satarupa22/MacromolecularLigandDB huggingface dataset:
Crystal structure of Aldo-Keto Reductase 1C3 (AKR1C3) complexed with inhibitor. (PDB entry 6GXK)
Macromolecule: Aldo-keto reductase family 1 member C3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1
Sequence length: 323 residues
Sequence: MDSKQQCVKLNDGHFMPVLGFGTYAPPEVPRSKALEVTKLAIEAGFRHIDSAHLYNNEEQVGLAIRSKIADGSVKREDIFYTSKLWSTFHRPELVRPALENSLKKAQLDYVDLYLIHSPMSLKPGEELSPTDENGKVIFDIVDLCTTWEAMEKCKDAGLAKSIGVSNFNRRQLEMILNKPGLKYKPVCNQVECHPYFNRSKLLDFCKSKDIVLVAYSALGSQRDKRWVDPNSPVLLEDPVLCALAKKHKRTPALIALRYQLQRGVVVLAKSYNEQRIRQNVQVFEFQLTAEDMKAIDGLDRNLHYFNSDSFASHPNYPYSDEY
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.7
R work: 0.1601
R free: 0.1987
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 277
Crystal growth procedure: 10mM MES pH6.0, 25% PEG8000
Matthews coefficient: 2.38
Solvent content (%): 48.32
Ligand: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE (NAP)
Ligand formula: C21 H28 N7 O17 P3
Ligand molecular weight: 743.405
Ligand SMILES: c1cc(c[n+](c1)C2C(C(C(O2)COP(=O)([O-])OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)OP(=O)(O)O)O)O)O)C(=O)N
Ligand InChI: InChI=1S/C21H28N7O17P3/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(44-46(33,34)35)14(30)11(43-21)6-41-48(38,39)45-47(36,37)40-5-10-13(29)15(31)20(42-10)27-3-1-2-9(4-27)18(23)32/h1-4,7-8,10-11,13-16,20-21,29-31H,5-6H2,(H7-,22,23,24,25,32,33,34,35,36,37,38,39)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
Release date: 2019-05-08
Non-receptor Protein Tyrosine Phosphatase SHP2 in Complex with Allosteric Inhibitor SHP099 (PDB entry 5EHR)
Macromolecule: Tyrosine-protein phosphatase non-receptor type 11
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 526 residues
Sequence: SMTSRRWFHPNITGVEAENLLLTRGVDGSFLARPSKSNPGDFTLSVRRNGAVTHIKIQNTGDYYDLYGGEKFATLAELVQYYMEHHGQLKEKNGDVIELKYPLNCADPTSERWFHGHLSGKEAEKLLTEKGKHGSFLVRESQSHPGDFVLSVRTGDDKGESNDGKSKVTHVMIRCQELKYDVGGGERFDSLTDLVEHYKKNPMVETLGTVLQLKQPLNTTRINAAEIESRVRELSKLAETTDKVKQGFWEEFETLQQQECKLLYSRKEGQRQENKNKNRYKNILPFDHTRVVLHDGDPNEPVSDYINANIIMPEFETKCNNSKPKKSYIATQGCLQNTVNDFWRMVFQENSRVIVMTTKEVERGKSKCVKYWPDEYALKEYGVMRVRNVKESAAHDYTLRELKLSKVGQGNTERTVWQYHFRTWPDHGVPSDPGGVLDFLEEVHHKQESIMDAGPVVVHCSAGIGRTGTFIVIDILIDIIREKGVDCDIDVPKTIQMVRSQRSGMVQTEAQYRFIYMAVQHYIETL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.7
R work: 0.1948
R free: 0.2207
Average B factor: 30.39
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 17% PEG3350, 200mM Ammonium Phosphate
Matthews coefficient: 2.27
Solvent content (%): 45.82
Ligand: PHOSPHATE ION (PO4)
Ligand formula: O4 P
Ligand molecular weight: 94.971
Ligand SMILES: [O-]P(=O)([O-])[O-]
Ligand InChI: InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4)/p-3
Release date: 2016-06-29
ATAD2 in complex with PepLite-Val (PDB entry 7Z9N)
Macromolecule: ATPase family AAA domain-containing protein 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.1.3
