficient: 2.66
Solvent content (%): 48.62
Ligand: 1,2-ETHANEDIOL (EDO)
Ligand formula: C2 H6 O2
Ligand molecular weight: 62.068
Ligand SMILES: C(CO)O
Ligand InChI: InChI=1S/C2H6O2/c3-1-2-4/h3-4H,1-2H2
Release date: 2015-09-16
Aurora-A in complex with CEP192 and an inhibitory monobody (PDB entry 8PR7)
Macromolecule: Aurora kinase A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 283 residues
Sequence: MESKKRQWALEDFEIGRPLGKGKFGNVYLAREKQSKFILALKVLFKAQLEKAGVEHQLRREVEIQSHLRHPNILRLYGYFHDATRVYLILEYAPLGTVYRELQKLSKFDEQRTATYITELANALSYCHSKRVIHRDIKPENLLLGSAGELKIANFGWSVHAPSSRRTTLAGTLDYLPPEMIEGRMHDEKVDLWSLGVLCYEFLVGKPPFEAATYAETYKRISRVEFAFPAFVTEGARDLISRLLKHNPSQRPMLREVLEHPWITANSSKPSNAQNKESASKQS
Oligomeric state: Hetero 6-mer
Stoichiometry: A2, B2, C1, D1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.76
R work: 0.2023
R free: 0.2564
Average B factor: 92.224
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 0.06M Divalents, Buffer system 1 pH 6.5, 40% Ethylene glycol, 20% PEG 8000
Matthews coefficient: 3.38
Solvent content (%): 63.56
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: 2024-07-24
Crystal structure of Aurora-A kinase in complex with an allosterically binding fragment (PDB entry 5OSF)
Macromolecule: Aurora kinase A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 265 residues
Sequence: QWALEDFEIGRPLGKGKFGNVYLAREKQSKFILALKVLFKAQLEKAGVEHQLRREVEIQSHLRHPNILRLYGYFHDATRVYLILEYAPLGTVYRELQKLSKFDEQRTATYITELANALSYCHSKRVIHRDIKPENLLLGSAGELKIADFGWSVHAPSSRRTTLAGTLDYLPPEMIEGRMHDEKVDLWSLGVLCYEFLVGKPPFEANTYQETYKRISRVEFTFPDFVTEGARDLISRLLKHNPSQRPMLREVLEHPWITANSSKPS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.89
R work: 0.2018
R free: 0.2541
Average B factor: 55.1139
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 298
Crystal growth procedure: 0.1 M Tris, pH 8.5: 0.5 M NaCl: 0.2 M MgCl2: 32.5 % v/v PEG 3350
Matthews coefficient: 2.77
Solvent content (%): 55.66
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: 2017-11-01
IDOL F3ab subdomain (PDB entry 6QLZ)
Macromolecule: E3 ubiquitin-protein ligase MYLIP
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2.27
Sequence length: 101 residues
Sequence: ENYGIEWHSVRDSEGQKLLIGVGPEGISICKDDFSPINRIAYPVVQMATQSGKNVYLTVTKESGNSIVLLFKMISTRAASGLYRAITETHAFYRCDTVTSA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.343
Average B factor: 63.5
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 293
Crystal growth procedure: 100mM Hepes pH 7.0
10% (w/v) PEG 6000
Matthews coefficient: 2.18
Solvent content (%): 43.6
Release date: 2020-02-19
HUMAN CD38 ECTODOMAIN BOUND TO COMPOUND 9-ADPR ADDUCT (PDB entry 8P8C)
Macromolecule: ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.2.2
Sequence length: 256 residues
