satarupa22/MacromolecularLigandDB huggingface dataset:
CRYSTAL STRUCTURE OF GLYCOGEN SYNTHASE KINASE 3 BETA COMPLEXED WITH 3-[(CYCLOPROPYLMETHYL)AMINO] -N-(4-PHENYLPYRIDIN-3-YL)IMIDAZO[1,2-B]PYRIDAZINE-8-CARBOX AMIDE (PDB entry 8DJE)
Macromolecule: Glycogen synthase kinase-3 beta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.26
Sequence length: 441 residues
Sequence: MHSSHHHHHHSSGENLYFQGHMSGRPRTTSFAESCKPVQQPSAFGSMKVSRDKDGSKVTTVVATPGQGPDRPQEVSYTDTKVIGNGSFGVVYQAKLCDSGELVAIKKVLQDKRFKNRELQIMRKLDHCNIVRLRYFFYSSGEKKDEVYLNLVLDYVPETVYRVARHYSRAKQTLPVIYVKLYMYQLFRSLAYIHSFGICHRDIKPQNLLLDPDTAVLKLCDFGSAKQLVRGEPNVSYICSRYYRAPELIFGATDYTSSIDVWSAGCVLAELLLGQPIFPGDSGVDQLVEIIKVLGTPTREQIREMNPNYTEFKFPQIKAHPWTKVFRPRTPPEAIALCSRLLEYTPTARLTPLEACAHSFFDELRDPNVKLPNGRDTPALFNFTTQELSSNPPLATILIPPHARIQAAASTPTNATAASDANTGDRGQTNNAASASASNST
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.374
R work: 0.2
R free: 0.2266
Average B factor: 51.48
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M MES pH 6.0, 20.0 %w/v PEG6K, 0.2 M NH4Cl
Matthews coefficient: 3.12
Solvent content (%): 60.64
Ligand: (4S)-3-[(cyclopropylmethyl)amino]-N-(4-phenylpyridin-3-yl)imidazo[1,2-b]pyridazine-8-carboxamide (U6S)
Ligand formula: C22 H20 N6 O
Ligand molecular weight: 384.434
Ligand SMILES: c1ccc(cc1)c2ccncc2NC(=O)c3ccnn4c3ncc4NCC5CC5
Ligand InChI: InChI=1S/C22H20N6O/c29-22(27-19-13-23-10-8-17(19)16-4-2-1-3-5-16)18-9-11-26-28-20(14-25-21(18)28)24-12-15-6-7-15/h1-5,8-11,13-15,24H,6-7,12H2,(H,27,29)
Release date: 2023-03-22
Crystal structure of TRIM21 E3 ligase, RING domain in complex with its cognate E2 conjugating enzyme UBE2E1 (PDB entry 6FGA)
Macromolecule: E3 ubiquitin-protein ligase TRIM21
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2.27
Sequence length: 101 residues
Sequence: GSHMASAARLTMMWEEVTCPICLDPFVEPVSIECGHSFCQECISQVGKGGGSVCPVCRQRFLLKNLRPNRQLANMVNNLKEISQEAREGTQGERCAVHGER
Oligomeric state: Hetero 4-mer
Stoichiometry: A2, B2
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.82
R work: 0.25283
R free: 0.29407
Average B factor: 90.688
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 100mM Bicine pH 9.0 and 5% w/v PEG 6000
Matthews coefficient: 3.1
Solvent content (%): 60.6
Ligand: ZINC ION (ZN)
Ligand formula: Zn
Ligand molecular weight: 65.409
Ligand SMILES: [Zn+2]
Ligand InChI: InChI=1S/Zn/q+2
Release date: 2019-06-12
tructure of DYRK1A in complex with compound 24 (PDB entry 7A5L)
Macromolecule: Dual specificity tyrosine-phosphorylation-regulated kinase 1A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.12.1
Sequence length: 359 residues
Sequence: MGSSHHHHHHSSGLVPRGSHMIVKNGEKWMDRYEIDSLIGKGSFGQVVKAYDRVEQEWVAIKIIKNKKAFLNQAQIEVRLLELMNKHDTEMKYYIVHLKRHFMFRNHLCLVFEMLSYNLYDLLRNTNFRGVSLNLTRKFAQQMCTALLFLATPELSIIHCDLKPENILLCNPKRSAIKIVDFGSSCQLGQRIYQYIQSRFYRSPEVLLGMPYDLAIDMWSLGCILVEMHTGEPLFSGANEVDQMNKIVEVLGIPPAHILDQAPKARKFFEKLPDGTWNLKKTKDGKREYKPPGTRKLHNILGVETGGPGGRRAGESGHTVADYLKFKDLILRMLDYDPKTRIQPYYALQHSFFKKTADE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.1
R work: 0.1675
R free: 0.2193
Average B factor: 32.348
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M MES buffer at pH 6.5, 12% Peg3350, 0.2M MgCl2
Matthews coefficient: 2.48
Solvent content (%): 50.5
Ligand: 4-[2-methyl-4-(thiophen-3-ylmethoxy)-7~{H}-pyrrolo[2,3-d]pyrimidin-5-yl]pyridin-2-amine (QZW)
Ligand formula: C17 H15 N5 O S
Ligand molecular weight: 337.399
