satarupa22/MacromolecularLigandDB huggingface dataset:
Crystal structure of human GPX4-U46C mutant K48A (PDB entry 7L8R)
Macromolecule: Isoform Cytoplasmic of Phospholipid hydroperoxide glutathione peroxidase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.11.1.12
Sequence length: 192 residues
Sequence: MGSSHHHHHHSSGLVPRGSHMLEAASRDDWRCARSMHEFSAKDIDGHMVNLDKYRGFVCIVTNVASQCGATEVNYTQLVDLHARYAECGLRILAFPCNQFGKQEPGSNEEIKEFAAGYNVKFDMFSKICVNGDDAHPLWKWMKIQPKGKGILGNAIKWNFTKFLIDKNGCVVKRYGPMEEPLVIEKDLPHYF
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.52
R work: 0.1576
R free: 0.1772
Average B factor: 21.4738
Crystallization method: MICROBATCH
Crystallization pH: 6
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M sodium chloride, 0.1 M MES, and 40% (w/v) PEG 8000
Matthews coefficient: 2.01
Solvent content (%): 38.83
Ligand: THIOCYANATE ION (SCN)
Ligand formula: C N S
Ligand molecular weight: 58.082
Ligand SMILES: C(#N)[S-]
Ligand InChI: InChI=1S/CHNS/c2-1-3/h3H/p-1
Release date: 2021-12-29
Crystal structure of human Casein Kinase II subunit alpha (CK2a1) in complex with 5-((4-((2-aminoethyl)(ethyl)amino)-3-(4H-1,2,4-triazol-4-yl)phenyl)amino)-7-(cyclopropylamino)pyrazolo[1,5-a]pyrimidine-3-carbonitrile (PDB entry 9EZG)
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): 2.18
R work: 0.20907
R free: 0.24235
Average B factor: 53.415
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M bis-tris pH 5.5 
23-26% (v/v) PEG 3350 
0.2 M ammonia sulphate
Matthews coefficient: 3.16
Solvent content (%): 61.04
Ligand: 5-[[4-[2-azanylethyl(ethyl)amino]-3-(1,2,4-triazol-4-yl)phenyl]amino]-7-(cyclopropylamino)pyrazolo[1,5-a]pyrimidine-3-carbonitrile (A1H8C)
Ligand formula: C22 H25 N11
Ligand molecular weight: 443.508
Ligand SMILES: CCN(CCN)c1ccc(cc1n2cnnc2)Nc3cc(n4c(n3)c(cn4)C#N)NC5CC5
Ligand InChI: InChI=1S/C22H25N11/c1-2-31(8-7-23)18-6-5-17(9-19(18)32-13-25-26-14-32)28-20-10-21(29-16-3-4-16)33-22(30-20)15(11-24)12-27-33/h5-6,9-10,12-14,16,29H,2-4,7-8,23H2,1H3,(H,28,30)
Release date: 2024-07-31
Crystal structure of human Biliverdin IX-beta reductase B with Febuxostat (TEI) (PDB entry 7ER9)
Macromolecule: Flavin reductase (NADPH)
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.5.1.30
Sequence length: 216 residues
Sequence: HHHHHHHHHHMAVKKIAIFGATGQTGLTTLAQAVQAGYEVTVLVRDSSRLPSEGPRPAHVVVGDVLQAADVDKTVAGQDAVIVLLGTRNDLSPTTVMSEGARNIVAAMKAHGVDKVVACTSAFLLWDPTKVPPRLQAVTDDHIRMHKVLRESGLKYVAVMPPHIGDQPLTGAYTVTLDGRGPSRVISKHDLGHFMLRCLTTDEYDGHSTYPSHQYQ
Oligomeric state: Homo 2-mer
Stoichiometry: A2
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.45
R work: 0.1552
R free: 0.1904
Average B factor: 24.35
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 291.15
Crystal growth procedure: 1.9-2.0M Ammonium sulfate, 0.1M Bis-tris (pH 6.5)
