satarupa22/MacromolecularLigandDB huggingface dataset:
Crystal structure of RCC1-Like domain 2 of ubiquitin ligase HERC2 in complex with DXDKDED motif of pericentriolar material 1 protein (PDB entry 7Q46)
Macromolecule: E3 ubiquitin-protein ligase HERC2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2.26
Sequence length: 405 residues
Sequence: GAMGSLIRKKAAGLESAATIRTKVFVWGLNDKDQLGGLKGSKIKVPSFSETLSALNVVQVAGGSKSLFAVTVEGKVYACGEATNGRLGLGISSGTVPIPRQITALSSYVVKKVAVHSGGRHATALTVDGKVFSWGEGDDGKLGHFSRMNCDKPRLIEALKTKRIRDIACGSSHSAALTSSGELYTWGLGEYGRLGHGDNTTQLKPKMVKVLLGHRVIQVACGSRDAQTLALTDEGLVFSWGDGDFGKLGRGGSEGCNIPQNIERLNGQGVCQIECGAQFSLALTKSGVVWTWGKGDYFRLGHGSDVHVRKPQVVEGLRGKKIVHVAVGALHCLAVTDSGQVYAWGDNDHGQQGNGTTTVNRKPTLVQGLEGQKITRVACGSSHSVAWTTVDVATPSVHEPVLFQT
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.46002538066
R work: 0.178644261638
R free: 0.245337109543
Average B factor: 36.7000727827
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8
Crystallization temperature (K): 293.15
Crystal growth procedure: hanging drop
20% PEG 3350
0.18M tris amonium citrate
Matthews coefficient: 2.61
Solvent content (%): 52.96
Ligand: CITRIC ACID (CIT)
Ligand formula: C6 H8 O7
Ligand molecular weight: 192.124
Ligand SMILES: C(C(=O)O)C(CC(=O)O)(C(=O)O)O
Ligand InChI: InChI=1S/C6H8O7/c7-3(8)1-6(13,5(11)12)2-4(9)10/h13H,1-2H2,(H,7,8)(H,9,10)(H,11,12)
Release date: 2022-11-16
Structure of Rad6~Ub (PDB entry 4R62)
Macromolecule: Ubiquitin-conjugating enzyme E2 2
Type: Protein, polypeptide(L)
Source organism: Saccharomyces cerevisiae S288C
EC number: 6.3.2.19
Sequence length: 172 residues
Sequence: MSTPARRRLMRDFKRMKEDAPPGVSASPLPDNVMVWNAMIIGPADTPYEDGTFRLLLEFDEEYPNKPPHVKFLSEMFHPNVYANGEIKLDILQNRWTPTYDVASILTSIQSLFNDPNPASPANVEAATLFKDHKSQYVKRVKETVEKSWEDDMDDMDDDDDDDDDDDDDEAD
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.28
R work: 0.2101
R free: 0.2645
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.4
Crystallization temperature (K): 293
Crystal growth procedure: 24% PEG 300, 50 mM sodium acetate, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Matthews coefficient: 1.99
Solvent content (%): 38.23
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: 2015-09-02
Apo structure of human Leukotriene A4 hydrolase (PDB entry 5FWQ)
Macromolecule: HUMAN LEUKOTRIENE A4 HYDROLASE
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.3.2.6
Sequence length: 633 residues