Ligand SMILES: Cc1nc2c(c(c[nH]2)c3ccnc(c3)N)c(n1)OCc4ccsc4
Ligand InChI: InChI=1S/C17H15N5OS/c1-10-21-16-15(17(22-10)23-8-11-3-5-24-9-11)13(7-20-16)12-2-4-19-14(18)6-12/h2-7,9H,8H2,1H3,(H2,18,19)(H,20,21,22)
Release date: 2021-06-30
The Crystal Structure of Tgf-Beta Type I Receptor (Alk5) from Biortus (PDB entry 8YHL)
Macromolecule: TGF-beta receptor type-1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.30
Sequence length: 306 residues
Sequence: GGTIARTIVLQESIGKGRFGEVWRGKWRGEEVAVKIFSSREERSWFREAEIYQTVMLRHENILGFIAADNKDNGTWTQLWLVSDYHEHGSLFDYLNRYTVTVEGMIKLALSTASGLAHLHMEIVGTQGKPAIAHRDLKSKNILVKKNGTCCIADLGLAVRHDSATDTIDIAPNHRVGTKRYMAPEVLDDSINMKHFESFKRADIYAMGLVFWEIARRCSIGGIHEDYQLPYYDLVPSDPSVEEMRKVVCEQKLRPNIPNRWQSCEALRVMAKIMRECWYANGAARLTALRIKKTLSQLSQQEGIKM
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.47
R work: 0.1634
R free: 0.1932
Average B factor: 18.485
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M MgAC2, 0.1M MES pH6.5, 10% PEG10,000
Matthews coefficient: 2.07
Solvent content (%): 40.72
Ligand: 2-fluoranyl-~{N}-[[5-(6-methylpyridin-2-yl)-4-([1,2,4]triazolo[1,5-a]pyridin-6-yl)-1~{H}-imidazol-2-yl]methyl]aniline (A1D6I)
Ligand formula: C22 H18 F N7
Ligand molecular weight: 399.424
Ligand SMILES: Cc1cccc(n1)c2c(nc([nH]2)CNc3ccccc3F)c4ccc5ncnn5c4
Ligand InChI: InChI=1S/C22H18FN7/c1-14-5-4-8-18(27-14)22-21(15-9-10-20-25-13-26-30(20)12-15)28-19(29-22)11-24-17-7-3-2-6-16(17)23/h2-10,12-13,24H,11H2,1H3,(H,28,29)
Release date: 2024-03-13
SARS CoV-2 PLpro in complex with ISG15 C-terminal domain propargylamide (PDB entry 6XA9)
Macromolecule: Non-structural protein 3
Type: Protein, polypeptide(L)
Source organism: Severe acute respiratory syndrome coronavirus 2
EC number: 3.4.22
Sequence length: 318 residues
Sequence: GPREVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYVLPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQVNGLTSIKWADNNCYLATALLTLQQIELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLDSCKRVLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGTFTCASEYTGNYQCGHYKHITSKETLYCIDGALLTKSSEYKGPITDVFYKENSYTTTIK
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.9
R work: 0.1997
R free: 0.2305
Average B factor: 102.03
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.2 M lithium sulfate, 25% PEG3350, 0.1 M Bis-Tris chloride, pH 6.5
Matthews coefficient: 3.4
Solvent content (%): 63.78
Ligand: GLYCEROL (GOL)
Ligand formula: C3 H8 O3
Ligand molecular weight: 92.094
Ligand SMILES: C(C(CO)O)O
Ligand InChI: InChI=1S/C3H8O3/c4-1-3(6)2-5/h3-6H,1-2H2
Release date: 2020-06-17
Human cyclophilin A at 278K, Data set 6 (PDB entry 5KV4)
Macromolecule: Peptidyl-prolyl cis-trans isomerase A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 5.2.1.8
Sequence length: 164 residues
Sequence: VNPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGFGYKGSCFHRIIPGFMCQGGDFTRHNGTGGKSIYGEKFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKTEWLDGKHVVFGKVKEGMNIVEAMERFGSRNGKTSKKITIADCGQLE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.7
R work: 0.1597
R free: 0.2004
Average B factor: 22.3612
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 291
Crystal growth procedure: CRYSTALS WERE GROWN BY MIXING EQUAL VOLUMES OF WELL SOLUTION (100 MM HEPES PH 7.5, 23% PEG 3350, 5 MM TCEP) AND PROTEIN (60 MG/ML IN 20 MM HEPES PH 7.5, 100 MM NACL, 0.5 MM TCEP) IN THE HANGING-DROP FORMAT.