Sequence length: 130 residues
Sequence: SMQEEDTFRELRIFLRNVTHRLAIDKRFRVFTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLRDIDLICSNALEYNPDRDPGDRLIRHRACALRDTAYAIIKEELDEDFEQLCEEIQESR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.34
R work: 0.2078
R free: 0.227
Average B factor: 30.216
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M BisTris pH 6-7, 1.7-2.1M Ammonium sulphate
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: 2022-11-23
Crystal structure of human Casein Kinase II subunit alpha (CK2a1) in complex with allosteric ligand FGC3336 (PDB entry 9EPW)
Macromolecule: Casein kinase II subunit alpha
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 338 residues
Sequence: SMSGPVPSRARVYTDVNTHRPREYWDYESHVVEWGNQDDYQLVRKLGRGKYSEVFEAINITNNEKVVVKILKPVKKKKIKREIKILENLRGGPNIITLADIVKDPVSRTPALVFEHVNNTDFKQLYQTLTDYDIRFYMYEILKALDYCHSMGIMHRDVKPHNVMIDHEHRKLRLIDWGLAEFYHPGQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRKEPFFHGHDNYDQLVRIAKVLGTEDLYDYIDKYNIELDPRFNDILGRHSRKRWERFVHSENQHLVSPEALDFLDKLLRYDHQSRLTAREAMEHPYFYTVVKDQARMGSS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.3
R work: 0.25888
R free: 0.30791
Average B factor: 46.536
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.2 M ammonia sulphate 0.1 M bis-tris pH 5.5 23-26% PEG 3350
Matthews coefficient: 2.15
Solvent content (%): 42.67
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: 2024-05-01
CRYSTAL STRUCTURE OF GLYCOGEN SYNTHASE KINASE 3 BETA COMPLEXED WITH (4S)-N-{4-[(2S)-2-methylmorpholin-4-yl] pyridin-3-yl}-2-phenylimidazo[1,2-b]pyridazine-8-carboxamide (PDB entry 8DJC)
Macromolecule: Glycogen synthase kinase-3 beta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.26
Sequence length: 441 residues
Sequence: MHSSHHHHHHSSGENLYFQGHMSGRPRTTSFAESCKPVQQPSAFGSMKVSRDKDGSKVTTVVATPGQGPDRPQEVSYTDTKVIGNGSFGVVYQAKLCDSGELVAIKKVLQDKRFKNRELQIMRKLDHCNIVRLRYFFYSSGEKKDEVYLNLVLDYVPETVYRVARHYSRAKQTLPVIYVKLYMYQLFRSLAYIHSFGICHRDIKPQNLLLDPDTAVLKLCDFGSAKQLVRGEPNVSYICSRYYRAPELIFGATDYTSSIDVWSAGCVLAELLLGQPIFPGDSGVDQLVEIIKVLGTPTREQIREMNPNYTEFKFPQIKAHPWTKVFRPRTPPEAIALCSRLLEYTPTARLTPLEACAHSFFDELRDPNVKLPNGRDTPALFNFTTQELSSNPPLATILIPPHARIQAAASTPTNATAASDANTGDRGQTNNAASASASNST
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.463
R work: 0.2156
R free: 0.2419
Average B factor: 48.87
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M MES pH 6.0, 20.0 %w/v PEG6K, 0.2 M NH4Cl
Matthews coefficient: 3.23
Solvent content (%): 61.95
Ligand: (4S)-N-{4-[(2S)-2-methylmorpholin-4-yl]pyridin-3-yl}-2-phenylimidazo[1,2-b]pyridazine-8-carboxamide (UAU)
Ligand formula: C23 H22 N6 O2
Ligand molecular weight: 414.46
Ligand SMILES: CC1CN(CCO1)c2ccncc2NC(=O)c3ccnn4c3nc(c4)c5ccccc5
Ligand InChI: InChI=1S/C23H22N6O2/c1-16-14-28(11-12-31-16)21-8-9-24-13-19(21)27-23(30)18-7-10-25-29-15-20(26-22(18)29)17-5-3-2-4-6-17/h2-10,13,15-16H,11-12,14H2,1H3,(H,27,30)/t16-/m0/s1
Release date: 2023-03-22