Matthews coefficient: 2.19
Solvent content (%): 43.9
Ligand: 2-(3-CYANO-4-ISOBUTOXY-PHENYL)-4-METHYL-5-THIAZOLE-CARBOXYLIC ACID (TEI)
Ligand formula: C16 H16 N2 O3 S
Ligand molecular weight: 316.375
Ligand SMILES: Cc1c(sc(n1)c2ccc(c(c2)C#N)OCC(C)C)C(=O)O
Ligand InChI: InChI=1S/C16H16N2O3S/c1-9(2)8-21-13-5-4-11(6-12(13)7-17)15-18-10(3)14(22-15)16(19)20/h4-6,9H,8H2,1-3H3,(H,19,20)
Release date: 2022-01-19
Human APE1 substrate complex with an G/G mismatch adjacent the THF (PDB entry 6BOR)
Macromolecule: DNA-(apurinic or apyrimidinic site) lyase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1
Sequence length: 318 residues
Sequence: MPKRGKKGAVAEDGDELRTEPEAKKSKTAAKKNDKEAAGEGPALYEDPPDQKTSPSGKPATLKICSWNVDGLRAWIKKKGLDWVKEEAPDILCLQQTKCSENKLPAELQELPGLSHQYWSAPSDKEGYSGVGLLSRQCPLKVSYGIGDEEHDQEGRVIVAEFDSFVLVTAYVPNAGRGLVRLEYRQRWDEAFRKFLKGLASRKPLVLCGNLNVAHEEIDLRNPKGNKKNAGFTPQERQGFGELLQAVPLADSFRHLYPNTPYAYTFWTYMMNARSKNVGWRLDYFLLSHSLLPALCDSKIRSKALGSDHCPITLYLAL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.84
R work: 0.1703
R free: 0.2092
Average B factor: 22.2407
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5
Crystallization temperature (K): 291
Crystal growth procedure: 7% PEG 20K, 100mM sodium Citrate, 15% glycerol, 5mM CaCl2
Matthews coefficient: 2.27
Solvent content (%): 45.88
Ligand: 1,2-ETHANEDIOL (EDO)
Ligand formula: C2 H6 O2
Ligand molecular weight: 62.068
Ligand SMILES: C(CO)O
Ligand InChI: InChI=1S/C2H6O2/c3-1-2-4/h3-4H,1-2H2
Release date: 2018-08-15
DNA Polymerase Mu, 8-oxodGTP:At Product State Ternary Complex, 10 mM Mn2+ (120min) (PDB entry 7KT5)
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): 1.46
R work: 0.1618
R free: 0.1825
Average B factor: 26.0838
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: 2.49
Solvent content (%): 50.66
Ligand: MANGANESE (II) ION (MN)
Ligand formula: Mn
Ligand molecular weight: 54.938
Ligand SMILES: [Mn+2]
Ligand InChI: InChI=1S/Mn/q+2
Release date: 2021-12-15
Human JMJD5 in complex with MN and 5-(benzylamino)pyridine-2,4-dicarboxylic acid. (PDB entry 7DYV)
Macromolecule: Bifunctional peptidase and arginyl-hydroxylase JMJD5
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11
Sequence length: 235 residues
Sequence: STVPRLHRPSLQHFREQFLVPGRPVILKGVADHWPCMQKWSLEYIQEIAGCRTVPVEVGSRYTDEEWSQTLMTVNEFISKYIVNEPRDVGYLAQHQLFDQIPELKQDISIPDYCSLGDGEEEEITINAWFGPQGTISPLHQDPQQNFLVQVMGRKYIRLYSPQESGALYPHDTHLLHNTSQVDVENPDLEKFPKFAKAPFLSCILSPGEILFIPVKYWHYVRALDLSFSVSFWWS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.92
R work: 0.2044
R free: 0.2401
Average B factor: 38.19
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 100mM HEPES sodium, 200mM magnesium chloride hexahydrate, 25% w/v PEG 3350, 1mM manganese chloride
Matthews coefficient: 2.32
Solvent content (%): 47.07