Sequence: RWRQQWSGPGTTKRFPETVLARCVKYTEIHPEMRHVDCQSVWDAFKGAFISKHPCDITEEDYQPLMKLGTQTVPCNKILLWSRIKDLAHQFTQVQRDMFTLEDTLLGYLADDLTWCGEFATSKINYQSCPDWRKDCSNNPVSVFWKTVSRRFAEAACDVVHVMLDGSRSKIFDKDSTFGSVEVHNLQPEKVQTLEAWVIHGGREDSRDLCQDPTIKELESIISKRNIQFSCKNIYRPDKFLQCVKNPEDSSCTSEI
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.653
R work: 0.2024
R free: 0.244
Average B factor: 26.11
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 9
Crystallization temperature (K): 277
Crystal growth procedure: 0.1 M bicine/NaOH pH 9.0, 20% w/v PEG 6000
Matthews coefficient: 1.94
Solvent content (%): 36.56
Ligand: [[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{R})-5-[4-[4-[[4-(2-methoxyethoxy)cyclohexyl]amino]-1-methyl-2-oxidanylidene-quinolin-6-yl]pyrazol-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate (X5T)
Ligand formula: C37 H49 N9 O16 P2
Ligand molecular weight: 937.783
Ligand SMILES: CN1c2ccc(cc2C(=CC1=O)NC3CCC(CC3)OCCOC)c4cnn(c4)C5C(C(C(O5)COP(=O)(O)OP(=O)(O)OCC6C(C(C(O6)n7cnc8c7ncnc8N)O)O)O)O
Ligand InChI: InChI=1S/C37H49N9O16P2/c1-44-25-8-3-19(11-23(25)24(12-28(44)47)43-21-4-6-22(7-5-21)57-10-9-56-2)20-13-42-46(14-20)37-33(51)31(49)27(61-37)16-59-64(54,55)62-63(52,53)58-15-26-30(48)32(50)36(60-26)45-18-41-29-34(38)39-17-40-35(29)45/h3,8,11-14,17-18,21-22,26-27,30-33,36-37,43,48-51H,4-7,9-10,15-16H2,1-2H3,(H,52,53)(H,54,55)(H2,38,39,40)/t21-,22-,26-,27-,30-,31-,32-,33-,36-,37-/m1/s1
Release date: 2023-07-26
Crystal structure of Tdp1 catalytic domain in complex with compound XZ519 (PDB entry 6MJ5)
Macromolecule: Tyrosyl-DNA phosphodiesterase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.4
Sequence length: 460 residues
Sequence: GEGQDIWDMLDKGNPFQFYLTRVSGVKPKYNSGALHIKDILSPLFGTLVSSAQFNYCFDVDWLVKQYPPEFRKKPILLVHGDKREAKAHLHAQAKPYENISLCQAKLDIAFGTHHTKMMLLLYEEGLRVVIHTSNLIHADWHQKTQGIWLSPLYPRIADGTHKSGESPTHFKADLISYLMAYNAPSLKEWIDVIHKHDLSETNVYLIGSTPGRFQGSQKDNWGHFRLKKLLKDHASSMPNAESWPVVGQFSSVGSLGADESKWLCSEFKESMLTLGKESKTPGKSSVPLYLIYPSVENVRTSLEGYPAGGSLPYSIQTAEKQNWLHSYFHKWSAETSGRSNAMPHIKTYMRPSPDFSKIAWFLVTSANLSKAAWGALEKNGTQLMIRSYELGVLFLPSAFGLDSFKVKQKFFAGSQEPMATFPVPYDLPPELYGSKDRPWIWNIPYVKAPDTHGNMWVPS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.853
R work: 0.1775
R free: 0.2183
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 292
Crystal growth procedure: protein 22 mg/mL

0.1M MOPS/HEPES-Na pH 7.5
10% w/v PEG 8000
20% v/v ethylene glycol
0.03M sodium fluoride
0.03M sodium bromide
0.03M sodium iodide
Matthews coefficient: 2.47
Solvent content (%): 50.2
Ligand: 1,2-ETHANEDIOL (EDO)
Ligand formula: C2 H6 O2
Ligand molecular weight: 62.068
Ligand SMILES: C(CO)O
Ligand InChI: InChI=1S/C2H6O2/c3-1-2-4/h3-4H,1-2H2
Release date: 2019-07-03
APE1 exonuclease substrate complex wild-type (PDB entry 6W3L)
Macromolecule: TCGACGGATCC
Type: DNA, polydeoxyribonucleotide
Source organism: synthetic construct
Sequence length: 11 residues
Sequence: TCGACGGATCC