Crystal structure of human low molecular weight protein tyrosine phosphatase (LMPTP) type A (PDB entry 5JNR)
Macromolecule: Low molecular weight phosphotyrosine protein phosphatase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 160 residues
Sequence: GSMAEQATKSVLFVCLGNICRSPIAEAVFRKLVTDQNISENWRVDSAATSGYEIGNPPDYRGQSCMKRHGIPMSHVARQITKEDFATFDYILCMDESNLRDLNRKSNQVKTCKAKIELLGSYDPQKQLIIEDPYYGNDSDFETVYQQCVRCCRAFLEKAH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2
R work: 0.1634
R free: 0.2136
Average B factor: 25.942
Crystallization method: EVAPORATION
Crystallization pH: 5.5
Crystallization temperature (K): 293
Crystal growth procedure: 7% PEG 10K, Bis Tris, Ammonium Acetate
Matthews coefficient: 2.4
Solvent content (%): 48.69
Release date: 2017-03-29
Ternary complex crystal structure of DNA polymerase Beta with "hot-spot sequence" with dGTP (PDB entry 6NKU)
Macromolecule: DNA (5'-D(P*TP*TP*CP*GP*G)-3')
Type: DNA, polydeoxyribonucleotide
Source organism: Homo sapiens
Sequence length: 5 residues
Sequence: TTCGG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.9
R work: 0.1741
R free: 0.2107
Average B factor: 32.1551
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 291
Crystal growth procedure: 16-18% PEG 3350, 350 mM Sodium Acetate, 50 mM Imidazole
Matthews coefficient: 2.28
Solvent content (%): 46.02
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: 2020-01-08
Crystal structure of human carbonic anhydrase I in complex with 4-(3-(2-((4-fluorobenzyl)amino)ethyl)ureido) benzenesulfonamide (PDB entry 6XZS)
Macromolecule: Carbonic anhydrase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 261 residues
Sequence: MASPDWGYDDKNGPEQWSKLYPIANGNNQSPVDIKTSETKHDTSLKPISVSYNPATAKEIINVGHSFHVNFEDNDNRSVLKGGPFSDSYRLFQFHFHWGSTNEHGSEHTVDGVKYSAELHVAHWNSAKYSSLAEAASKADGLAVIGVLMKVGEANPKLQKVLDALQAIKTKGKRAPFTNFDPSTLLPSSLDFWTYPGSLTHPPLYESVTWIICKESISVSSEQLAQFRSLLSNVEGDNAVPMQHNNRPTQPLKGRTVRASF
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.53
R work: 0.1962
R free: 0.2184
Average B factor: 28.72
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 9
Crystallization temperature (K): 293
Crystal growth procedure: 200 mM Na-acetate, 30% PEG 4000, 100 mM Tris-HCl pH 9.
Inhibitor: 150 mM NaCl, 10% DMSO,  50 mM Tris pH 7
Matthews coefficient: 2.36
Solvent content (%): 47.84
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
CRYSTAL STRUCTURE OF MONOBODY AS25/ABL1 SH2 DOMAIN COMPLEX, CRYSTAL A (PDB entry 5DC4)
Macromolecule: Tyrosine-protein kinase ABL1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 123 residues
Sequence: GSPSNYITPVNSLEKHSWYHGPVSRNAAEYLLSSGINGSFLVRESESSPGQRSISLRYEGRVYHYRINTASDGKLYVSSESRFNTLAELVHHHSTVADGLITTLHYPAPKRNKPTVYGVSPNY
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.48
R work: 0.14447
R free: 0.18965
Average B factor: 15.81
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.83
Crystallization temperature (K): 291
Crystal growth procedure: 0.1M Imidazole pH 7.83 and 3.5M NaCl