Ligand: 5-(benzylamino)pyridine-2,4-dicarboxylic acid (HRF)
Ligand formula: C14 H12 N2 O4
Ligand molecular weight: 272.256
Ligand SMILES: c1ccc(cc1)CNc2cnc(cc2C(=O)O)C(=O)O
Ligand InChI: InChI=1S/C14H12N2O4/c17-13(18)10-6-11(14(19)20)16-8-12(10)15-7-9-4-2-1-3-5-9/h1-6,8,15H,7H2,(H,17,18)(H,19,20)
Release date: 2022-02-02
Zn- Carbonic Anhydrase II pH 7.8 0 atm CO2 (PDB entry 6LUW)
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): 1.2
R work: 0.1165
R free: 0.1409
Average B factor: 13.109
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.8
Crystallization temperature (K): 293
Crystal growth procedure: 1.3 M sodium citrate, 50 mM Tris-HCl
Matthews coefficient: 2.08
Solvent content (%): 40.88
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: 2020-08-19
PKCeta kinase domain in complex with compound 2 (PDB entry 8FP1)
Macromolecule: Protein kinase C eta type
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.13
Sequence length: 353 residues
Sequence: GSKESSKEGNGIGVNSSNRLGIDNFEFIRVLGKGSFGKVMLARVKETGDLYAVKVLKKDVILQDDDVECTMTEKRILSLARNHPFLTQLFCCFQTPDRLFFVMEFVNGGDLMFHIQKSRRFDEARARFYAAEIISALMFLHDKGIIYRDLKLDNVLLDHEGHCKLADFGMCKEGICNGVTTATFCGTPDYIAPEILQEMLYGPAVDWWAMGVLLYEMLCGHAPFEAENEDDLFEAILNDEVVYPTWLHEDATGILKSFMTKNPTMRLGSLTQGGEHAILRHPFFKEIDWAQLNHRQIEPPFRPRIKSREDVSNFDPDFIKEEPVLTPIDEGHLPMINQDEFRNFEYVSPELQP
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.85
R work: 0.1978
R free: 0.2344
Average B factor: 29.4
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6
Crystallization temperature (K): 286.15
Crystal growth procedure: Well Ingredients:
Precipitant: 21.0 %w/v (21.0 uL of stock 50.0 %w/v) PEG 3350
Salt: 0.7 M (4.375 uL of stock 8.0 M) lithium nitrate
Buffer: 0.1 M (5.0 uL of stock 1.0 M) MES (pH 6.00)
Organic (non-volatile): 7.0 % w/v (4.375 uL of stock 80.0 % w/v) Glycerol
Matthews coefficient: 2.35
Solvent content (%): 47.56
Ligand: (3P)-3-[6-chloro-4-(9-methyl-1-oxa-4,9-diazaspiro[5.5]undecan-4-yl)-7H-pyrrolo[2,3-d]pyrimidin-5-yl]benzonitrile (XXF)
Ligand formula: C22 H23 Cl N6 O
Ligand molecular weight: 422.911
Ligand SMILES: CN1CCC2(CC1)CN(CCO2)c3c4c(c([nH]c4ncn3)Cl)c5cccc(c5)C#N
Ligand InChI: InChI=1S/C22H23ClN6O/c1-28-7-5-22(6-8-28)13-29(9-10-30-22)21-18-17(16-4-2-3-15(11-16)12-24)19(23)27-20(18)25-14-26-21/h2-4,11,14H,5-10,13H2,1H3,(H,25,26,27)
Release date: 2023-04-05
Crystal structure of the DHR-2 domain of DOCK10 in complex with Rac1 (PDB entry 8I5W)
Macromolecule: Dedicator of cytokinesis protein 10
Type: Protein, polypeptide(L)
Source organism: Mus musculus
Sequence length: 282 residues
Sequence: GSSGSSGRYYRVAFYGQGFFEEEEGKEYIYKEPKLTGLSEISQRLLKLYADKFGADNVKIIQDSNKVNPKDLDPKYAYIQVTYVTPFFEEKEIEDRKTDFEMHHNINRFVFETPFTLSGKKHGGVAEQCKRRTVLTTSHLFPYVKKRIQVISQSSTELNPIEVAIDEMSRKVSELNQLCTTEEVDMIRLQLKLQGSVSVKVNAGPMAYARAFLEETNAKKYPDNQVKLLKEIFRQFADACGQALDVNERLIKEDQLEYQEELRSHYKDMLSELSAIMNEQIT