Sequence: MASMTGGQQMGRGSMPEIVDTCSLASPASVCRTKHLHLRCSVDFTRRTLTGTAALTVQSQEDNLRSLVLDTKDLTIEKVVINGQEVKYALGERQSYKGSPMEISLPIALSKNQEIVIEISFETSPKSSALQWLTPEQTSGKEHPYLFSQCQAIHCRAILPCQDTPSVKLTYTAEVSVPKELVALMSAIRDGETPDPEDPSRKIYKFIQKVPIPCYLIALVVGALESRQIGPRTLVWSEKEQVEKSAYEFSETESMLKIAEDLGGPYVWGQYDLLVLPPSFPYGGMENPCLTFVTPTLLAGDKSLSNVIAHEISHSWTGNLVTNKTWDHFWLNEGHTVYLERHICGRLFGEKFRHFNALGGWGELQNSVKTFGETHPFTKLVVDLTDIDPDVAYSSVPYEKGFALLFYLEQLLGGPEIFLGFLKAYVEKFSYKSITTDDWKDFLYSYFKDKVDVLNQVDWNAWLYSPGLPPIKPNYDMTLTNACIALSQRWITAKEDDLNSFNATDLKDLSSHQLNEFLAQTLQRAPLPLGHIKRMQEVYNFNAINNSEIRFRWLRLCIQSKWEDAIPLALKMATEQGRMKFTRPLFKDLAAFDKSHDQAVRTYQEHKASMHPVTAMLVGKDLKVDLEHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.047
R work: 0.1934
R free: 0.223
Average B factor: 22.8
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 290.55
Crystal growth procedure: PROTEIN SOLUTION: 10 MM TRIS-HCL, 25 MM KCL, 4-8 MG/ML PROTEIN (PH8); PRECIPITATE SOLUTION: 0,15M IMIDAZOL/HCL PH6.5; 0,1 M NAACETAT, 14% PEG8000, 5 MM YBCL3 AND 25 MM 5-CHLORO-3-HYDROXYPYRIDINE; HANGING DROP VAPOR-DIFFUSION AT 290.55 K
Matthews coefficient: 2.23
Solvent content (%): 44.75
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: 2016-10-05
Nocturnin with bound NADPH substrate (PDB entry 6NF0)
Macromolecule: Nocturnin
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.13.4
Sequence length: 312 residues
Sequence: GPPPRFQRDFVDLRTDCPSTHPPIRVMQWNILAQALGEGKDNFVQCPVEALKWEERKCLILEEILAYQPDILCLQEVDHYFDTFQPLLSRLGYQGTFFPKPWSPCLDVEHNNGPDGCALFFLQNRFKLVNSANIRLTAMTLKTNQVAIAQTLECKESGRQFCIAVTHLKARTGWERFRSAQGCDLLQNLQNITQGAKIPLIVCGDFNAEPTEEVYKHFASSSLNLNSAYKLLSADGQSEPPYTTWKIRTSGECRHTLDYIWYSKHALNVRSALDLLTEEQIGPNRLPSFNYPSDHLSLVCDFSFTEESDGLS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.7
R work: 0.2063
R free: 0.264
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: Co-crystals were grown using the hanging drop vapor diffusion method by mixing the crystallization complex 1:1 with reservoir solution (100 mM HEPES pH 7.5, 10% (v/v) Isopropanol, 50 mM Sodium Acetate, and 12% (w/v) PEG 4,000)
Matthews coefficient: 2.14
Solvent content (%): 42.51
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: 2019-05-01
PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with XST00000752b (PDB entry 7GT2)
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): 1.9
R work: 0.2
R free: 0.2393
Average B factor: 46.147
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.3 M magnesium acetate, 0.1 M HEPES pH 7.5, 0.1% beta-mercaptoethanol, 13-14% PEG 8000, 2% ethanol
Matthews coefficient: 3.39
Solvent content (%): 63.71
Ligand: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL (TRS)
Ligand formula: C4 H12 N O3
Ligand molecular weight: 122.143
Ligand SMILES: C(C(CO)(CO)[NH3+])O
Ligand InChI: InChI=1S/C4H11NO3/c5-4(1-6,2-7)3-8/h6-8H,1-3,5H2/p+1
Release date: 2024-01-24
RING-DTC domains of Deltex 2, Form 2 (PDB entry 6Y2X)