Matthews coefficient: 1.88
Solvent content (%): 34.46
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: 2016-03-02
Disulfide between E3 HECT ligase Smurf2 and Ubiquitin G76C (PDB entry 6FX4)
Macromolecule: E3 ubiquitin-protein ligase SMURF2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2.26
Sequence length: 122 residues
Sequence: GAMGKIDVNDWKVNTRLKHATPDSNIVKWFWKAVEFFDEERRARLLQFVTGSSRVPLQGFKALQGAAGPRLFTIHQIDANTNNLPKAHTCFNRIDIPPYESYEKLYEKLLTAIEETSGFAVE
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.5
R work: 0.1873
R free: 0.239
Average B factor: 39.1772
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 1.36M tri-Sodium citrat pH6.5, 15% (v/v) Glycerol
Matthews coefficient: 2.51
Solvent content (%): 51.07
Ligand: GLYCEROL (GOL)
Ligand formula: C3 H8 O3
Ligand molecular weight: 92.094
Ligand SMILES: C(C(CO)O)O
Ligand InChI: InChI=1S/C3H8O3/c4-1-3(6)2-5/h3-6H,1-2H2
Release date: 2018-07-11
Co-crystal structure of FTO bound to 22 (PDB entry 8IT9)
Macromolecule: Alpha-ketoglutarate-dependent dioxygenase FTO
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11
Sequence length: 491 residues
Sequence: HHHHHHSSGLVPRGSHMTPKDDEFYQQWQLKYPKLILREASSVSEELHKEVQEAFLTLHKHGCLFRDLVRIQGKDLLTPVSRILIGNPGCTYKYLNTRLFTVPWPVKGSNIKHTEAEIAAACETFLKLNDYLQIETIQALEELAAKEKANEDAVPLCMSADFPRVGMGSSYNGQDEVDIKSRAAYNVTLLNFMDPQKMPYLKEEPYFGMGKMAVSWHHDENLVDRSAVAVYSYSCEGPEEESEDDSHLEGRDPDIWHVGFKISWDIETPGLAIPLHQGDCYFMLDDLNATHQHCVLAGSQPRFSSTHRVAECSTGTLDYILQRCQLALQNVCDDVDNDDVSLKSFEPAVLKQGEEIHNEVEFEWLRQFWFQGNRYRKCTDWWCQPMAQLEALWKKMEGVTNAVLHEVKREGLPVEQRNEILTAILASLTARQNLRREWHARCQSRIARTLPADQKPECRPYWEKDDASMPLPFDLTDIVSELRGQLLEAKP
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.14
R work: 0.22159
R free: 0.2392
Average B factor: 41.946
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 100 mM sodium citrate, pH 5.4, 11.5% (w/v) polyethylene glycol (PEG) 3350, and 8% isopropanol
Matthews coefficient: 2.91
Solvent content (%): 57.68
Ligand: 2-[(2,6-diethyl-4-pyridin-4-yl-phenyl)amino]-6-(1,4-oxazepan-4-ylmethyl)benzoic acid (ZL6)
Ligand formula: C28 H33 N3 O3
Ligand molecular weight: 459.58
Ligand SMILES: CCc1cc(cc(c1Nc2cccc(c2C(=O)O)CN3CCCOCC3)CC)c4ccncc4
Ligand InChI: InChI=1S/C28H33N3O3/c1-3-20-17-24(22-9-11-29-12-10-22)18-21(4-2)27(20)30-25-8-5-7-23(26(25)28(32)33)19-31-13-6-15-34-16-14-31/h5,7-12,17-18,30H,3-4,6,13-16,19H2,1-2H3,(H,32,33)
Release date: 2024-02-14
Crystal Structure of HDM2 in complex with Nutlin-3a (PDB entry 5C5A)
Macromolecule: E3 ubiquitin-protein ligase Mdm2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 6.3.2
Sequence length: 92 residues
Sequence: PASEQETLVRPKPLLLKLLKSVGAQKDTYTMKEVLFYLGQYIMTKRLYDEKQQHIVYCSNDLLGDLFGVPSFSVKEHRKIYTMIYRNLVVVN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.146
R work: 0.1531
R free: 0.1683
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.2M Potassium iodide, 2.2M Ammonium Sulfate
