satarupa22/MacromolecularLigandDB huggingface dataset:
The crystal structure of uPA in complex with 4-Iodobenzylamine at pH7.4 (PDB entry 5Z1C)
Macromolecule: Urokinase-type plasminogen activator
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.73
Sequence length: 245 residues
Sequence: IIGGEFTTIENQPWFAAIYRRHRGGSVTYVCGGSLISPCWVISATHCFIDYPKKEDYIVYLGRSRLNSNTQGEMKFEVENLILHKDYSADTLAHHNDIALLKIRSKEGRCAQPSRTIQTIALPSMYNDPQFGTSCEITGFGKEQSTDYLYPEQLKMTVVKLISHRECQQPHYYGSEVTTKMLCAADPQWKTDSCQGDSGGPLVCSLQGRMTLTGIVSWGRGCALKDKPGVYTRVSHFLPWIRSHT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.45
R work: 0.11791
R free: 0.14284
Average B factor: 30.576
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 298
Crystal growth procedure: 50mM sodium citrate (pH 4.6), 2.0M ammonium sulfate supplemented with 5% PEG 400
Matthews coefficient: 2.16
Solvent content (%): 43.15
Ligand: 1-(4-iodophenyl)methanamine (ZXI)
Ligand formula: C7 H8 I N
Ligand molecular weight: 233.05
Ligand SMILES: c1cc(ccc1CN)I
Ligand InChI: InChI=1S/C7H8IN/c8-7-3-1-6(5-9)2-4-7/h1-4H,5,9H2
Release date: 2018-12-26
Crystal Structure of EGFR-T790M/V948R in Complex with Reversible Aminopyrimidine 13 (PDB entry 7ZYQ)
Macromolecule: Epidermal growth factor receptor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 333 residues
Sequence: GSHMASGEAPNQALLRILKETEFKKIKVLGSGAFGTVYKGLWIPEGEKVKIPVAIKELREATSPKANKEILDEAYVMASVDNPHVCRLLGICLTSTVQLIMQLMPFGCLLDYVREHKDNIGSQYLLNWCVQIAKGMNYLEDRRLVHRDLAARNVLVKTPQHVKITDFGLAKLLGAEEKEYHAEGGKVPIKWMALESILHRIYTHQSDVWSYGVTVWELMTFGSKPYDGIPASEISSILEKGERLPQPPICTIDVYMIMRKCWMIDADSRPKFRELIIEFSKMARDPQRYLVIQGDERMHLPSPTDSNFYRALMDEEDMDDVVDADEYLIPQQG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.1
R work: 0.1978
R free: 0.223
Average B factor: 50.739
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 27.5 % PEG3350, 100 mM MgSO4, 2 % ethylen glycole, 6.4 mg/mL EGFR-T790M/V948R (in 100 mM NaCl, 25 mM Tris-HCl, 10 % glycerol, 1 mM TCEP, pH 8.0) 1 ul reservoir + 1 ul protein solution)
Ligand: phenyl 2-[[4-[4-(dimethylamino)piperidin-1-yl]-2-methoxy-phenyl]amino]-4-(1H-indol-3-yl)pyrimidine-5-carboxylate (V58)
Ligand formula: C33 H34 N6 O3
Ligand molecular weight: 562.661
Ligand SMILES: CN(C)C1CCN(CC1)c2ccc(c(c2)OC)Nc3ncc(c(n3)c4c[nH]c5c4cccc5)C(=O)Oc6ccccc6
Ligand InChI: InChI=1S/C33H34N6O3/c1-38(2)22-15-17-39(18-16-22)23-13-14-29(30(19-23)41-3)36-33-35-21-27(32(40)42-24-9-5-4-6-10-24)31(37-33)26-20-34-28-12-8-7-11-25(26)28/h4-14,19-22,34H,15-18H2,1-3H3,(H,35,36,37)
Release date: 2023-05-03
PanDDA analysis group deposition of models with modelled events (e.g. bound ligands) -- Crystal Structure of NUDT7 in complex with FMOPL000022a (PDB entry 5QGR)
Macromolecule: Peroxisomal coenzyme A diphosphatase NUDT7
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.1
Sequence length: 196 residues