Macromolecule: Probable E3 ubiquitin-protein ligase DTX2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2.27
Sequence length: 235 residues
Sequence: GSEPEPEQVIKNYTEELKVPPDEDCIICMEKLSTASGYSDVTDSKAIGSLAVGHLTKCSHAFHLLCLLAMYCNGNKDGSLQCPSCKTIYGEKTGTQPQGKMEVLRFQMSLPGHEDCGTILIVYSIPHGIQGPEHPNPGKPFTARGFPRQCYLPDNAQGRKVLELLKVAWKRRLIFTVGTSSTTGETDTVVWNEIHHKTEMDRNITGHGYPDPNYLQNVLAELAAQGVTEDCLEQQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.77
R work: 0.2421
R free: 0.2741
Average B factor: 56.2907
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.6
Crystallization temperature (K): 292
Crystal growth procedure: Morpheus condition 60
Matthews coefficient: 2.44
Solvent content (%): 49.69
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: 2020-09-02
Human Pim-1 kinase in complex with an inhibitor identified by virtual screening (PDB entry 6YKD)
Macromolecule: Serine/threonine-protein kinase pim-1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 329 residues
Sequence: MGSSHHHHHHSQDPNSMLLSKINSLAHLRAAPCNDLHATKLAPGKEKEPLESQYQVGPLLGSGGFGSVYSGIRVSDNLPVAIKHVEKDRISDWGELPNGTRVPMEVVLLKKVSSGFSGVIRLLDWFERPDSFVLILERPEPVQDLFDFITERGALQEELARSFFWQVLEAVRHCHNCGVLHRDIKDENILIDLNRGELKLIDFGSGALLKDTVYTDFDGTRVYSPPEWIRYHRYHGRSAAVWSLGILLYDMVCGDIPFEHDEEIIRGQVFFRQRVSSECQHLIRWCLALRPSDRPTFEEIQNHPWMQDVLLPQETAEIHLHSLSPGPSK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.86
R work: 0.1584
R free: 0.1942
Average B factor: 43.51
Crystallization method: COUNTER-DIFFUSION
Crystallization pH: 6.3
Crystallization temperature (K): 277
Crystal growth procedure: 0.1 M imidazole pH 6.3
1 M sodium acetate
Matthews coefficient: 3.02
Solvent content (%): 59.25
Ligand: ~{N}-[3-[6-[(3~{R})-piperidin-3-yl]-2-pyridin-4-yl-pyrimidin-4-yl]oxyphenyl]ethanamide (OWB)
Ligand formula: C22 H23 N5 O2
Ligand molecular weight: 389.45
Ligand SMILES: CC(=O)Nc1cccc(c1)Oc2cc(nc(n2)c3ccncc3)C4CCCNC4
Ligand InChI: InChI=1S/C22H23N5O2/c1-15(28)25-18-5-2-6-19(12-18)29-21-13-20(17-4-3-9-24-14-17)26-22(27-21)16-7-10-23-11-8-16/h2,5-8,10-13,17,24H,3-4,9,14H2,1H3,(H,25,28)/t17-/m1/s1
Release date: 2020-07-01
Multiconformer model of WT PTP1B with BB3 at 273 K (PDB entry 6B8Z)
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): 1.8
R work: 0.1687
R free: 0.1991
Average B factor: 47.7507
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: well solution: 0.3 M magnesium acetate, 0.1 M HEPES pH 7.5, 0.1% beta-mercaptoethanol, 13-14% PEG 8000, 2% ethanol
Matthews coefficient: 3.63
Solvent content (%): 66.16
Ligand: 3-(3,5-DIBROMO-4-HYDROXY-BENZOYL)-2-ETHYL-BENZOFURAN-6-SULFONIC ACID [4-(THIAZOL-2-YLSULFAMOYL)-PHENYL]-AMIDE (FRJ)