Matthews coefficient: 2.19
Solvent content (%): 43.9
Ligand: 4-({(4S,5R)-4,5-bis(4-chlorophenyl)-2-[4-methoxy-2-(propan-2-yloxy)phenyl]-4,5-dihydro-1H-imidazol-1-yl}carbonyl)piperazin-2-one (NUT)
Ligand formula: C30 H30 Cl2 N4 O4
Ligand molecular weight: 581.49
Ligand SMILES: CC(C)Oc1cc(ccc1C2=NC(C(N2C(=O)N3CCNC(=O)C3)c4ccc(cc4)Cl)c5ccc(cc5)Cl)OC
Ligand InChI: InChI=1S/C30H30Cl2N4O4/c1-18(2)40-25-16-23(39-3)12-13-24(25)29-34-27(19-4-8-21(31)9-5-19)28(20-6-10-22(32)11-7-20)36(29)30(38)35-15-14-33-26(37)17-35/h4-13,16,18,27-28H,14-15,17H2,1-3H3,(H,33,37)/t27-,28+/m0/s1
Release date: 2016-06-29
Crystal structure of human NEIL1(R242, Y244H) bound to duplex DNA containing 2'-fluoro-2'-deoxy-5,6-dihydrouridine (PDB entry 6LWO)
Macromolecule: Endonuclease 8-like 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.2.2
Sequence length: 295 residues
Sequence: MPEGPELHLASQFVNEACRALVFGGCVEKSSVSRNPEVPFESSAYRISASARGKELRLILSPLPGAQPQQEPLALVFRFGMSGSFQLVPREELPRHAHLRFYTAPPGPRLALCFVDIRRFGRWDLGGKWQPGRGPCVLQEYQQFRENVLRNLADKAFDRPICEALLDQRFFNGIGNYLRAEILYRLKIPPFEKARSVLEALQQHRPSPELTLSQKIRTKLQNPDLLELCHSVPKEVVQLGGRGHGSESGEEDFAAFRAWLRCYGMPGMSSLQDRHGRTIWFQGDPGPLAPKGRKS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.51
R work: 0.2027
R free: 0.2428
Average B factor: 75.438
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 277.15
Crystal growth procedure: 0.1 M cacodylic acid (pH 6.5), 0.1 M NaCl, 0.05 M MgCl2 and 18% (w/v) PEG 8000
Matthews coefficient: 3.04
Solvent content (%): 59.5
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: 2021-06-09
Crystal Structure of SIRT3 in complex with H3K4bhb peptide (PDB entry 5Z94)
Macromolecule: NAD-dependent protein deacetylase sirtuin-3, mitochondrial
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.5.1
Sequence length: 283 residues
Sequence: SSDKGKLSLQDVAELIRARACQRVVVMVGAGISTPSGIPDFRSPGSGLYSNLQQYDLPYPEAIFELPFFFHNPKPFFTLAKELYPGNYKPNVTHYFLRLLHDKGLLLRLYTQNIDGLERVSGIPASKLVEAHGTFASATCTVCQRPFPGEDIRADVMADRVPRCPVCTGVVKPDIVFFGEPLPQRFLLHVVDFPMADLLLILGTSLEVEPFASLTEAVRSSVPRLLINRDLVGPLAWHPRSRDVAQLGDVVHGVESLVELLGWTEEMRDLVQRETGKLDGPDK
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.899
R work: 0.1607
R free: 0.1911
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 0.2M Li2SO4, 0.1M sodium citrate, pH 6.0, 19% PEG 3,350
Matthews coefficient: 2.95
Solvent content (%): 58.37
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: 2019-02-06
DNA Polymerase Mu (K438D), 8-oxodGTP:Ct Product State Ternary Complex, 50 mM Mn2+ (90min) (PDB entry 7KTL)
Macromolecule: DNA-directed DNA/RNA polymerase mu
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 356 residues
Sequence: GSAAAPLSPAWMPAYACQRPTPLTHHNTGLSEALEILAEAAGFEGSEGRLLTFCRAASVLKALPSPVTTLSQLQGLPHFGEHSSRVVQELLEHGVCEEVERVRRSERYQTMKLFTQIFGVGVKTADRWYREGLRTLDDLREQPQKLTQQQKAGLQHHQDLSTPVLRSDVDALQQVVEEAVGQALPGATVTLTGGFRRGKLQGHDVDFLITHPKEGQEAGLLPRVMCRLQDQGLILYHQHQHSCCESPTRLAQQSHMDAFERSFCIFRLPQPGSWKAVRVDLVVAPVSQFPFALLGWTGSDLFQRELRRFSRKEKGLWLNSHGLFDPEQKTFFQAASEEDIFRHLGLEYLPPEQRNA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.421