Sequence: SMLDDAKARLRKYDIGGKYSHLPYNKYSVLLPLVAKEGKLHLLFTVRSEKLRRAPGEVCFPGGKRDPTDMDDAATALREAQEEVGLRPHQVEVVCCLVPCLIDTDTLITPFVGLIDHNFQAQPNPAEVKDVFLVPLAYFLHPQVHDQHYVTRLGHRFINHIFEYTNPEDGVTYQIKGMTANLAVLVAFIILEKKPT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.96
R work: 0.2126
R free: 0.2438
Average B factor: 42.554
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M bis-tris pH 5.5 -- 0.1M ammonium acetate -- 5%(w/v) PEG10K
Matthews coefficient: 4.32
Solvent content (%): 71.54
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: 2019-03-27
Structure of the human Nocturnin catalytic domain (PDB entry 6BT1)
Macromolecule: Nocturnin
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.13.4
Sequence length: 313 residues
Sequence: STRPPRFQRDFVDLRTDCPSTHPPIRVMQWNILAQALGEGKDNFVQCPVEALKWEERKCLILEEILAYQPDILCLQEVDHYFDTFQPLLSRLGYQGTFFPKPWSPCLDVEHNNGPDGCALFFLQNRFKLVNSANIRLTAMTLKTNQVAIAQTLECKESGRQFCIAVTHLKARTGWERFRSAQGCDLLQNLQNITQGAKIPLIVCGDFNAEPTEEVYKHFASSSLNLNSAYKLLSADGQSEPPYTTWKIRTSGECRHTLDYIWYSKHALNVRSALDLLTEEQIGPNRLPSFNYPSDHLSLVCDFSFTEESDGLS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.48
R work: 0.1511
R free: 0.1865
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 294
Crystal growth procedure: 3', 5' Adenosine Diphosphate, Magnesium Chloride, Tris, Sodium Citrate, PEG 4000
Matthews coefficient: 2.09
Solvent content (%): 41.07
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: 2018-05-16
Crystal structure of DNMT3a ADD domain G550D mutant bound to H3 peptide (PDB entry 4QBR)
Macromolecule: DNA (cytosine-5)-methyltransferase 3A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1.37
Sequence length: 137 residues
Sequence: SRERLVYEVRQKCRNIEDICISCGSLNVTLEHPLFVGGMCQNCKNCFLECAYQYDDDGYQSYCTICCGGREVLMCDNNNCCRCFCVECVDLLVGPGAAQAAIKEDPWNCYMCGHKGTYGLLRRREDWPSRLQMFFAN
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.902
R work: 0.1779
R free: 0.2252
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 291
Crystal growth procedure: 25% PEG3350, 0.1M Bis-Tris-HCL, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Matthews coefficient: 1.97
Solvent content (%): 37.67
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: 2015-05-13
Complex structure of JMJD5 and substrate (PDB entry 5FBJ)
Macromolecule: Lysine-specific demethylase 8
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11.27
Sequence length: 236 residues
Sequence: GSTVPRLHRPSLQHFREQFLVPGRPVILKGVADHWPCMQKWSLEYIQEIAGCRTVPVEVGSRYTDEEWSQTLMTVNEFISKYIVNEPRDVGYLAQHQLFDQIPELKQDISIPDYCSLGDGEEEEITINAWFGPQGTISPLHQDPQQNFLVQVMGRKYIRLYSPQESGALYPHDTHLLHNTSQVDVENPDLEKFPKFAKAPFLSCILSPGEILFIPVKYWHYVRALDLSFSVSFWWS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.42
R work: 0.1898
R free: 0.2458
Crystallization method: EVAPORATION
Crystallization temperature (K): 281
Crystal growth procedure: PEG3350