Ligand formula: C26 H19 Br2 N3 O7 S3
Ligand molecular weight: 741.448
Ligand SMILES: CCc1c(c2ccc(cc2o1)S(=O)(=O)Nc3ccc(cc3)S(=O)(=O)Nc4nccs4)C(=O)c5cc(c(c(c5)Br)O)Br
Ligand InChI: InChI=1S/C26H19Br2N3O7S3/c1-2-21-23(24(32)14-11-19(27)25(33)20(28)12-14)18-8-7-17(13-22(18)38-21)41(36,37)30-15-3-5-16(6-4-15)40(34,35)31-26-29-9-10-39-26/h3-13,30,33H,2H2,1H3,(H,29,31)
Release date: 2018-06-20
DNA Polymerase Mu, 8-oxodGTP:Ct Pre-Catalytic Ground State Ternary Complex, 20 mM Ca2+ (120min) (PDB entry 7KTA)
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: GSAAAPLSPAWMPAYACQRPTPLTHHNTGLSEALEILAEAAGFEGSEGRLLTFCRAASVLKALPSPVTTLSQLQGLPHFGEHSSRVVQELLEHGVCEEVERVRRSERYQTMKLFTQIFGVGVKTADRWYREGLRTLDDLREQPQKLTQQQKAGLQHHQDLSTPVLRSDVDALQQVVEEAVGQALPGATVTLTGGFRRGKLQGHDVDFLITHPKEGQEAGLLPRVMCRLQDQGLILYHQHQHSCCESPTRLAQQSHMDAFERSFCIFRLPQPGSWKAVRVDLVVAPVSQFPFALLGWTGSKLFQRELRRFSRKEKGLWLNSHGLFDPEQKTFFQAASEEDIFRHLGLEYLPPEQRNA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.844
R work: 0.1672
R free: 0.1984
Average B factor: 38.5364
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: 2.52
Solvent content (%): 51.12
Ligand: 8-OXO-2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE (8DG)
Ligand formula: C10 H16 N5 O14 P3
Ligand molecular weight: 523.18
Ligand SMILES: C1C(C(OC1N2C3=C(C(=O)NC(=N3)N)NC2=O)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O
Ligand InChI: InChI=1S/C10H16N5O14P3/c11-9-13-7-6(8(17)14-9)12-10(18)15(7)5-1-3(16)4(27-5)2-26-31(22,23)29-32(24,25)28-30(19,20)21/h3-5,16H,1-2H2,(H,12,18)(H,22,23)(H,24,25)(H2,19,20,21)(H3,11,13,14,17)/t3-,4+,5+/m0/s1
Release date: 2021-12-15
X-ray structure of human CD38 catalytic domain with 2'-Cl-araNAD+ (PDB entry 6VUA)
Macromolecule: ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.2.2.6
Sequence length: 257 residues
Sequence: SRWRQQWSGPGTTKRFPETVLARCVKYTEIHPEMRHVDCQSVWDAFKGAFISKHPCDITEEDYQPLMKLGTQTVPCNKILLWSRIKDLAHQFTQVQRDMFTLEDTLLGYLADDLTWCGEFATSKINYQSCPDWRKDCSNNPVSVFWKTVSRRFAEAACDVVHVMLDGSRSKIFDKDSTFGSVEVHNLQPEKVQTLEAWVIHGGREDSRDLCQDPTIKELESIISKRNIQFSCKNIYRPDKFLQCVKNPEDSSCTSEI
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.5
R work: 0.1664
R free: 0.1902
Average B factor: 30.512
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7
Crystallization temperature (K): 295
Crystal growth procedure: 1) 100mM HEPES pH 7.0, 2) 38-42%  Morpheus Precipitant mix 1 (MD2-250-84) containing PEG 1K, 3350 and MPD, 3) 100mM Potassium phosphate dibasic
Matthews coefficient: 2.73
Solvent content (%): 55
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~{R},4~{R})-4-chloranyl-3-oxidanyl-oxolan-2-yl]methyl hydrogen phosphate (ROJ)
Ligand formula: C15 H22 Cl N5 O12 P2