R work: 0.1584
R free: 0.1738
Average B factor: 26.2035
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 85-90mM HEPES pH 7.5, 17-18% PEG4000
Matthews coefficient: 2.44
Solvent content (%): 49.66
Ligand: SODIUM ION ()
Ligand formula: Na
Ligand molecular weight: 22.99
Ligand SMILES: [Na+]
Ligand InChI: InChI=1S/Na/q+1
Release date: 2022-05-11
Crystal Structure of human Legumain in complex with (2S)-N-[(3S)-5-amino-5-oxopent-1-yn-3-yl]-1-[1-[4-(cyclopropylmethoxy)phenyl]cyclopropanecarbonyl]pyrrolidine-2-carboxamide (PDB entry 7FQH)
Macromolecule: Legumain
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.22.34
Sequence length: 444 residues
Sequence: MKLCILLAVVAFVGLSLGVPIDDPEDGGKHWVVIVAGSNGWYNYRHQADACHAYQIIHRNGIPDEQIVVMMYDDIAYSEDNPTPGIVINRPNGTDVYQGVPKDYTGEDVTPQNFLAVLRGDAEAVKGIGSGKVLKSGPQDHVFIYFTNHGSTGILVFPNEDLHVKDLNETIHYMYKHKMYRKMVFYIEACESGSMMNHLPDNINVYATTAANPRESSYACYYDEKRSTYLGDWYSVNWMEDSDVEDLTKETLHKQYHLVKSHTNTSHVMQYGQKTISTMKVMQFQGMKRKASSPVPLPPVTHLDLTPSPDVPLTIMKRKLMNTNDLEESRQLTEEIQRHLDARHLIEKSVRKIVSLLAASEAEVEQLLSERAPLTGHSCYPEALLHFRTHCFNWHSPTYEYALRHLYVLVNLCEKPYPLHRIKLSMDHVCLGHYVDHHHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.18
R work: 0.2234
R free: 0.2724
Average B factor: 38.796
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 26mg/mL deglycosylated protein in 25mM HEPES/NaOH pH7, 300 mM NaCl, 200mM Trehalose incubated with 10-fold excess of ligand, then mixed 50-70% with 50-30% reservoir consisting of 22.5% PEG smear low, 0.1M MES/NaOH, 10% v/v 2-Propanol, total volume 200nL
Matthews coefficient: 1.4
Solvent content (%): 11.98
Ligand: N-[(3S)-5-amino-5-oxopent-1-en-3-yl]-1-{1-[4-(cyclopropylmethoxy)phenyl]cyclopropane-1-carbonyl}-L-prolinamide (WR9)
Ligand formula: C24 H31 N3 O4
Ligand molecular weight: 425.521
Ligand SMILES: C=CC(CC(=O)N)NC(=O)C1CCCN1C(=O)C2(CC2)c3ccc(cc3)OCC4CC4
Ligand InChI: InChI=1S/C24H31N3O4/c1-2-18(14-21(25)28)26-22(29)20-4-3-13-27(20)23(30)24(11-12-24)17-7-9-19(10-8-17)31-15-16-5-6-16/h2,7-10,16,18,20H,1,3-6,11-15H2,(H2,25,28)(H,26,29)/t18-,20+/m1/s1
Release date: 2023-10-11
Structure of cyclin-dependent kinase 2 with small-molecule ligand 3-(4,7-dichloro-1H-indol-3-yl)prop-2-yn-1-ol (AT17833) in an alternate binding site. (PDB entry 5FP6)
Macromolecule: CYCLIN-DEPENDENT KINASE 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.22
Sequence length: 298 residues
Sequence: MENFQKVEKIGEGTYGVVYKARNKLTGEVVALKKIRLDTETEGVPSTAIREISLLKELNHPNIVKLLDVIHTENKLYLVFEFLHQDLKKFMDASALTGIPLPLIKSYLFQLLQGLAFCHSHRVLHRDLKPQNLLINTEGAIKLADFGLARAFGVPVRTYTHEVVTLWYRAPEILLGCKYYSTAVDIWSLGCIFAEMVTRRALFPGDSEIDQLFRIFRTLGTPDEVVWPGVTSMPDYKPSFPKWARQDFSKVVPPLDEDGRSLLSQMLHYDPNKRISAKAALAHPFFQDVTKPVPHLRL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.85
R work: 0.207
R free: 0.2403
Average B factor: 30.85
Crystallization pH: 7.4