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.432
R work: 0.2195
R free: 0.28
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: ammonium sulfate, sodium cacodylate, PEG 8000, glycerol
Matthews coefficient: 2.91
Solvent content (%): 57.67
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: 2023-03-15
Structure of BRCA1 BRCT domains in complex with Abraxas single phosphorylated peptide (PDB entry 4Y2G)
Macromolecule: Breast cancer type 1 susceptibility protein
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 6.3.2
Sequence length: 224 residues
Sequence: MSHHHHHHSMVNKRMSMVVSGLTPEEFMLVYKFARKHHITLTNLITEETTHVVMKTDAEFVCERTLKYFLGIAGGKWVVSYFWVTQSIKERKMLNEHDFEVRGDVVNGRNHQGPKRARESQDRKIFRGLEICCYGPFTNMPTDQLEWMVQLCGASVVKELSSFTLGTGVHPIVVVQPDAWTEDNGFHAIGQMCEAPVVTREWVLDSVALYQCQELDTYLIPQIP
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.5
R work: 0.2149
R free: 0.2521
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8
Crystallization temperature (K): 291
Crystal growth procedure: Lithium chloride, Tris, PEG 6000
Matthews coefficient: 2.05
Solvent content (%): 40.14
Release date: 2016-01-27
Crystal Structures of the bispecific ubiquitin/FAT10 activating enzyme, Uba6 (PDB entry 7SOL)
Macromolecule: Ubiquitin-like modifier-activating enzyme 6
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 6.2.1.45
Sequence length: 1020 residues
Sequence: GAMGVEIDDALYSRQRYVLGDTAMQKMAKSHVFLSGMGGLGLEIAKNLVLAGIKAVTIHDTEKCQAWDLGTNFFLSEDDVVNKRNRAEAVLKHIAELNPYVHVTSSSVPFNETTDLSFLDKYQCVVLTEMKLPLQKKINDFCRSQCPPIKFISADVHGIWSRLFCDFGDEFEVLDTTGEEPKEIFISNITQANPGIVTCLENHPHKLETGQFLTFREINGMTGLNGSIQQITVISPFSFSIGDTTELEPYLHGGIAVQVKTPKTVFFESLERQLKHPKCLIVDFSNPEAPLEIHTAMLALDQFQEKYSRKPNVGCQQDSEELLKLATSISETLEEKPDVNADIVHWLSWTAQGFLSPLAAAVGGVASQEVLKAVTGKFSPLCQWLYLEAADIVESLGKPECEEFLPRGDRYDALRACIGDTLCQKLQNLNIFLVGCGAIGCEMLKNFALLGVGTSKEKGMITVTDPDLIEKSNLNRQFLFRPHHIQKPKSYTAADATLKINSQIKIDAHLNKVCPTTETIYNDEFYTKQDVIITALDNVEARRYVDSRCLANLRPLLDSGTMGTKGHTEVIVPHLTESYNSHRDPPEEEIPFATLKSFPAAIEHTIQWARDKFESSFSHKPSLFNKFWQTYSSAEEVLQKIQSGHSLEGCFQVIKLLSRRPRNWSQCVELARLKFEKYFNHKALQLLHCFPLDIRLKDGSLFWQSPKRPPSPIKFDLNEPLHLSFLQNAAKLYATVYCIPFAEEDLSADALLNILSEVKIQEFKPSNKVVQTDETARKPDHVPISSEDERNAIFQLEKAILSNEATKSDLQMAVLSFEKDDDHNGHIDFITAASNLRAKMYSIEPADRFKTKRIAGKIIPAIATTTATVSGLVALEMIKVTGGYPFEAYKNCFLNLAIPIVVFTETTEVRKTKIRNGISFTIWDRWTVHGKEDFTLLDFINAVKEKYGIEPTMVVQGVKMLYVPVMPGHAKRLKLTMHKLVKPTTEKKYVDLTVSFAPDIDGDEDLPGPPVRYYFSHDTD
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.25000635563
R work: 0.165797872043
R free: 0.205701836009
Average B factor: 54.0402852294
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 20 % PEG 3350, 0.2 M NaF
Matthews coefficient: 2.75
Solvent content (%): 55.23
Ligand: INOSITOL HEXAKISPHOSPHATE (IHP)
Ligand formula: C6 H18 O24 P6