Ligand molecular weight: 561.762
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(C(CO4)Cl)O)O)O)N
Ligand InChI: InChI=1S/C15H22ClN5O12P2/c16-6-1-29-7(10(6)22)2-30-34(25,26)33-35(27,28)31-3-8-11(23)12(24)15(32-8)21-5-20-9-13(17)18-4-19-14(9)21/h4-8,10-12,15,22-24H,1-3H2,(H,25,26)(H,27,28)(H2,17,18,19)/t6-,7-,8-,10+,11-,12-,15-/m1/s1
Release date: 2020-06-03
dAb3/HOIP-RBR-HOIPIN-8 (PDB entry 6SC9)
Macromolecule: E3 ubiquitin-protein ligase RNF31
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2.31
Sequence length: 376 residues
Sequence: QECAVCGWALPHNRMQALTSCECTICPDCFRQHFTIALKEKHITDMVCPACGRPDLTDDTQLLSYFSTLDIQLRESLEPDAYALFHKKLTEGVLMRDPKFLWCAQCSFGFIYEREQLEATCPQCHQTFCVRCKRQWEEQHRGRSCEDFQNWKRMNDPEYQAQGLAMYLQENGIDCPKCKFSYALARGGCMHFHCTQCRHQFCSGCYNAFYAKNKCPEPNCRVKKSLHGHHPRDCLFYLRDWTALRLQKLLQDNNVMFNTEPPAGARAVPGGGCRVIEQKEVPNGLRDEACGKETPAGYAGLCQAHYKEYLVSLINAHSLDPATLYEVEELETATERYLHVRPQPLAGEDPPAYQARLLQKLTEEVPLGQSIPRRRK
Oligomeric state: Hetero 3-mer
Stoichiometry: A2, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.47
R work: 0.2098
R free: 0.2524
Average B factor: 67.34
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: Ammonium sulfate, sodium chloride, HEPES
Matthews coefficient: 2.59
Solvent content (%): 52.44
Ligand: 2-[3-[2,6-bis(fluoranyl)-4-(1~{H}-pyrazol-4-yl)phenyl]-3-oxidanylidene-prop-1-enyl]-4-(1-methylpyrazol-4-yl)benzoic acid (L68)
Ligand formula: C23 H16 F2 N4 O3
Ligand molecular weight: 434.395
Ligand SMILES: Cn1cc(cn1)c2ccc(c(c2)C=CC(=O)c3c(cc(cc3F)c4c[nH]nc4)F)C(=O)O
Ligand InChI: InChI=1S/C23H16F2N4O3/c1-29-12-17(11-28-29)13-2-4-18(23(31)32)14(6-13)3-5-21(30)22-19(24)7-15(8-20(22)25)16-9-26-27-10-16/h2-12H,1H3,(H,26,27)(H,31,32)/b5-3+
Release date: 2019-11-27
DHODH in complex with Ligand 10 (PDB entry 9BKM)
Macromolecule: Dihydroorotate dehydrogenase (quinone), mitochondrial
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.3.5.2
Sequence length: 369 residues
Sequence: GAMATGDERFYAEHLMPTLQGLLDPESAHRLAVRFTSLGLLPRARFQDSDMLEVRVLGHKFRNPVGIAAGFDKHGEAVDGLYKMGFGFVEIGSVTPKPQEGNPRPRVFRLPEDQAVINRYGFNSHGLSVVEHRLRARQQKQAKLTEDGLPLGVNLGKNKTSVDAAEDYAEGVRVLGPLADYLVVNVSSPNTAGLRSLQGKAELRRLLTKVLQERDGLRRVHRPAVLVKIAPDLTSQDKEDIASVVKELGIDGLIVTNTTVSRPAGLQGALRSETGGLSGKPLRDLSTQTIREMYALTQGRVPIIGVGGVSSGQDALEKIRAGASLVQLYTALTFWGPPVVGKVKRELEALLKEQGFGGVTDAIGADHRR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.08
R work: 0.19063
R free: 0.22795
Average B factor: 34.763
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 293
Crystal growth procedure: 0.10 M NaAcetat_pH4.8, 2.30 M (NH4)2SO4, 30 % Glycerol, 18% (w/v) PEG 4000, 0.1M Na3Citrate pH=5.75
Matthews coefficient: 3.65