Crystal growth procedure: PROTEIN CONCENTRATION: 13.6 MG/ML, pH 7.4
Matthews coefficient: 2.25
Solvent content (%): 45
Ligand: 3-(4,7-dichloro-1H-indol-3-yl)prop-2-yn-1-ol (MFZ)
Ligand formula: C11 H7 Cl2 N O
Ligand molecular weight: 240.085
Ligand SMILES: c1cc(c2c(c1Cl)c(c[nH]2)C#CCO)Cl
Ligand InChI: InChI=1S/C11H7Cl2NO/c12-8-3-4-9(13)11-10(8)7(6-14-11)2-1-5-15/h3-4,6,14-15H,5H2
Release date: 2015-12-23
phosphorylated ERK2 with GDC-0994 (PDB entry 6OPH)
Macromolecule: Mitogen-activated protein kinase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.24
Sequence length: 354 residues
Sequence: SGAGPEMVRGQVFDVGPRYTNLSYIGEGAYGMVCSAYDNVNKVRVAIKKISPFEHQTYCQRTLREIKILLRFRHENIIGINDIIRAPTIEQMKDVYIVQDLMETDLYKLLKTQHLSNDHICYFLYQILRGLKYIHSANVLHRDLKPSNLLLNTTCDLKICDFGLARVADPDHDHTGFLTEYVATRWYRAPEIMLNSKGYTKSIDIWSVGCILAEMLSNRPIFPGKHYLDQLNHILGILGSPSQEDLNCIINLKARNYLLSLPHKNKVPWNRLFPNADSKALDLLDKMLTFNPHKRIEVEQALAHPYLEQYYDPSDEPIAEAPFKFDMELDDLPKEKLKELIFEETARFQPGYRS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.4
R work: 0.19291
R free: 0.24287
Average B factor: 55.747
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 9
Crystallization temperature (K): 293
Crystal growth procedure: 36% PEG3350, 100mM bicine pH 9.0
Matthews coefficient: 2.99
Solvent content (%): 58.8
Ligand: 1-[(1~{S})-1-(4-chloranyl-3-fluoranyl-phenyl)-2-oxidanyl-ethyl]-4-[2-[(2-methylpyrazol-3-yl)amino]pyrimidin-4-yl]pyridin-2-one (6QB)
Ligand formula: C21 H18 Cl F N6 O2
Ligand molecular weight: 440.858
Ligand SMILES: Cn1c(ccn1)Nc2nccc(n2)C3=CC(=O)N(C=C3)C(CO)c4ccc(c(c4)F)Cl
Ligand InChI: InChI=1S/C21H18ClFN6O2/c1-28-19(5-8-25-28)27-21-24-7-4-17(26-21)13-6-9-29(20(31)11-13)18(12-30)14-2-3-15(22)16(23)10-14/h2-11,18,30H,12H2,1H3,(H,24,26,27)/t18-/m1/s1
Release date: 2019-07-31
Structure of DYRK1A in complex with compound 4 (PDB entry 7A4Z)
Macromolecule: Dual specificity tyrosine-phosphorylation-regulated kinase 1A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.12.1
Sequence length: 359 residues
Sequence: MGSSHHHHHHSSGLVPRGSHMIVKNGEKWMDRYEIDSLIGKGSFGQVVKAYDRVEQEWVAIKIIKNKKAFLNQAQIEVRLLELMNKHDTEMKYYIVHLKRHFMFRNHLCLVFEMLSYNLYDLLRNTNFRGVSLNLTRKFAQQMCTALLFLATPELSIIHCDLKPENILLCNPKRSAIKIVDFGSSCQLGQRIYQYIQSRFYRSPEVLLGMPYDLAIDMWSLGCILVEMHTGEPLFSGANEVDQMNKIVEVLGIPPAHILDQAPKARKFFEKLPDGTWNLKKTKDGKREYKPPGTRKLHNILGVETGGPGGRRAGESGHTVADYLKFKDLILRMLDYDPKTRIQPYYALQHSFFKKTADE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.9
R work: 0.1728
R free: 0.2151
Average B factor: 32.671
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M MES buffer at pH 6.5, 12% Peg3350, 0.2M MgCl2
Matthews coefficient: 2.5
Solvent content (%): 50.74
Ligand: 3-(4-methoxyphenyl)-1~{H}-pyrazol-5-amine (6SD)
Ligand formula: C10 H11 N3 O
Ligand molecular weight: 189.214
Ligand SMILES: COc1ccc(cc1)c2cc([nH]n2)N
Ligand InChI: InChI=1S/C10H11N3O/c1-14-8-4-2-7(3-5-8)9-6-10(11)13-12-9/h2-6H,1H3,(H3,11,12,13)
Release date: 2021-06-30