HEPEPS-Na
Matthews coefficient: 2.3
Solvent content (%): 46.49
Ligand: (2S)-2-amino-5-[(N-methylcarbamimidoyl)amino]pentanoic acid (NMM)
Ligand formula: C7 H16 N4 O2
Ligand molecular weight: 188.228
Ligand SMILES: [H]N=C(NC)NCCCC(C(=O)O)N
Ligand InChI: InChI=1S/C7H16N4O2/c1-10-7(9)11-4-2-3-5(8)6(12)13/h5H,2-4,8H2,1H3,(H,12,13)(H3,9,10,11)/t5-/m0/s1
Release date: 2016-12-14
ARHGEF2 PanDDA analysis group deposition -- ARHGEF2 and RhoA in complex with Z1203730981 (PDB entry 7G96)
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): 2.3
R work: 0.1979
R free: 0.2657
Average B factor: 62.977
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: 2.47
Solvent content (%): 50.25
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 the human METTL3-METTL14 complex bound to Compound 17 (ADO_AE_005) (PDB entry 7O27)
Macromolecule: N6-adenosine-methyltransferase catalytic subunit
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1.348
Sequence length: 246 residues
Sequence: MGHHHHHHSSGRENLYFQGALTQSVGGDSSADRLFPPQWICCDIRYLDVSILGKFAVVMADPPWDIHMELPYGTLTDDEMRRLNIPVLQDDGFLFLWVTGRAMELGRECLNLWGYERVDEIIWVKTNQLQRIIRTGRTGHWLNHGKEHCLVGVKGNPQGFNQGLDCDVIVAEVRSTSHKPDEIYGMIERLSPGTRKIELFGRPHNVQPNWITLGNQLDGIHLLDPDVVARFKQRYPDGIISKPKNL
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.4
R work: 0.2078
R free: 0.2541
Average B factor: 65.42
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 295
Crystal growth procedure: 20% PEG 3350, 400mM Mg acetate
Matthews coefficient: 2.16
Solvent content (%): 43.09
Ligand: 4-[4-[(4,4-dimethylpiperidin-1-yl)methyl]phenyl]-9-(7H-pyrrolo[2,3-d]pyrimidin-4-yl)-1,4,9-triazaspiro[5.5]undecan-2-one (UYZ)
Ligand formula: C28 H37 N7 O
Ligand molecular weight: 487.64
Ligand SMILES: CC1(CCN(CC1)Cc2ccc(cc2)N3CC(=O)NC4(C3)CCN(CC4)c5c6cc[nH]c6ncn5)C
Ligand InChI: InChI=1S/C28H37N7O/c1-27(2)8-13-33(14-9-27)17-21-3-5-22(6-4-21)35-18-24(36)32-28(19-35)10-15-34(16-11-28)26-23-7-12-29-25(23)30-20-31-26/h3-7,12,20H,8-11,13-19H2,1-2H3,(H,32,36)(H,29,30,31)
Release date: 2021-09-15
Crystal structure of the EGFR kinase domain (L858R, T790M, V948R) in complex with a covalent inhibitor N-[(3R,4R)-4-fluoro-1-{6-[(1-methyl-1H-pyrazol-4-yl)amino]-9-(propan-2-yl)-9H-purin-2-yl}pyrrolidin-3-yl]propanamide (PDB entry 5UG8)
Macromolecule: Epidermal growth factor receptor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 329 residues
Sequence: GSGEAPNQALLRILKETEFKKIKVLGSGAFGTVYKGLWIPEGEKVKIPVAIKELREATSPKANKEILDEAYVMASVDNPHVCRLLGICLTSTVQLIMQLMPFGCLLDYVREHKDNIGSQYLLNWCVQIAKGMNYLEDRRLVHRDLAARNVLVKTPQHVKITDFGRAKLLGAEEKEYHAEGGKVPIKWMALESILHRIYTHQSDVWSYGVTVWELMTFGSKPYDGIPASEISSILEKGERLPQPPICTIDVYMIMRKCWMIDADSRPKFRELIIEFSKMARDPQRYLVIQGDERMHLPSPTDSNFYRALMDEEDMDDVVDADEYLIPQQG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.46
R work: 0.192
R free: 0.207