Ligand molecular weight: 660.035
Ligand SMILES: C1(C(C(C(C(C1OP(=O)(O)O)OP(=O)(O)O)OP(=O)(O)O)OP(=O)(O)O)OP(=O)(O)O)OP(=O)(O)O
Ligand InChI: InChI=1S/C6H18O24P6/c7-31(8,9)25-1-2(26-32(10,11)12)4(28-34(16,17)18)6(30-36(22,23)24)5(29-35(19,20)21)3(1)27-33(13,14)15/h1-6H,(H2,7,8,9)(H2,10,11,12)(H2,13,14,15)(H2,16,17,18)(H2,19,20,21)(H2,22,23,24)/t1-,2-,3-,4+,5-,6-
Release date: 2022-11-02
Anaerobic crystal structure of HIF prolyl hydroxylase 2 (PHD2 181-407) in complex with HIF2alpha-CODD peptide (523-542), Fe(II) and 2-oxoglutarate (2OG) (PDB entry 8Q6D)
Macromolecule: Egl nine homolog 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11.29
Sequence length: 233 residues
Sequence: GSHMASPNGQTKPLPALKLALEYIVPCMNKHGICVVDDFLGKETGQQIGDEVRALHDTGKFTDGQLVSQKSDSSKDIRGDKITWIEGKEPGCETIGLLMSSMDDLIRHCNGKLGSYKINGRTKAMVACYPGNGTGYVRHVDNPNGDGRCVTCIYYLNKDWDAKVSGGILRIFPEGKAQFADIEPKFDRLLFFWSDRRNPHEVQPAYATRYAITVWYFDADERARAKVKYLTGE
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.4
R work: 0.1671
R free: 0.1899
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 298
Crystal growth procedure: 10-35% PEG 4K, 0.2 ammonium acetate, sodium ammonium acetate trihydrate pH (4.1-5.6)
Matthews coefficient: 1.86
Solvent content (%): 34
Ligand: FE (III) ION (FE)
Ligand formula: Fe
Ligand molecular weight: 55.845
Ligand SMILES: [Fe+3]
Ligand InChI: InChI=1S/Fe/q+3
Release date: 2024-08-21
Fragment-based discovery of pyrazolopyridones as JAK1 inhibitors with excellent subtype selectivity (PDB entry 6TPD)
Macromolecule: Tyrosine-protein kinase JAK2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 289 residues
Sequence: TQFEERHLKFLQQLGKGNFGSVEMCRYDPLQDNTGEVVAVKKLQHSTEEHLRDFEREIEILKSLQHDNIVKYKGVCYSAGRRNLKLIMEYLPYGSLRDYLQKHKERIDHIKLLQYTSQICKGMEYLGTKRYIHRDLATRNILVENENRVKIGDFGLTKVLPQDKEFFKVKEPGESPIFWYAPESLTESKFSVASDVWSFGVVLYELFTYIEKSKSPPAEFMRMIGNDKQGQSIVTHLIELLKNNGRLPRPDGCPDEIYMIMTECWNNNVNQRPSFRDLALRVDQIRDNM
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.99
R work: 0.22341
R free: 0.27759
Average B factor: 25.233
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 2.1M Na Malonate pH 6.0/6.5, 0.1M glycine pH 8.2
Matthews coefficient: 2.77
Solvent content (%): 55.57
Ligand: 3-methyl-4-phenyl-2,7-dihydropyrazolo[3,4-b]pyridin-6-one (QZ8)
Ligand formula: C13 H11 N3 O
Ligand molecular weight: 225.246
Ligand SMILES: Cc1c2c(n[nH]1)NC(=O)C=C2c3ccccc3
Ligand InChI: InChI=1S/C13H11N3O/c1-8-12-10(9-5-3-2-4-6-9)7-11(17)14-13(12)16-15-8/h2-7H,1H3,(H2,14,15,16,17)
Release date: 2020-06-10
PAK4 kinase domain in complex with FRAX486 (PDB entry 5VEE)
Macromolecule: Serine/threonine-protein kinase PAK 4
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 319 residues