Matthews coefficient: 2.82
Solvent content (%): 56.31
Release date: 2016-08-10
Strategic design of catalytic lysine-targeting reversible covalent BCR-ABL Inhibitors (PDB entry 7DT2)
Macromolecule: Tyrosine-protein kinase ABL1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 310 residues
Sequence: MGSSHHHHHHSSGLVPRGSHMENLYFQSSPNYDKWEMERTDITMKHKLGGGQYGEVYEGVWKKYSLTVAVKTLKEDTMEVEEFLKEAAVMKEIKHPNLVQLLGVCTREPPFYIITEFMTYGNLLDYLRECNRQEVNAVVLLYMATQISSAMEYLEKKNFIHRDLAARNCLVGENHLVKVADFGLSRLMTGDTYTAHAGAKFPIKWTAPESLAYNKFSIKSDVWAFGVLLWEIATYGMSPYPGIDLSQVYELLEKDYRMERPEGCPEKVYELMRACWQWNPSDRPSFAEIHQAFETMFQESSISDEVEKEL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.3
R work: 0.2058
R free: 0.2371
Average B factor: 44.1429
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7
Crystallization temperature (K): 277.15
Crystal growth procedure: 1% Tryptone, 0.05M Hepes sodium pH 7, 
20% w/v Polyethylene glycol 3350
Matthews coefficient: 2.74
Solvent content (%): 55.17
Ligand: [4-[5-[5-(dimethylcarbamoyl)pyridin-3-yl]-1H-pyrrolo[2,3-b]pyridin-3-yl]-2-methanoyl-5-methoxy-phenyl]boronic acid (HJ9)
Ligand formula: C23 H21 B N4 O5
Ligand molecular weight: 444.248
Ligand SMILES: B(c1cc(c(cc1C=O)c2c[nH]c3c2cc(cn3)c4cc(cnc4)C(=O)N(C)C)OC)(O)O
Ligand InChI: InChI=1S/C23H21BN4O5/c1-28(2)23(30)15-4-13(8-25-9-15)14-5-18-19(11-27-22(18)26-10-14)17-6-16(12-29)20(24(31)32)7-21(17)33-3/h4-12,31-32H,1-3H3,(H,26,27)
Release date: 2021-06-09
PanDDA analysis group deposition -- Crystal Structure of DCP2 (NUDT20) in complex with NUOOA000023a (PDB entry 5QOP)
Macromolecule: DCP2 (NUDT20)
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.1.62
Sequence length: 167 residues
Sequence: SMGVPTYGAIILDETLENVLLVQGYLAKSGWGFPKGKVNKEEAPHDCAAREVFEETGFDIKDYICKDDYIELRINDQLARLYIIPGIPKDTKFNPKTRREIRNIEWFSIEKLPCHRNDMTPKSKLGLAPNKFFMAIPFIRPLRDWLSRRFGDSSDSDNGFSSTGSTP
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.86
R work: 0.1987
R free: 0.2473
Average B factor: 33.769
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 4.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.1 M acetate, pH 4.5, 5-25% PEG3350
Matthews coefficient: 2.6
Solvent content (%): 52.61
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: 2019-05-08
PI3Kg IN COMPLEX WITH 5d (PDB entry 5T23)
Macromolecule: Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.1.153
Sequence length: 966 residues