Average B factor: 23.1
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 286
Crystal growth procedure: Salt: 0.2 M Ammonium sulfate
Precipitant: 11.4 %w/v PEG 8000
Buffer: 0.1 M HEPES (pH 7.50)
Precipitant: 10.0 %v/v iso-propanol
Matthews coefficient: 1.84
Solvent content (%): 33.11
Ligand: N-[(3R,4R)-4-fluoro-1-{6-[(1-methyl-1H-pyrazol-4-yl)amino]-9-(propan-2-yl)-9H-purin-2-yl}pyrrolidin-3-yl]propanamide (8BP)
Ligand formula: C19 H26 F N9 O
Ligand molecular weight: 415.468
Ligand SMILES: CCC(=O)NC1CN(CC1F)c2nc(c3c(n2)n(cn3)C(C)C)Nc4cnn(c4)C
Ligand InChI: InChI=1S/C19H26FN9O/c1-5-15(30)24-14-9-28(8-13(14)20)19-25-17(23-12-6-22-27(4)7-12)16-18(26-19)29(10-21-16)11(2)3/h6-7,10-11,13-14H,5,8-9H2,1-4H3,(H,24,30)(H,23,25,26)/t13-,14-/m1/s1
Release date: 2017-03-22
Crystal Structure of human cyclic GMP-AMP synthase in complex with 2-[(4-phenylphenyl)methylamino]-5-propyl-4H-[1,2,4]triazolo[1,5-a]pyrimidin-7-one:2,2,2-trifluoroacetic acid (PDB entry 7FTY)
Macromolecule: Cyclic GMP-AMP synthase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.86
Sequence length: 362 residues
Sequence: GASKLRAVLEKLKLSRDDISTAAGMVKGVVDHLLLRLKCDSAFRGVGLLNTGSYYEHVKISAPNEFDVMFKLEVPRIQLEEYSNTRAYYFVKFKRNPKENPLSQFLEGEILSASKMLSKFRKIIKEEINDIKDTDVIMKRKRGGSPAVTLLISEKISVDITLALESKSSWPASTQEGLRIQNWLSAKVRKQLRLKPFYLVPKHAKEGNGFQEETWRLSFSHIEKEILNNHGKSKTCCENKEEKCCRKDCLKLMKYLLEQLKERFKDKKHLDKFSSYHVKTAFFHVCTQNPQDSQWDRKDLGLCFDNCVTYFLQCLRTEKLENYFIPEFNLFSSNLIDKRSKEFLTKQIEYERNNEFPVFDEF
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.3
R work: 0.23
R free: 0.29
Average B factor: 93.7
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 293
Crystal growth procedure: 10-12 mg/mL protein in 25 mM Tris/HCl pH7.5, 500mM NaCl, 2mM TCEP, supplemented with 10x molar excess of ligand and, if needed, with 10 mM MgCl2 and 5mM ATP, then mixed 1:1 with reservoir of the Procomplex screen. Several conditions resulted in crystals.
Matthews coefficient: 2.58
Solvent content (%): 52.41
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: 2024-02-21
Crystal Structure of Human Vaccinia-related kinase 2 (VRK-2) bound to JA-47 (PDB entry 9FET)
Macromolecule: Serine/threonine-protein kinase VRK2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 324 residues
Sequence: SMPFPEGKVLDDMEGNQWVLGKKIGSGGFGLIYLAFPTNKPEKDARHVVKVEYQENGPLFSELKFYQRVAKKDCIKKWIERKQLDYLGIPLFYGSGLTEFKGRSYRFMVMERLGIDLQKISGQNGTFKKSTVLQLGIRMLDVLEYIHENEYVHGDIKAANLLLGYKNPDQVYLADYGLSYRYCPNGNHKQYQENPRKGHNGTIEFTSLDAHKGVALSRRSDVEILGYCMLRWLCGKLPWEQNLKDPVAVQTAKTNLLDELPQSVLKWAPSGSSCCEIAQFLVCAHSLAYDEKPNYQALKKILNPHGIPLGPLDFSTKGQSINVH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.4
R work: 0.22183
R free: 0.2687
Average B factor: 61.088
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293.15
Crystal growth procedure: 20% PEG6000 -- 10% ethylene glycol -- 0.1M tris pH 7.5 -- 0.1M calcium chloride