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.59
R work: 0.217
R free: 0.277
Average B factor: 61.25
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 7% PEG20000, 100 mM sodium citrate, 15% glycerol, 5 mM calcium chloride
Matthews coefficient: 2.65
Solvent content (%): 53.55
Ligand: CALCIUM ION (CA)
Ligand formula: Ca
Ligand molecular weight: 40.078
Ligand SMILES: [Ca+2]
Ligand InChI: InChI=1S/Ca/q+2
Release date: 2020-06-10
crystal structure of PARP14 bound to N-{4-[4-(diphenylmethoxy)piperidin-1-yl]butyl}[1,2,4]triazolo[4,3-b]pyridazin-6-amine inhibitor (PDB entry 5V7T)
Macromolecule: Poly [ADP-ribose] polymerase 14
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.4.2.30
Sequence length: 194 residues
Sequence: GGSDMKQQNFCVVELLPSDPEYNTVASKFNQTCSHFRIEKIERIQNPDLWNSYQAKKKTMDAKNGQTMNEKQLFHGTDAGSVPHVNRNGFNRSYAGKNAVAYGKGTYFAVNANYSANDTYSRPDANGRKHVYYVRVLTGIYTHGNHSLIVPPSKNPQNPTDLYDTVTDNVHHPSLFVAFYDYQAYPEYLITFRK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.3
R work: 0.22098
R free: 0.29097
Average B factor: 65.976
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 298
Crystal growth procedure: 20% PEG3350, 0.2M Sodium-malonate, pH 7.2-7.8
Matthews coefficient: 2.94
Solvent content (%): 58.22
Ligand: N-{4-[4-(diphenylmethoxy)piperidin-1-yl]butyl}[1,2,4]triazolo[4,3-b]pyridazin-6-amine (91V)
Ligand formula: C27 H32 N6 O
Ligand molecular weight: 456.583
Ligand SMILES: c1ccc(cc1)C(c2ccccc2)OC3CCN(CC3)CCCCNc4ccc5nncn5n4
Ligand InChI: InChI=1S/C27H32N6O/c1-3-9-22(10-4-1)27(23-11-5-2-6-12-23)34-24-15-19-32(20-16-24)18-8-7-17-28-25-13-14-26-30-29-21-33(26)31-25/h1-6,9-14,21,24,27H,7-8,15-20H2,(H,28,31)
Release date: 2017-05-03
pMob1-Lats1 complex (PDB entry 5BRK)
Macromolecule: MOB kinase activator 1A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 217 residues
Sequence: GMSFLFSSRSSKTFKPKKNIPEGSHQYELLKHAEATLGSGNLRQAVMLPEGEDLNEWIAVNTVDFFNQINMLYGTITEFCTEASCPVMSAGPRYEYHWADGTNIKKPIKCSAPKYIDYLMTWVQDQLDDETLFPSKIGVPFPKNFMSVAKTILKRLFRVYAHIYHQHFDSVMQLQEEAHLNTSFKHFIFFVQEFNLIDRRELAPLQELIEKLGSKDR
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.3
R work: 0.1857
R free: 0.2205
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5
Crystallization temperature (K): 293
Crystal growth procedure: 0.2 M di-Ammonium citrate
20% (W/V) PEG 3,350
Matthews coefficient: 2.42
Solvent content (%): 49.08
Ligand: ZINC ION (ZN)
Ligand formula: Zn
Ligand molecular weight: 65.409
Ligand SMILES: [Zn+2]
Ligand InChI: InChI=1S/Zn/q+2
Release date: 2015-07-08
The KNL1-PP1 Holoenzyme (PDB entry 6CZO)
Macromolecule: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.16
Sequence length: 299 residues
Sequence: GHMGSLNLDSIIGRLLEVQGSRPGKNVQLTENEIRGLCLKSREIFLSQPILLELEAPLKICGDIHGQYYDLLRLFEYGGFPPESNYLFLGDYVDRGKQSLETICLLLAYKIKYPENFFLLRGNHECASINRIYGFYDECKRRYNIKLWKTFTDCFNCLPIAAIVDEKIFCCHGGLSPDLQSMEQIRRIMRPTDVPDQGLLCDLLWSDPDKDVQGWGENDRGVSFTFGAEVVAKFLHKHDLDLICRAHQVVEDGYEFFAKRQLVTLFSAPNYCGEFDNAGAMMSVDETLMCSFQILKPAD