Sequence: GARARQENGMPEKPPGPRSPQREPQRVSHEQFRAALQLVVDPGDPRSYLDNFIKIGEGSTGIVCIATVRSSGKLVAVKKMDLRKQQRRELLFNEVVIMRDYQHENVVEMYNSYLVGDELWVVMEFLEGGALTDIVTHTRMNEEQIAAVCLAVLQALSVLHAQGVIHRDIKSDSILLTHDGRVKLSDFGFCAQVSKEVPRRKSLVGTPYWMAPELISRLPYGPEVDIWSLGIMVIEMVDGEPPYFNEPPLKAMKMIRDNLPPRLKNLHKVSPSLKGFLDRLLVRDPAQRATAAELLKHPFLAKAGPPASIVPLMRQNRTR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.5
R work: 0.22839
R free: 0.27564
Average B factor: 115.572
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 298
Crystal growth procedure: 0.1 M Tris-HCl (pH 7.5) and 1.5 - 2.0 M Na acetate
Matthews coefficient: 2.52
Solvent content (%): 51.26
Ligand: 6-(2,4-dichlorophenyl)-8-ethyl-2-{[3-fluoro-4-(piperazin-1-yl)phenyl]amino}pyrido[2,3-d]pyrimidin-7(8H)-one (981)
Ligand formula: C25 H23 Cl2 F N6 O
Ligand molecular weight: 513.394
Ligand SMILES: CCN1c2c(cnc(n2)Nc3ccc(c(c3)F)N4CCNCC4)C=C(C1=O)c5ccc(cc5Cl)Cl
Ligand InChI: InChI=1S/C25H23Cl2FN6O/c1-2-34-23-15(11-19(24(34)35)18-5-3-16(26)12-20(18)27)14-30-25(32-23)31-17-4-6-22(21(28)13-17)33-9-7-29-8-10-33/h3-6,11-14,29H,2,7-10H2,1H3,(H,30,31,32)
Release date: 2017-10-18
Ni-Carbonic Anhydrase II complexed with 3NPA after UV at 140 K (PDB entry 7Y2U)
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): 1.2
R work: 0.12527
R free: 0.1523
Average B factor: 15.29
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.8
Crystallization temperature (K): 293
Crystal growth procedure: 1.3 M sodium citrate, 50 mM Tris-HCl
Matthews coefficient: 2.08
Solvent content (%): 40.91
Ligand: NICKEL (II) ION (NI)
Ligand formula: Ni
Ligand molecular weight: 58.693
Ligand SMILES: [Ni+2]
Ligand InChI: InChI=1S/Ni/q+2
Release date: 2023-12-20
Crystal structure of MGAT5 (alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase V) luminal domain with a Lys329-Ile345 loop truncation, in complex with biantennary pentasaccharide M592 (PDB entry 6YJS)
Macromolecule: Alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.4.1.155
Sequence length: 515 residues
Sequence: SLAEIRTDFNILYSMMKKHEEFRWMRLRIRRMADAWIQAIKSLAEKQNLEKRKRKKVLVHLGLLTKESGFKIAETAFSGGPLGELVQWSDLITSLYLLGHDIRISASLAELKEIMGGGGVELIYIDIVGLAQFKKTLGPSWVHYQCMLRVLDSFGTEPEFNHANYAQSKGHKTPWGKWNLNPQQFYTMFPHTPDNSFLGFVVEQHLNSSDIHHINEIKRQNQSLVYGKVDSFWKNKKIYLDIIHTYMEVHATVYGSSTKNIPSYVKNHGILSGRDLQFLLRETKLFVGLGFPYEGPAPLEAIANGCAFLNPKFNPPKSSKNTDFFIGKPTLRELTSQHPYAEVFIGRPHVWTVDLNNQEEVEDAVKAILNQKIEPYMPYEFTCEGMLQRINAFIEKQDFCHGQVMWPPLSALQVKLAEPGQSCKQVCQESQLICEPSFFQHLNKDKDMLKYKVTCQSSELAKDILVPSFDPKNKHCVFQGDLLLFSCAGAHPRHQRVCPCRDFIKGQVALCKDCL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.6
R work: 0.1841
R free: 0.2145
Average B factor: 34.716
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M HEPES pH 8.0, 
0.3 M Li2SO4, 
30 % (w/v) PEG 3350, 
10 % (v/v) ethylene glycol
wXHPcQHrME
Matthews coefficient: 2.16
Solvent content (%): 43.01
Ligand: 1,2-ETHANEDIOL (EDO)
Ligand formula: C2 H6 O2