Matthews coefficient: 2.25
Solvent content (%): 45.27
Ligand: [4-({4-[(5-cyclopropyl-1H-pyrazol-3-yl)amino]pyrimidin-2-yl}amino)phenyl]acetonitrile (REB)
Ligand formula: C18 H17 N7
Ligand molecular weight: 331.374
Ligand SMILES: c1cc(ccc1CC#N)Nc2nccc(n2)Nc3cc([nH]n3)C4CC4
Ligand InChI: InChI=1S/C18H17N7/c19-9-7-12-1-5-14(6-2-12)21-18-20-10-8-16(23-18)22-17-11-15(24-25-17)13-3-4-13/h1-2,5-6,8,10-11,13H,3-4,7H2,(H3,20,21,22,23,24,25)
Release date: 2024-09-11
Structure of human Bruton's Tyrosine Kinase in complex with Evobrutinib (PDB entry 6OMU)
Macromolecule: Tyrosine-protein kinase BTK
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 271 residues
Sequence: GLGYGSWEIDPKDLTFLKELGTGQFGVVKYGKWRGQYDVAIKMIKEGSMSEDEFIEEAKVMMNLSHEKLVQLYGVCTKQRPIFIITEYMANGCLLNYLREMRHRFQTQQLLEMCKDVCEAMEYLESKQFLHRDLAARNCLVNDQGVVKVSDFGLSRYVLDDEYTSSVGSKFPVRWSPPEVLMYSKFSSKSDIWAFGVLMWEIYSLGKMPYERFTNSETAEHIAQGLRLYRPHLASEKVYTIMYSCWHEKADERPTFKILLSNILDVMDEES
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.41
R work: 0.1902
R free: 0.226
Average B factor: 10.287
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 295
Crystal growth procedure: 20% PEG 3350, 0.1 M Bis Tris Propane pH 7.5, 0.2 M Sodium acetate trihydrate
Matthews coefficient: 2.27
Solvent content (%): 45.74
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: 2019-08-14
HDAC2 complexed with an inhibitory ligand (PDB entry 7ZZS)
Macromolecule: Histone deacetylase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.5.1.98
Sequence length: 498 residues
Sequence: MAYSQGGGKKKVCYYYDGDIGNYYYGQGHPMKPHRIRMTHNLLLNYGLYRKMEIYRPHKATAEEMTKYHSDEYIKFLRSIRPDNMSEYSKQMQRFNVGEDCPVFDGLFEFCQLSTGGSVAGAVKLNRQQTDMAVNWAGGLHHAKKSEASGFCYVNDIVLAILELLKYHQRVLYIDIDIHHGDGVEEAFYTTDRVMTVSFHKYGEYFPGTGDLRDIGAGKGKYYAVNFPMRDGIDDESYGQIFKPIISKVMEMYQPSAVVLQCGADSLSGDRLGCFNLTVKGHAKCVEVVKTFNLPLLMLGGGGYTIRNVARCWTYETAVALDCEIPNELPYNDYFEYFGPDFKLHISPSNMTNQNTPEYMEKIKQRLFENLRMLPHAPGVQMQAIPEDAVHEDSGDEDGEDPDKRISIRASDKRIACDEEFSDSEDEGEGGRRNVADHKKGAKKARIEEDKKETEDKKTDVKEEDKSKDNSGEKTDTKGTKSEQLSNPGSSGHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.88
R work: 0.1664
R free: 0.2068
Average B factor: 44.138
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 40% PEG 300
0.1M pH=8.6 CHES/NaOH
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: 2022-09-21
X-ray structure of furin in complex with the guanylhydrazone-based inhibitor 2 (mi307) soaked at 0.25 M NaCl (PDB entry 7O1Y)
Macromolecule: Furin
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.75
Sequence length: 480 residues
