satarupa22/MacromolecularLigandDB huggingface dataset:
Structure of human monoacylglycerol lipase bound to a covalent inhibitor (PDB entry 6AX1)
Macromolecule: Monoglyceride lipase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.1.23
Sequence length: 348 residues
Sequence: MASRGSHHHHHHGAGDRGPEFPSSMPEESSPRRTPQSIPYQDLPHLVNADGQYLFCRYWKPTGTPKALIFVSHGAGEHSGRYEELARMLMGLDLLVFAHDHVGHGQSEGERMVVSDFHVFVRDVLQHVDSMQKDYPGLPVFLLGHSMGGAIAILTAAERPGHFAGMVLISPLVLANPESATTFKVLAAKVLNLVLPNLSLGPIDSSVLSRNKTEVDIYNSDPLICRAGLKVCFGIQLLNAVSRVERALPKLTVPFLLLQGSADRLCDSKGAYLLMELAKSQDKTLKIYEGAYHVLHKELPEVTNSVFHEINMWVSQRTATAGTASPPLEVDLQGDHGLSAWSHPQFEK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.26
R work: 0.163
R free: 0.1984
Average B factor: 44.77
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 298
Crystal growth procedure: Reservoir Buffer: 0.07M sodium cacodylate pH 5.1-5.9 and 33-51% MPD

The protein is 20 mg/mL in a buffer of 15 mM HEPES pH 8.2; 2 mM TCEP; and 10% glycerol, with hexaethylene glycol monododecyl ether added to 0.1 mM.

Apo protein crystals obtained in this manner were transferred to a cryo-protectant solution consisting of 70 mM NaCacodylate pH 5.1; 10% MPD; 30% PEG-MME-2K, and 1mM of inhibitor compound. Crystals were soaked overnight, then flash-frozen in LN2.
Matthews coefficient: 2.46
Solvent content (%): 50.04
Ligand: 1,1,1,3,3,3-hexafluoropropan-2-yl 3-(3-phenyl-1,2,4-oxadiazol-5-yl)azetidine-1-carboxylate (C0S)
Ligand formula: C15 H11 F6 N3 O3
Ligand molecular weight: 395.257
Ligand SMILES: c1ccc(cc1)c2nc(on2)C3CN(C3)C(=O)OC(C(F)(F)F)C(F)(F)F
Ligand InChI: InChI=1S/C15H11F6N3O3/c16-14(17,18)12(15(19,20)21)26-13(25)24-6-9(7-24)11-22-10(23-27-11)8-4-2-1-3-5-8/h1-5,9,12H,6-7H2
Release date: 2017-12-27
The crystal structure of CK2alpha in complex with compound 22 (PDB entry 5OUU)
Macromolecule: Casein kinase II subunit alpha
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 352 residues
Sequence: GSMDIEFDDDADDDGSGSGSGSGSSGPVPSRARVYTDVNTHRPSEYWDYESHVVEWGNQDDYQLVRKLGRGKYSEVFEAINITNNEKVVVKILKPVKKKKIKREIKILENLRGGPNIITLADIVKDPVSRTPALVFEHVNNTDFKQLYQTLTDYDIRFYMYEILKALDYCHSMGIMHRDVKPHNVMIDHEHRKLRLIDWGLAEFYHPGQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRKEPFFHGHDNYDQLVRIAKVLGTEDLYDYIDKYNIELDPRFNDILGRHSRKRWERFVHSENQHLVSPEALDFLDKLLRYDHQSRLTAREAMEHPYFYTVVK
Oligomeric state: Homo 2-mer
Stoichiometry: A2
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.81
R work: 0.186
R free: 0.203
Average B factor: 49.2
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 298
Crystal growth procedure: 112.5mM Mes pH 6.5, 35% glycerol ethoxylate, 180 mM ammonium acetate
Matthews coefficient: 2.2
Solvent content (%): 44.2
Ligand: ACETATE ION (ACT)
Ligand formula: C2 H3 O2
Ligand molecular weight: 59.044
Ligand SMILES: CC(=O)[O-]
Ligand InChI: InChI=1S/C2H4O2/c1-2(3)4/h1H3,(H,3,4)/p-1
Release date: 2018-02-28
Human Carbonic Anhydrase II complexed with an inhibitor with a benzenesulfonamide group (5). (PDB entry 4YYT)
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): 1.07
R work: 0.143
R free: 0.1658
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 2.5 uL of the protein solution (10 mg/ml hCAII in 50 mM Tris pH 7.8) were mixed with 2.5 uL of the well solution (2.7 M (NH4)SO4, 100 mM Tris, pH 7.8, saturated with p-chloromercurybenzoicacid) and placed as a hanging drop. Crystals appeared after several days. The crystals were soaked in 3.0 M (NH4)SO4, 100 mM Tris, pH 7.8, saturated with the inhibitor, for 1 day.