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.95
R work: 0.169
R free: 0.213
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 10% PEG 6000, 0.1 M HEPES, VAPOR
 DIFFUSION, TEMPERATURE 277K
Matthews coefficient: 3.43
Solvent content (%): 68.14
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: 2019-01-23
SMYD2 in complex with AZ506 (PDB entry 5KJN)
Macromolecule: N-lysine methyltransferase SMYD2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1
Sequence length: 429 residues
Sequence: GLGGLERFCSPGKGRGLRALQPFQVGDLLFSCPAYAYVLTVNERGNHCEYCFTRKEGLSKCGRCKQAFYCNVECQKEDWPMHKLECSPMVVFGENWNPSETVRLTARILAKQKIHPERTPSEKLLAVKEFESHLDKLDNEKKDLIQSDIAALHHFYSKHLEFPDNDSLVVLFAQVNCNGFTIEDEELSHLGSAIFPDVALMNHSCCPNVIVTYKGTLAEVRAVQEIKPGEEVFTSYIDLLYPTEDRNDRLRDSYFFTCECQECTTKDKDKAKVEIRKLSDPPKAEAIRDMVRYARNVIEEFRRAKHYKSPSELLEICELSQEKMSSVFEDSNVYMLHMMYQAMGVCLYMQDWEGALQYGQKIIKPYSKHYPLYSLNVASMWLKLGRLYMGLEHKAAGEKALKKAIAIMEVAHGKDHPYISEIKQEIESH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.72
R work: 0.162
R free: 0.225
Average B factor: 57.18
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: 20% PEG 3350, 0.1 M Tris-HCl, 5% ethanol
Matthews coefficient: 3.18
Solvent content (%): 61.28
Ligand: S-ADENOSYLMETHIONINE (SAM)
Ligand formula: C15 H22 N6 O5 S
Ligand molecular weight: 398.437
Ligand SMILES: C[S+](CCC(C(=O)[O-])N)CC1C(C(C(O1)n2cnc3c2ncnc3N)O)O
Ligand InChI: InChI=1S/C15H22N6O5S/c1-27(3-2-7(16)15(24)25)4-8-10(22)11(23)14(26-8)21-6-20-9-12(17)18-5-19-13(9)21/h5-8,10-11,14,22-23H,2-4,16H2,1H3,(H2-,17,18,19,24,25)/t7-,8+,10+,11+,14+,27-/m0/s1
Release date: 2016-12-07
Structure of the N-SH2 domain of the human tyrosine-protein phosphatase non-receptor type 11 in complex with the phosphorylated immune receptor tyrosine-based inhibitory motif (PDB entry 6ROY)
Macromolecule: Tyrosine-protein phosphatase non-receptor type 11
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 104 residues
Sequence: MASRRWFHPNITGVEAENLLLTRGVDGSFLARPSKSNPGDFTLSVRRNGAVTHIKIQNTGDYYDLYGGEKFATLAELVQYYMEHHGQLKEKNGDVIELKYPLNC
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.1
R work: 0.22525
R free: 0.2785
Average B factor: 35.16
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.1
Crystallization temperature (K): 291
Crystal growth procedure: 31.7% (w/v) PEG3350, 0.1 M HEPES, 0.233 M MgSO4
Matthews coefficient: 1.82
Solvent content (%): 32.39
Release date: 2020-02-19
Crystal structure of human KDM4A in complex with compound 37 (PDB entry 5F39)
Macromolecule: Lysine-specific demethylase 4A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11
Sequence length: 360 residues