Sequence: DVYQEPTDPKFPQQWYLSGVTQRDLNVKAAWAQGYTGHGIVVSILDDGIEKNHPDLAGNYDPGASFDVNDQDPDPQPRYTQMNDNRHGTRCAGEVAAVANNGVCGVGVAYNARIGGVRMLDGEVTDAVEARSLGLNPNHIHIYSASWGPEDDGKTVDGPARLAEEAFFRGVSQGRGGLGSIFVWASGNGGREHDSCNCDGYTNSIYTLSISSATQFGNVPWYSEACSSTLATTYSSGNQNEKQIVTTDLRQKCTESHTGTSASAPLAAGIIALTLEANKNLTWRDMQHLVVQTSKPAHLNANDWATNGVGRKVSHSYGYGLLDAGAMVALAQNWTTVAPQRKCIIDILTEPKDIGKRLEVRKTVTACLGEPNHITRLEHAQARLTLSYNRRGDLAIHLVSPMGTRSTLLAARPHDYSADGFNDWAFMTTHSWDEDPSGEWVLEIENTSEANNYGTLTKFTLVLYGTASGSLVPRGSHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.7
R work: 0.1622
R free: 0.177
Average B factor: 29.48
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 293.15
Crystal growth procedure: CRYSTALLIZATION SOLUTION: 100mM MES, 200mM K/NAH2PO4, PH 5.5, 2 M NACL; RESERVOIR SOLUTION: 3.0-3.2M NACL
Matthews coefficient: 3.72
Solvent content (%): 66.95
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: 2021-09-01
A histone H3K9M mutation traps histone methyltransferase Clr4 to prevent heterochromatin spreading (PDB entry 5T0M)
Macromolecule: Histone-lysine N-methyltransferase EHMT2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1
Sequence length: 281 residues
Sequence: NRAIRTEKIICRDVARGYENVPIPCVNGVDGEPCPEDYKYISENCETSTMNIDRNITHLQHCTCVDDCSSSNCLCGQLSIRCWYDKDGRLLQEFNKIEPPLIFECNQACSCWRNCKNRVVQSGIKVRLQLYRTAKMGWGVRALQTIPQGTFICEYVGELISDAEADVREDDSYLFDLDNKDGEVYCIDARYYGNISRFINHLCDPNIIPVRVFMLHQDLRFPRIAFFSSRDIRTGEELGFDYGDRFWDIKSKYFTCQCGSEKCKHSAEAIALEQSRLARLD
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.896
R work: 0.1845
R free: 0.224
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293.15
Crystal growth procedure: 0.1 M Bis-Tris propane (pH 7.5), 18% (w/v) PEG3350, 0.2 M NaF, and 5% (v/v) ethylene glycol
Matthews coefficient: 2.34
Solvent content (%): 47.42
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: 2016-10-05
Crystal structure of apo-hGSTA1-1 exhibiting a new conformation of C-terminal helix (PDB entry 6ATQ)
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): 2
R work: 0.1687
R free: 0.2348
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, 6.5
Matthews coefficient: 2.26
Solvent content (%): 45.66
Ligand: (4S)-2-METHYL-2,4-PENTANEDIOL (MPD)
Ligand formula: C6 H14 O2
Ligand molecular weight: 118.174
Ligand SMILES: CC(CC(C)(C)O)O
Ligand InChI: InChI=1S/C6H14O2/c1-5(7)4-6(2,3)8/h5,7-8H,4H2,1-3H3/t5-/m0/s1
Release date: 2018-09-12
Human DNA polymerase eta-DNA ternary mismatch complex:reaction with 1.0 mM Mg2+ for 80s (PDB entry 7U78)
Macromolecule: DNA polymerase eta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 435 residues
Sequence: GPHMATGQDRVVALVDMDCFFVQVEQRQNPHLRNKPCAVVQYKSWKGGGIIAVSYEARAFGVTRSMWADDAKKLCPDLLLAQVRESRGKANLTKYREASVEVMEIMSRFAVIERASIDEAYVDLTSAVQERLQKLQGQPISADLLPSTYIEGLPQGPTTAEETVQKEGMRKQGLFQWLDSLQIDNLTSPDLQLTVGAVIVEEMRAAIERETGFQCSAGISHNKVLAKLACGLNKPNRQTLVSHGSVPQLFSQMPIRKIRSLGGKLGASVIEILGIEYMGELTQFTESQLQSHFGEKNGSWLYAMCRGIEHDPVKPRQLPKTIGCSKNFPGKTALATREQVQWWLLQLAQELEERLTKDRNDNDRVATQLVVSIRVQGDKRLSSLRRCCALTRYDAHKMSHDAFTVIKNCNTSGIQTEWSPPLTMLFLCATKFSAS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.61