Matthews coefficient: 2.09
Solvent content (%): 41.03
Ligand: MERCURIBENZOIC ACID (MBO)
Ligand formula: C7 H5 Hg O2
Ligand molecular weight: 321.703
Ligand SMILES: c1cc(ccc1C(=O)O)[Hg]
Ligand InChI: InChI=1S/C7H5O2.Hg/c8-7(9)6-4-2-1-3-5-6;/h2-5H,(H,8,9);
Release date: 2016-02-03
H-Ras Y137F (PDB entry 4XVR)
Macromolecule: GTPase HRas
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.5.2
Sequence length: 166 residues
Sequence: MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHQYREQIKRVKDSDDVPMVLVGNKCDLAARTVESRQAQDLARSFGIPYIETSAKTRQGVEDAFYTLVREIRQH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.031
R work: 0.2218
R free: 0.2857
Average B factor: 42.23
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 291.15
Crystal growth procedure: 139mM Ca(OAc)2, 22.6% PEG 3350, 13% stabilization buffer at pH 7.5
Matthews coefficient: 1.91
Solvent content (%): 35.63
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: 2015-06-17
Structure of cyclophilin A in complex with 3-amino-1H-pyridin-2-one (PDB entry 5NOS)
Macromolecule: Peptidyl-prolyl cis-trans isomerase A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 5.2.1.8
Sequence length: 165 residues
Sequence: MVNPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGFGYKGSCFHRIIPGFMCQGGDFTRHNGTGGKSIYGEKFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKTEWLDGKHVVFGKVKEGMNIVEAMERFGSRNGKTSKKITIADCGQLE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.35
R work: 0.13135
R free: 0.16478
Average B factor: 15.096
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8
Crystallization temperature (K): 279.15
Crystal growth procedure: PEG 8000, Tris-HCl
Matthews coefficient: 2.73
Solvent content (%): 54.98
Ligand: 5-azanyl-3~{H}-pyridin-6-one (92Z)
Ligand formula: C5 H6 N2 O
Ligand molecular weight: 110.114
Ligand SMILES: C1C=C(C(=O)N=C1)N
Ligand InChI: InChI=1S/C5H6N2O/c6-4-2-1-3-7-5(4)8/h2-3H,1,6H2
Release date: 2017-07-12
The complex of Src with GW8510 (PDB entry 8HAQ)
Macromolecule: Isoform 2 of Proto-oncogene tyrosine-protein kinase Src
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 277 residues
Sequence: KDAWEIPRESLRLEVKLGQGCFGEVWMGTWNGTTRVAIKTLKPGTMSPEAFLQEAQVMKKLRHEKLVQLYAVVSEEPIYIVTEYMSKGSLLDFLKGETGKYLRLPQLVDMAAQIASGMAYVERMNYVHRDLRAANILVGENLVCKVADFGLARLIEDNEYTARQGAKFPIKWTAPEAALYGRFTIKSDVWSFGILLTELTTKGRVPYPGMVNREVLDQVERGYRMPCPPECPESLHDLMCQCWRKEPEERPTFEYLQAFLEDYFTSTEPQYQPGENL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.27
R work: 0.2074
R free: 0.2499
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M MOPS pH 7.0, 18% PEG 3350, 5% Glycerol, 5 mM TCEP
Matthews coefficient: 3
Solvent content (%): 59.04
Ligand: 4-[(~{E})-(7-oxidanyl-6~{H}-pyrrolo[2,3-g][1,3]benzothiazol-8-yl)methylideneamino]-~{N}-pyridin-2-yl-benzenesulfonamide (L1N)
Ligand formula: C21 H15 N5 O3 S2
Ligand molecular weight: 449.506