Sequence: SMASESETLNPSARIMTFYPTMEEFRNFSRYIAYIESQGAHRAGLAKVVPPKEWKPRASYDDIDDLVIPAPIQQLVTGQSGLFTQYNIQKKAMTVREFRKIANSDKYCTPRYSEFEELERKYWKNLTFNPPIYGADVNGTLYEKHVDEWNIGRLRTILDLVEKESGITIEGVNTPYLYFGMWKTSFAWHTEDMDLYSINYLHFGEPKSWYSVPPEHGKRLERLAKGFFPGSAQSCEAFLRHKMTLISPLMLKKYGIPFDKVTQEAGEFMITFPYGYHAGFNHGFNCAESTNFATRRWIEYGKQAVLCSCRKDMVKISMDVFVRKFQPERYKLWKAGKDNTVIDHTLPTPEAAEFLKESEL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.65
R work: 0.169
R free: 0.2097
Average B factor: 73.75
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 291
Crystal growth procedure: Crystallisation solution is 0.1M Bis-Tris-Propane pH7.5, 12-16% PEG-4000. Inhibitor is soaked in crystals by addition directly to the drops of DMSO dissolved compound
Matthews coefficient: 2.52
Solvent content (%): 51.13
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: 2016-01-20
ARHGEF2 PanDDA analysis group deposition -- ARHGEF2 and RhoA in complex with Z1037511924 (PDB entry 7G8C)
Macromolecule: Transforming protein RhoA
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.5.2
Sequence length: 185 residues
Sequence: SMAAIRKKLVIVGDGACGKTCLLIVFSKDQFPEVYVPTVFENYVADIEVDGKQVELALWDTAGQEDYDRLRPLSYPDTDVILMCFSIDSPDSLENIPEKWTPEVKHFCPNVPIILVGNKKDLRNDEHTRRELAKMKQEPVKPEEGRDMANRIGAFGYMECSAKTKDGVREVFEMATRAALQARRG
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.176
R work: 0.2024
R free: 0.2552
Average B factor: 43.36
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 293
Crystal growth procedure: 100 mM Tris, 2.6M sodium formate
Matthews coefficient: 2.56
Solvent content (%): 51.91
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: 2023-07-12
Crystal structure of Steroid 5-alpha-reductase 2 in complex with Finasteride (PDB entry 7BW1)
Macromolecule: 3-oxo-5-alpha-steroid 4-dehydrogenase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.3.1.22
Sequence length: 258 residues
Sequence: GGGTMQVQCQQSPVLAGSATLVALGALALYVAKPSGYGKHTESLKPAATRLPARAAWFLQELPSFAVPAGILARQPLSLFGPPGTVLLGLFCVHYFHRTFVYSLLNRGRPYPAILILRGTAFCTGNGVLQGYYLIYCAEYPDGWYTDIRFSLGVFLFILGMGINIHSDYILRQLRKPGEISYRIPQGGLFTYVSGANFLGEIIEWIGYALATWSLPALAFAFFSLCFLGLRAFHHHRFYLKMFEDYPKSRKALIPFIF
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.8
R work: 0.2391
R free: 0.2646
Average B factor: 75.84
Crystallization method: LIPIDIC CUBIC PHASE
Crystallization temperature (K): 293
Crystal growth procedure: 30% v/v PEG600, 100mM tris-sodium citrate ph5.0, 100mM sodium chloride, 100mM Lithium sulfate
Matthews coefficient: 3
Solvent content (%): 59.02
Ligand: (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate (OLC)
Ligand formula: C21 H40 O4
Ligand molecular weight: 356.54
Ligand SMILES: CCCCCCCCC=CCCCCCCCC(=O)OCC(CO)O
Ligand InChI: InChI=1S/C21H40O4/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-21(24)25-19-20(23)18-22/h9-10,20,22-23H,2-8,11-19H2,1H3/b10-9-/t20-/m1/s1
Release date: 2020-08-05