Solvent content (%): 66.29
Ligand: FLAVIN MONONUCLEOTIDE (FMN)
Ligand formula: C17 H21 N4 O9 P
Ligand molecular weight: 456.344
Ligand SMILES: Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)CC(C(C(COP(=O)(O)O)O)O)O
Ligand InChI: InChI=1S/C17H21N4O9P/c1-7-3-9-10(4-8(7)2)21(15-13(18-9)16(25)20-17(26)19-15)5-11(22)14(24)12(23)6-30-31(27,28)29/h3-4,11-12,14,22-24H,5-6H2,1-2H3,(H,20,25,26)(H2,27,28,29)/t11-,12+,14-/m0/s1
Release date: 2024-07-03
Crystal Structure of human cyclic GMP-AMP synthase in complex with 8-chloro-2-(2-hydroxyphenyl)quinoline-4-carboxylic acid (PDB entry 7FTL)
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): 2.2
R work: 0.2361
R free: 0.2868
Average B factor: 75.9929
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: 2.59
Solvent content (%): 52.54
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
BACE2 xaperone complex with N-{3-[(4R,5R,6R)-2-amino-5-fluoro-4,6-dimethyl-5,6-dihydro-4H-1,3-thiazin-4-yl]-4-fluorophenyl}-2H,3H-[1,4]dioxino[2,3-c]pyridine-7-carboxamide (PDB entry 7F1G)
Macromolecule: Beta-secretase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.23.45
Sequence length: 386 residues
Sequence: ANFLAMVDNLQGDSGRGYYLEMLIGTPPQKLQILVDTGSSNFAVAGTPHSYIDTYFDTERSSTYRSKGFDVTVKYTQGSWTGFVGEDLVTIPKGFNTSFLVNIATIFESENFFLPGIKWNGILGLAYATLAKPSSSLETFFDSLVTQANIPNVFSMQMCGAGLPVAGSGTNGGSLVLGGIEPSLYKGDIWYTPIKEEWYYQIEILKLEIGGQSLNLDCREYNADKAIVDSGTTLLRLPQKVFDAVVEAVARASLIPEFSDGFWTGSQLACWTNSETPWSYFPKISIYLRDENSSRSFRITILPQLYIQPMMGAGLNYECYRFGISPSTNALVIGATVMEGFYVIFDRAQKRVGFAASPCAEIAGAAVSEISGPFSTEDVASNCVPA
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.5
R work: 0.2255
R free: 0.2446
Average B factor: 27.607
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: not available
Matthews coefficient: 2.26
Solvent content (%): 45.5
Ligand: N-[3-[(4R,5R,6R)-2-azanyl-5-fluoranyl-4,6-dimethyl-5,6-dihydro-1,3-thiazin-4-yl]-4-fluoranyl-phenyl]-2,3-dihydro-[1,4]dioxino[2,3-c]pyridine-7-carboxamide (0QQ)
Ligand formula: C20 H20 F2 N4 O3 S
Ligand molecular weight: 434.46
Ligand SMILES: CC1C(C(N=C(S1)N)(C)c2cc(ccc2F)NC(=O)c3cc4c(cn3)OCCO4)F
Ligand InChI: InChI=1S/C20H20F2N4O3S/c1-10-17(22)20(2,26-19(23)30-10)12-7-11(3-4-13(12)21)25-18(27)14-8-15-16(9-24-14)29-6-5-28-15/h3-4,7-10,17H,5-6H2,1-2H3,(H2,23,26)(H,25,27)/t10-,17+,20-/m1/s1
Release date: 2022-02-23
Structure of human NNMT in complex with macrocyclic peptide 8 (PDB entry 7EI2)
Macromolecule: Nicotinamide N-methyltransferase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1.1
Sequence length: 259 residues