Ligand SMILES: c1ccnc(c1)NS(=O)(=O)c2ccc(cc2)N=Cc3c4c(ccc5c4scn5)[nH]c3O
Ligand InChI: InChI=1S/C21H15N5O3S2/c27-21-15(19-16(25-21)8-9-17-20(19)30-12-24-17)11-23-13-4-6-14(7-5-13)31(28,29)26-18-3-1-2-10-22-18/h1-12,25,27H,(H,22,26)/b23-11+
Release date: 2023-11-01
PTP1B in complex with TCS401 by Native S-SAD at Room Temperature (PDB entry 7MM1)
Macromolecule: Tyrosine-protein phosphatase non-receptor type 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 321 residues
Sequence: MEMEKEFEQIDKSGSWAAIYQDIRHEASDFPSRVAKLPKNKNRNRYRDVSPFDHSRIKLHQEDNDYINASLIKMEEAQRSYILTQGPLPNTVGHFWEMVWEQKSRGVVMLNRVMEKGSLKCAQYWPQKEEKEMIFEDTNLKLTLISEDIKSYYTVRQLELENLTTQETREILHFHYTTWPDFGVPESPASFLNFLFKVRESGSLSPEHGPVVVHCSAGIGRSGTFCLADTCLLLMDKRKDPSSVDIKKVLLEMRKFRMGLIQTADQLRFSYLAVIEGAKFIMGDSSVQDQWKELSHEDLEPPPEHIPPPPRPPKRILEPHN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.85
R work: 0.129
R free: 0.1385
Average B factor: 34.16
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 100mM HEPES (pH 6.8 - 7.6), 250mM magnesium acetate, 11-15% PEG8000 (w/v), 10% glycerol (v/v), 6% ethanol (v/v),  0.1% BME (v/v). TCS401 was co-crystallized using a >5-fold molar excess.
Matthews coefficient: 3.26
Solvent content (%): 62.29
Ligand: 2-(OXALYL-AMINO)-4,5,6,7-TETRAHYDRO-THIENO[2,3-C]PYRIDINE-3-CARBOXYLIC ACID (OTA)
Ligand formula: C10 H10 N2 O5 S
Ligand molecular weight: 270.262
Ligand SMILES: C1CNCc2c1c(c(s2)NC(=O)C(=O)O)C(=O)O
Ligand InChI: InChI=1S/C10H10N2O5S/c13-7(10(16)17)12-8-6(9(14)15)4-1-2-11-3-5(4)18-8/h11H,1-3H2,(H,12,13)(H,14,15)(H,16,17)
Release date: 2021-05-12
Kinase domain of mutant human ULK1 in complex with compound MRT68921 (PDB entry 8P5K)
Macromolecule: Serine/threonine-protein kinase ULK1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 284 residues
Sequence: SMEPGRGGTETVGKFEFSRKDLIGHGAFAVVFKGRHREKHDLEVAVKCINKKNLAKSQTLLGKEIKILKELKHENIVALYDFQEMANSVYLVMEYCNGGDLADYLHAMRTLSEDTIRLFLQQIAGAMRLLHSKGIIHRDLKPQNILLSNPAGRRANPNSIRVKIADFGFARYLQSNMMAATLCGSPMYMAPEVIMSQHYDGKADLWSIGTIVYQCLTGKAPFQASSPQDLRLFYEKNKTLVPTIPAATSAPLRQLLLALLQRNHKDRMDFDEFFHHPFLDASPS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.209
R work: 0.177
R free: 0.2043
Average B factor: 40.344
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6
Crystallization temperature (K): 277.15
Crystal growth procedure: 0.3-0.8 M NaAcetate pH 6, 20-26% w/v PEG3350
Matthews coefficient: 3.5
Solvent content (%): 64.88
Ligand: ~{N}-[3-[[5-cyclopropyl-2-[(2-methyl-3,4-dihydro-1~{H}-isoquinolin-6-yl)amino]pyrimidin-4-yl]amino]propyl]cyclobutanecarboxamide (HVH)
Ligand formula: C25 H34 N6 O
Ligand molecular weight: 434.577
Ligand SMILES: CN1CCc2cc(ccc2C1)Nc3ncc(c(n3)NCCCNC(=O)C4CCC4)C5CC5
Ligand InChI: InChI=1S/C25H34N6O/c1-31-13-10-19-14-21(9-8-20(19)16-31)29-25-28-15-22(17-6-7-17)23(30-25)26-11-3-12-27-24(32)18-4-2-5-18/h8-9,14-15,17-18H,2-7,10-13,16H2,1H3,(H,27,32)(H2,26,28,29,30)