Ligand molecular weight: 62.068
Ligand SMILES: C(CO)O
Ligand InChI: InChI=1S/C2H6O2/c3-1-2-4/h3-4H,1-2H2
Release date: 2020-08-05
Crystal structure of farnesylated hGBP1 (PDB entry 6K1Z)
Macromolecule: Guanylate-binding protein 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.5
Sequence length: 594 residues
Sequence: GSMASEIHMTGPMCLIENTNGRLMANPEALKILSAITQPMVVVAIVGLYRTGKSYLMNKLAGKKKGFSLGSTVQSHTKGIWMWCVPHPKKPGHILVLLDTEGLGDVEKGDNQNDSWIFALAVLLSSTFVYNSIGTINQQAMDQLYYVTELTHRIRSKSSPDENENEVEDSADFVSFFPDFVWTLRDFSLDLEADGQPLTPDEYLTYSLKLKKGTSQKDETFNLPRLCIRKFFPKKKCFVFDRPVHRRKLAQLEKLQDEELDPEFVQQVADFCSYIFSNSKTKTLSGGIQVNGPRLESLVLTYVNAISSGDLPCMENAVLALAQIENSAAVQKAIAHYEQQMGQKVQLPTETLQELLDLHRDSEREAIEVFIRSSFKDVDHLFQKELAAQLEKKRDDFCKQNQEASSDRCSALLQVIFSPLEEEVKAGIYSKPGGYRLFVQKLQDLKKKYYEEPRKGIQAEEILQTYLKSKESMTDAILQTDQTLTEKEKEIEVERVKAESAQASAKMLQEMQRKNEQMMEQKERSYQEHLKQLTEKMENDRVQLLKEQERTLALKLQEQEQLLKEGFQKESRIMKNEIQDLQTKMRRRKACTIS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.307
R work: 0.2195
R free: 0.2668
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293.15
Crystal growth procedure: 0.02M Citric acid/0.08M BIS-TRIS propane (pH 8.8), 16% w/v Polyethylene glycol 3350
Matthews coefficient: 2.57
Solvent content (%): 52.09
Ligand: FARNESYL (FAR)
Ligand formula: C15 H26
Ligand molecular weight: 206.367
Ligand SMILES: CC=C(C)CCC=C(C)CCC=C(C)C
Ligand InChI: InChI=1S/C15H26/c1-6-14(4)10-8-12-15(5)11-7-9-13(2)3/h6,9,12H,7-8,10-11H2,1-5H3/b14-6+,15-12+
Release date: 2019-06-12
Structure of Bace-1 (Beta-Secretase) in complex with : N-(3-((1R,5S,6R)-3-amino-5-methyl-2-oxa-4-azabicyclo[4.1.0]hept-3-en-5-yl)-4-fluorophenyl)-5-methoxypyrazine-2-carboxamide (PDB entry 6C2I)
Macromolecule: Beta-secretase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.23.46
Sequence length: 411 residues
Sequence: LPRETDEEPEEPGKKGSFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHPFLHRYYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTVRANIAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTHVPNLFSLQLCGAGFPLNQSEVLASVGGSMIIGGIDHSLYTGSLWYTPIRREWYYEVIIVRVEINGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVKSIKAASSTEKFPDGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRITILPQQYLRPVEDVATSQDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSACHVHDEFRTAAVEGPFVTLDMEDCGYNIPQTDES
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.95
R work: 0.1575
R free: 0.1838
Average B factor: 28.5896
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 20 % (w/v) PEG 5000 monomethylethyl ether (MME), 200 mM sodium citrate (pH 6.6) and 200 mM sodium iodide
Matthews coefficient: 2.82
Solvent content (%): 56.36
Ligand: IODIDE ION (IOD)
Ligand formula: I
Ligand molecular weight: 126.904
Ligand SMILES: [I-]
Ligand InChI: InChI=1S/HI/h1H/p-1
Release date: 2018-02-21