R work: 0.1863
R free: 0.2174
Average B factor: 31.8631
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6
Crystallization temperature (K): 298
Crystal growth procedure: 10% PEG 2000MME, 0.1 M MES
Matthews coefficient: 2.06
Solvent content (%): 40.36
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: 2022-05-04
Crystal Structure of KRAS4a (GMPPNP) in complex with RAF1 (RBD-CRD) (PDB entry 8T75)
Macromolecule: RAF proto-oncogene serine/threonine-protein kinase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 137 residues
Sequence: SKTSNTIRVFLPNKQRTVVNVRNGMSLHDCLMKALKVRGLQPECCAVFRLLHEHKGKKARLDWNTDAASLIGEELQVDFLDHVPLTTHNFARKTFLKLAFCDICQKFLLNGFRCQTCGYKFHEHCSTKVPTMCVDWS
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.65
R work: 0.178
R free: 0.219
Average B factor: 76.6592
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M sodium acetate (pH 4.6), 2 M sodium formate
Matthews coefficient: 3.96
Solvent content (%): 68.93
Ligand: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER (GNP)
Ligand formula: C10 H17 N6 O13 P3
Ligand molecular weight: 522.196
Ligand SMILES: c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(NP(=O)(O)O)O)O)O)N=C(NC2=O)N
Ligand InChI: InChI=1S/C10H17N6O13P3/c11-10-13-7-4(8(19)14-10)12-2-16(7)9-6(18)5(17)3(28-9)1-27-32(25,26)29-31(23,24)15-30(20,21)22/h2-3,5-6,9,17-18H,1H2,(H,25,26)(H3,11,13,14,19)(H4,15,20,21,22,23,24)/t3-,5-,6-,9-/m1/s1
Release date: 2024-02-14
DCN1 bound to DI-1859 (PDB entry 6XOO)
Macromolecule: Lysozyme, DCN1-like protein 1 chimera
Type: Protein, polypeptide(L)
Source organism: Tequatrovirus T4
EC number: 3.2.1.17
Sequence length: 386 residues
Sequence: MHHHHHHSSGVDLGTENLYFQSNAMNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTNSLRMLQQKRWAEAAVNLAKSRWYNQTPNRTKRVITTFATGTWDAYKNLRKKLEQLYNRYKDPQDENKIGIDGIQQFCDDLALDPASISVLIIAWKFRAATQCEFSKQEFMDGMTELGCDSIEKLKAQIPKMEQELKEPGRFKDFYQFTFNFAKNPGQKGLDLEMAIAYWNLVLNGRFKFLDLWNKFLLEHHKRSIPKDTWNLLLDFSTMIADDMSNYDEEGAWPVLIDDFVEFARPQIAGTKSTTV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.06
R work: 0.197
R free: 0.242
Average B factor: 32.25
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: 28-33% PEG 3350, 200 mM Ammonium formate
Matthews coefficient: 2.14
Solvent content (%): 42.47
Ligand: N-{(1S)-1-cyclohexyl-2-[(2-methylpropanoyl)amino]ethyl}-N~2~-propanoyl-3-[6-(propan-2-yl)-1,3-benzothiazol-2-yl]-L-alaninamide (H8S)
Ligand formula: C28 H42 N4 O3 S
Ligand molecular weight: 514.723
Ligand SMILES: CCC(=O)NC(Cc1nc2ccc(cc2s1)C(C)C)C(=O)NC(CNC(=O)C(C)C)C3CCCCC3
Ligand InChI: InChI=1S/C28H42N4O3S/c1-6-25(33)30-22(15-26-31-21-13-12-20(17(2)3)14-24(21)36-26)28(35)32-23(16-29-27(34)18(4)5)19-10-8-7-9-11-19/h12-14,17-19,22-23H,6-11,15-16H2,1-5H3,(H,29,34)(H,30,33)(H,32,35)/t22-,23+/m0/s1
Release date: 2021-06-02