Release date: 2024-06-05
APE1 phosphorothioate substrate complex with abasic ribonucleotide DNA (PDB entry 7LPI)
Macromolecule: DNA (5'-D(*GP*GP*AP*TP*CP*CP*GP*TP*CP*GP*AP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')
Type: DNA, polydeoxyribonucleotide
Source organism: synthetic construct
Sequence length: 21 residues
Sequence: GGATCCGTCGAGCGCATCAGC
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.05
R work: 0.1968
R free: 0.2447
Average B factor: 37.12
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 4
Crystallization temperature (K): 291
Crystal growth procedure: 50 mM tri-Sodium Citrate (pH 4), 100 mM NaCl, 10% Peg 6,000
Matthews coefficient: 2.53
Solvent content (%): 51.45
Release date: 2021-08-04
Mutant Human DNA Polymerase Eta Q38A/R61A Inserting dCTP Opposite an 8-Oxoguanine Lesion (PDB entry 4YP3)
Macromolecule: DNA polymerase eta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 435 residues
Sequence: GPHMATGQDRVVALVDMDCFFVQVEQRQNPHLRNKPCAVVAYKSWKGGGIIAVSYEARAFGVTASMWADDAKKLCPDLLLAQVRESRGKANLTKYREASVEVMEIMSRFAVIERASIDEAYVDLTSAVQERLQKLQGQPISADLLPSTYIEGLPQGPTTAEETVQKEGMRKQGLFQWLDSLQIDNLTSPDLQLTVGAVIVEEMRAAIERETGFQCSAGISHNKVLAKLACGLNKPNRQTLVSHGSVPQLFSQMPIRKIRSLGGKLGASVIEILGIEYMGELTQFTESQLQSHFGEKNGSWLYAMCRGIEHDPVKPRQLPKTIGCSKNFPGKTALATREQVQWWLLQLAQELEERLTKDRNDNDRVATQLVVSIRVQGDKRLSSLRRCCALTRYDAHKMSHDAFTVIKNCNTSGIQTEWSPPLTMLFLCATKFSAS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.89
R work: 0.1685
R free: 0.2155
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6
Crystallization temperature (K): 291
Crystal growth procedure: NaMES (pH 6.0), polyethylene glycol monomethyl ether 2000, and calcium chloride
Matthews coefficient: 2.11
Solvent content (%): 41.83
Ligand: 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE (DCP)
Ligand formula: C9 H16 N3 O13 P3
Ligand molecular weight: 467.157
Ligand SMILES: C1C(C(OC1N2C=CC(=NC2=O)N)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O
Ligand InChI: InChI=1S/C9H16N3O13P3/c10-7-1-2-12(9(14)11-7)8-3-5(13)6(23-8)4-22-27(18,19)25-28(20,21)24-26(15,16)17/h1-2,5-6,8,13H,3-4H2,(H,18,19)(H,20,21)(H2,10,11,14)(H2,15,16,17)/t5-,6+,8+/m0/s1
Release date: 2015-05-13
Crystal structure of hGSTA1-1 complexed with two GSH analogues in each subunit (PDB entry 6ATR)
Macromolecule: Glutathione S-transferase A1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.5.1.18
Sequence length: 221 residues
Sequence: AEKPKLHYFNARGRMESTRWLLAAAGVEFEEKFIKSAEDLDKLRNDGYLMFQQVPMVEIDGMKLVQTRAILNYIASKYNLYGKDIKERALIDMYIEGIADLGEMILLLPVCPPEEKDAKLALIKEKIKNRYFPAFEKVLKSHGQDYLVGNKLSRADIHLVELLYYVEELDSSLISSFPLLKALKTRISNLPTVKKFLQPGSPRKPPMDEKSLEEARKIFRF
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.29
R work: 0.1683
R free: 0.1823
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: PEG 2000 MME, 25% (w/v), 0.1 M MES, pH 6.5