Sequence: GSGFTSKDTYLSHFNPRDYLEKYYKFGSRHSAESQILKHLLKNLFKIFCLDGVKGDLLIDIGSGPTIYQLLSACESFKEIVVTDYSDQNLQELEKWLKKEPAAFDWSPVVTYVCDLEGNRVKGPEKEEKLRQAVKQVLKCDVTQSQPLGAVPLPPADCVLSTLCLDAACPDLPTYCRALRNLGSLLKPGGFLVIMDALKSSYYMIGEQKFSSLPLGREAVEAAVKEAGYTIEWFEVISQSYSSTMANNEGLFSLVARKL
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.08
R work: 0.184
R free: 0.2464
Average B factor: 46.734
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 0.2M Sodium iodide, 0.1M Bis-Tris propane pH7.5, 20% w/v PEG 3350
Matthews coefficient: 2.02
Solvent content (%): 39.21
Release date: 2022-03-30
GSK3-beta in complex with compound (S)-5c (PDB entry 7B6F)
Macromolecule: Glycogen synthase kinase-3 beta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.26
Sequence length: 365 residues
Sequence: MKVSRDKDGSKVTTVVATPGQGPDRPQEVSYTDTKVIGNGSFGVVYQAKLCDSGELVAIKKVLQDKRFKNRELQIMRKLDHCNIVRLRYFFYSSGEKKDEVYLNLVLDYVPETVYRVARHYSRAKQTLPVIYVKLYMYQLFRSLAYIHSFGICHRDIKPQNLLLDPDTAVLKLCDFGSAKQLVRGEPNVSYICSRYYRAPELIFGATDYTSSIDVWSAGCVLAELLLGQPIFPGDSGVDQLVEIIKVLGTPTREQIREMNPNYTEFKFPQIKAHPWTKVFRPRTPPEAIALCSRLLEYTPTARLTPLEACAHSFFDELRDPNVKLPNGRDTPALFNFTTQELSSNPPLATILIPPHARAHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.05
R work: 0.1739
R free: 0.2093
Average B factor: 43.91
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: protein solution: 10 mg/ml in buffer 25mM HEPES, pH 7.5, 200mM NaCl, 5% glycerol, 0.5mM TCEP
reservoir:12% PEG 8000, 1 mM MgCl2, 0.5M NaCl and 0.1M Tris pH 8.0
Matthews coefficient: 2.87
Solvent content (%): 57.08
Ligand: 3-[(3~{S})-3-[(7-chloranyl-9~{H}-pyrimido[4,5-b]indol-4-yl)-methyl-amino]piperidin-1-yl]propanenitrile (SZW)
Ligand formula: C19 H21 Cl N6
Ligand molecular weight: 368.863
Ligand SMILES: CN(c1c2c3ccc(cc3[nH]c2ncn1)Cl)C4CCCN(C4)CCC#N
Ligand InChI: InChI=1S/C19H21ClN6/c1-25(14-4-2-8-26(11-14)9-3-7-21)19-17-15-6-5-13(20)10-16(15)24-18(17)22-12-23-19/h5-6,10,12,14H,2-4,8-9,11H2,1H3,(H,22,23,24)/t14-/m0/s1
Release date: 2020-12-16
The Crystal Structure of TNIK from Biortus. (PDB entry 8X88)
Macromolecule: TRAF2 and NCK-interacting protein kinase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 304 residues
Sequence: DEIDLSALRDPAGIFELVELVGNGTYGQVYKGRHVKTGQLAAIKVMDVTGDEEEEIKQEINMLKKYSHHRNIATYYGAFIKKNPPGMDDQLWLVMEFCGAGSVTDLIKNTKGNTLKEEWIAYICREILRGLSHLHQHKVIHRDIKGQNVLLTENAEVKLVDFGVSAQLDRTVGRRNTFIGTPYWMAPEVIACDENPDATYDFKSDLWSLGITAIEMAEGAPPLCDMHPMRALFLIPRNPAPRLKSKKWSKKFQSFIESCLVKNHSQRPATEQLMKHPFIRDQPNERQVRIQLKDHIDRTKKKRG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.7
R work: 0.1981
R free: 0.2561
Average B factor: 80.368
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 2.4M Sodium malonate dibasic monohydrate,7
Matthews coefficient: 3.3
Solvent content (%): 62.78
Release date: 2023-12-13