Matthews coefficient: 2.4
Solvent content (%): 48.67
Ligand: L-gamma-glutamyl-L-alanylglycine (BWS)
Ligand formula: C10 H17 N3 O6
Ligand molecular weight: 275.258
Ligand SMILES: CC(C(=O)NCC(=O)O)NC(=O)CCC(C(=O)O)N
Ligand InChI: InChI=1S/C10H17N3O6/c1-5(9(17)12-4-8(15)16)13-7(14)3-2-6(11)10(18)19/h5-6H,2-4,11H2,1H3,(H,12,17)(H,13,14)(H,15,16)(H,18,19)/t5-,6-/m0/s1
Release date: 2018-09-12
MAP4K4 in complex with inhibitor compound 12 (N3-methyl-10-(3-methyl-3-(5-methyloxazol-2-yl)but-1-yn-1-yl)-6,7-dihydro-5H-5,7-methanobenzo[c]imidazo[1,2-a]azepine-2,3-dicarboxamide) (PDB entry 5W5Q)
Macromolecule: Mitogen-activated protein kinase kinase kinase kinase 4
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 332 residues
Sequence: GSANDSPAKSLVDIDLSSLRDPAGIFELVEVVGNGTYGQVYKGRHVKTGQLAAIKVMDVTEDEEEEIKLEINMLKKYSHHRNIATYYGAFIKKSPPGHDDQLWLVMEFCGAGSITDLVKNTKGNTLKEDWIAYISREILRGLAHLHIHHVIHRDIKGQNVLLTENAEVKLVDFGVSAQLDRTVGRRNTFIGTPYWMAPEVIACDENPDATYDYRSDLWSCGITAIEMAEGAPPLCDMHPMRALFLIPRNPPPRLKSKKWSKKFFSFIEGCLVKNYMQRPSTEQLLKHPFIRDQPNERQVRIQLKDHIDRTRKKRGEKDETEYEYSGSEEGNS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.33
R work: 0.2095
R free: 0.2355
Average B factor: 55.71
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M MES pH 6.5, 35% PEG 3350
Matthews coefficient: 2.16
Solvent content (%): 43.13
Ligand: (5s,7s)-N~3~-methyl-10-[3-methyl-3-(5-methyl-1,3-oxazol-2-yl)but-1-yn-1-yl]-6,7-dihydro-5H-5,7-methanoimidazo[2,1-a][2]benzazepine-2,3-dicarboxamide (9X4)
Ligand formula: C25 H25 N5 O3
Ligand molecular weight: 443.498
Ligand SMILES: Cc1cnc(o1)C(C)(C)C#Cc2ccc3c(c2)-c4nc(c(n4C5CC3C5)C(=O)NC)C(=O)N
Ligand InChI: InChI=1S/C25H25N5O3/c1-13-12-28-24(33-13)25(2,3)8-7-14-5-6-17-15-10-16(11-15)30-20(23(32)27-4)19(21(26)31)29-22(30)18(17)9-14/h5-6,9,12,15-16H,10-11H2,1-4H3,(H2,26,31)(H,27,32)/t15-,16+
Release date: 2018-06-20
Crystal structure of RBR E3 ligase RNF216 in complex with K63-linked di-ubiquitin (PDB entry 7M4N)
Macromolecule: E3 ubiquitin-protein ligase RNF216
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2.27
Sequence length: 138 residues
Sequence: GPEELAEKDDIKYRTSIEEKMTAARIRKCHKCGTGLIKSEGANRMSCRCGAQMCYLCRVSINGYDHFCQHPRSPGAPCQECSRCSLWTDPTEDDEKLIEEIQKEAEEEQKRKNGENTFKRIGPPLEKPVEKVQRVEAL
Oligomeric state: Hetero 3-mer
Stoichiometry: A2, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.52
R work: 0.2163
R free: 0.2732
Average B factor: 46.24
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.9
Crystallization temperature (K): 293
Crystal growth procedure: 0.2M ammonium sulfate, 30% PEG 4000
Matthews coefficient: 2.52
Solvent content (%): 51.28
Ligand: ZINC ION (ZN)
Ligand formula: Zn
Ligand molecular weight: 65.409
Ligand SMILES: [Zn+2]
Ligand InChI: InChI=1S/Zn/q+2
Release date: 2022-01-05
Hybrid dihydroorotase domain of human CAD with E. coli flexible loop in apo state (PDB entry 6HG1)
Macromolecule: CAD protein,Dihydroorotase,CAD protein
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 6.3.5.5
Sequence length: 371 residues
Sequence: AKLVRLPGLIDVHVHLREPGGTHKEDFASGTAAALAGGITMVCAMPNTRPPIIDAPALALAQKLAEAGARCDFALFLGASSENAGTLGTVAGSAAGLKLYLANATTNSSHGVTSVVQWMEHFETWPSHLPIVAHAEEQTVAAVLMVAQLTQRSVHICHVARKEEILLIKAAKARGLPVTCEVAPHHLFLSHDDLERLGPGKGEVRPELGSRQDVEALWENMAVIDCFASDHAPHTLEEKCGSRPPPGFPGLETMLPLLLTAVSEGRLSLDDLLQRLHHNPRRIFHLPPQEDTYVEVDLEHEWTIPSHMPFSKAHWTPFEGQKVKGTVRRVVLRGEVAYIDGQVLVPPGYGQDVRKWPQGAVPQLPPSAPAA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.12
R work: 0.1737
R free: 0.2091
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 291
Crystal growth procedure: Protein at 2-3 mg/ml in 20 mM Tris pH 8, 0.15 M NaCl, 0.02 mM zinc sulfate, 0.2 mM TCEP
Mother liquor: 2.5-3 M potassium formate, 0.1 M HEPES pH 7.5
Matthews coefficient: 2.39
Solvent content (%): 48.48
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: 2018-10-24
DNA Polymerase Lambda, TTP:At Ca2+ Ground State Ternary Complex (PDB entry 7M43)
Macromolecule: DNA polymerase lambda
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 329 residues
Sequence: AQPSSQKATNHNLHITEKLEVLAKAYSVQGDKWRALGYAKAINALKSFHKPVTSYQEACSIPGIGKRMAEKIIEILESGHLRKLDHISESVPVLELFSNIWGAGTKTAQMWYQQGFRSLEDIRSQASLTTQQAIGLKHYSDFLERMPREEATEIEQTVQKAAQAFNSGLLCVACGSYRRGKATCGDVDVLITHPDGRSHRGIFSRLLDSLRQEGFLTDDLVKGETKYLGVCRLPGPGRRHRRLDIIVVPYSEFACALLYFTGSAHFNRSMRALAKTKGMSLSEHALSTAVVRNTHGCKVGPGRVLPTPTEKDVFRLLGLPYREPAERDW
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.978
R work: 0.1925
R free: 0.231
Average B factor: 41.5763
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 80-95mM BICINE pH 8.3, 0.3M Na-K Tartrate, 18-22.5% PolyPure PEG
Matthews coefficient: 2.86
Solvent content (%): 56.94
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: 2022-07-06
Structure of Tdp1 catalytic domain in complex with inhibitor XZ634p (PDB entry 6W7K)
Macromolecule: Tyrosyl-DNA phosphodiesterase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.4
Sequence length: 461 residues
Sequence: SGEGQDIWDMLDKGNPFQFYLTRVSGVKPKYNSGALHIKDILSPLFGTLVSSAQFNYCFDVDWLVKQYPPEFRKKPILLVHGDKREAKAHLHAQAKPYENISLCQAKLDIAFGTHHTKMMLLLYEEGLRVVIHTSNLIHADWHQKTQGIWLSPLYPRIADGTHKSGESPTHFKADLISYLMAYNAPSLKEWIDVIHKHDLSETNVYLIGSTPGRFQGSQKDNWGHFRLKKLLKDHASSMPNAESWPVVGQFSSVGSLGADESKWLCSEFKESMLTLGKESKTPGKSSVPLYLIYPSVENVRTSLEGYPAGGSLPYSIQTAEKQNWLHSYFHKWSAETSGRSNAMPHIKTYMRPSPDFSKIAWFLVTSANLSKAAWGALEKNGTQLMIRSYELGVLFLPSAFGLDSFKVKQKFFAGSQEPMATFPVPYDLPPELYGSKDRPWIWNIPYVKAPDTHGNMWVPS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.7
R work: 0.187
R free: 0.219
Average B factor: 26.8934
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 292
Crystal growth procedure: 0.1M MOPS/HEPES-Na pH 7.5 10% w/v PEG 8000 20% v/v ethylene glycol 0.03 M sodium fluoride 0.03 M sodium bromide 0.03 M sodium iodide
Matthews coefficient: 2.44
Solvent content (%): 49.52
Ligand: 4-[(2-phenylimidazo[1,2-a]pyridin-3-yl)amino]benzene-1,2-dicarboxylic acid (TG7)
Ligand formula: C21 H15 N3 O4
Ligand molecular weight: 373.362
Ligand SMILES: c1ccc(cc1)c2c(n3ccccc3n2)Nc4ccc(c(c4)C(=O)O)C(=O)O
Ligand InChI: InChI=1S/C21H15N3O4/c25-20(26)15-10-9-14(12-16(15)21(27)28)22-19-18(13-6-2-1-3-7-13)23-17-8-4-5-11-24(17)19/h1-12,22H,(H,25,26)(H,27,28)
Release date: 2021-03-24
Nek2 bound to arylaminopurine compound 8 (PDB entry 5M51)
Macromolecule: Serine/threonine-protein kinase Nek2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 279 residues
Sequence: MPSRAEDYEVLYTIGTGSYGRCQKIRRKSDGKILVWKELDYGSMTEAEKQMLVSEVNLLRELKHPNIVRYYDRIIDRTNTTLYIVMEYCEGGDLASVITKGTKERQYLDEEFVLRVMTQLTLALKECHRRSDGGHTVLHRDLKPANVFLDGKQNVKLGDFGLARILNHDTSFAKTFVGTPYYMSPEQMNRMSYNEKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIREGKFRRIPYRYSDELNEIITRMLNLKDYHRPSVEEILENPLILEHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.899
R work: 0.222
R free: 0.2567
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 3 % PEG 8000, 50 mM Tris pH 8.5
Matthews coefficient: 2.4
Solvent content (%): 48.82
Ligand: 3-[[6-(cyclohexylmethoxy)-9~{H}-purin-2-yl]amino]benzamide (NU6)
Ligand formula: C19 H22 N6 O2
Ligand molecular weight: 366.417
Ligand SMILES: c1cc(cc(c1)Nc2nc3c(c(n2)OCC4CCCCC4)nc[nH]3)C(=O)N
Ligand InChI: InChI=1S/C19H22N6O2/c20-16(26)13-7-4-8-14(9-13)23-19-24-17-15(21-11-22-17)18(25-19)27-10-12-5-2-1-3-6-12/h4,7-9,11-12H,1-3,5-6,10H2,(H2,20,26)(H2,21,22,23,24,25)
Release date: 2016-11-09
Crystal structure of Glucokinase in complex with compound 72 (PDB entry 6E0I)
Macromolecule: Glucokinase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.1.2
Sequence length: 458 residues
Sequence: MLDDRARMEAAKKEKVEQILAEFQLQEEDLKKVMRRMQKEMDRGLRLETHEEASVKMLPTYVRSTPEGSEVGDFLSLDLGGTNFRVMLVKVGEGEEGQWSVKTKHQMYSIPEDAMTGTAEMLFDYISECISDFLDKHQMKHKKLPLGFTFSFPVRHEDIDKGILLNWTKGFKASGAEGNNVVGLLRDAIKRRGDFEMDVVAMVNDTVATMISCYYEDHQCEVGMIVGTGCNACYMEEMQNVELVEGDEGRMCVNTEWGAFGDSGELDEFLLEYDRLVDESSANPGQQLYEKLIGGKYMGELVRLVLLRLVDENLLFHGEASEQLRTRGAFETRFVSQVESDTGDRKQIYNILSTLGLRPSTTDCDIVRRACESVSTRAAHMCSAGLAGVINRMRESRSEDVMRITVGVDGSVYKLHPSFKERFHASVRRLTPSCEITFIESEEGSGRGAALVSAVACK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.9
R work: 0.19134
R free: 0.22873
Average B factor: 22.644
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M Hepes pH7.5, 28% PEG3350
Matthews coefficient: 2.41
Solvent content (%): 49.04
Ligand: alpha-D-glucopyranose (GLC)
Ligand formula: C6 H12 O6
Ligand molecular weight: 180.156
Ligand SMILES: C(C1C(C(C(C(O1)O)O)O)O)O
Ligand InChI: InChI=1S/C6H12O6/c7-1-2-3(8)4(9)5(10)6(11)12-2/h2-11H,1H2/t2-,3-,4+,5-,6+/m1/s1
Release date: 2019-07-10