Sequence: MSEESQAFQRQLTALIGYDVTDVSNVHDDELEFTRRGLVTPRMAEVASRDPKLYAMHPWVTSKPLPEYLWKKIANNCIFIVIHRSTTSQTIKVSPDDTPGAILQSFFTKMAKKKSLMDIPESQSEQDFVLRVCGRDEYLVGETPIKNFQWVRHCLKNGEEIHVVLDTPPDPALDEVRKEEWPLVDDCTGVTGYHEQLTIHGKDHESVFTVSLWDCDRKFRVKIRGIDIPVLPRNTDLTVFVEANIQHGQQVLCQRRTSPKPFTEEVLWNVWLEFSIKIKDLPKGALLNLQIYCGKAPALSSKASAESPSSESKGKVQLLYYVNLLLIDHRFLLRRGEYVLHMWQISGKGEDQGSFNADKLTSATNPDKENSMSISILLDNYCHPIALPKHQPTPDPEGDRVRAEMPNQLRKQLEAIIATDPLNPLTAEDKELLWHFRYESLKHPKAYPKLFSSVKWGQQEIVAKTYQLLARREVWDQSALDVGLTMQLLDCNFSDENVRAIAVQKLESLEDDDVLHYLLQLVQAVKFEPYHDSALARFLLKRGLRNKRIGHFLFWFLRSEIAQSRHYQQRFAVILEAYLRGCGTAMLHDFTQQVQVIEMLQKVTLDIKSLSAEKYDVSSQVISQLKQKLENLQNSQLPESFRVPYDPGLKAGALAIEKCKVMASKKKPLWLEFKCADPTALSNETIGIIFKHGDDLRQDMLILQILRIMESIWETESLDLCLLPYGCISTGDKIGMIEIVKDATTIAKIQQSTVGNTGAFKDEVLNHWLKEKSPTEEKFQAAVERFVYSCAGYCVATFVLGIGDRHNDNIMITETGNLFHIDFGHILGNYKSFLGINKERVPFVLTPDFLFVMGTSGKKTSPHFQKFQDICVKAYLALRHHTNLLIILFSMMLMTGMPQLTSKEDIEYIRDALTVGKNEEDAKKYFLDQIEVCRDKGWTVQFNWFLHLVLGIKQGEKHSAHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.78
R work: 0.25469
R free: 0.33923
Average B factor: 86.127
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 100mM Hepes pH 7.7-8.2, 18-19% PEG3350, 175mM (NH4)2SO4, 10mM DTT
Matthews coefficient: 2.81
Solvent content (%): 56.29
Ligand: 3-(benzotriazol-1-yl)-5-[1-methyl-5-[(1~{S})-1-morpholin-4-ylethyl]-1,2,4-triazol-3-yl]pyrazin-2-amine (74F)
Ligand formula: C19 H22 N10 O
Ligand molecular weight: 406.444
Ligand SMILES: CC(c1nc(nn1C)c2cnc(c(n2)n3c4ccccc4nn3)N)N5CCOCC5
Ligand InChI: InChI=1S/C19H22N10O/c1-12(28-7-9-30-10-8-28)18-23-17(25-27(18)2)14-11-21-16(20)19(22-14)29-15-6-4-3-5-13(15)24-26-29/h3-6,11-12H,7-10H2,1-2H3,(H2,20,21)/t12-/m0/s1
Release date: 2017-04-19
Crystal structure of human valosin-containing protein methyltransferase (PDB entry 8HL6)
Macromolecule: Protein N-lysine methyltransferase METTL21D
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1
Sequence length: 235 residues
Sequence: MADTLESSLEDPLRSFVRVLEKRDGTVLRLQQYSSGGVGCVVWDAAIVLSKYLETPEFSGDGAHALSRRSVLELGSGTGAVGLMAATLGADVVVTDLEELQDLLKMNINMNKHLVTGSVQAKVLKWGEEIEGFPSPPDFILMADCIYYEESLEPLLKTLKDISGFETCIICCYEQRTMGKNPEIEKKYFELLQLDFDFEKIPLEKHDEEYRSEDIHIIYIRKKKSKFPSHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.1918
R free: 0.2262
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 295
Crystal growth procedure: 20 % PEG 1000, 0.1 M Na/K phosphate (pH 6.2), and 0.2M sodium chloride
Matthews coefficient: 2.44
Solvent content (%): 49.67
Ligand: S-ADENOSYLMETHIONINE (SAM)
Ligand formula: C15 H22 N6 O5 S
Ligand molecular weight: 398.437
Ligand SMILES: C[S+](CCC(C(=O)[O-])N)CC1C(C(C(O1)n2cnc3c2ncnc3N)O)O
Ligand InChI: InChI=1S/C15H22N6O5S/c1-27(3-2-7(16)15(24)25)4-8-10(22)11(23)14(26-8)21-6-20-9-12(17)18-5-19-13(9)21/h5-8,10-11,14,22-23H,2-4,16H2,1H3,(H2-,17,18,19,24,25)/t7-,8+,10+,11+,14+,27-/m0/s1
Release date: 2023-07-12
Carbonic Anhydrase II Complexed with 3-((2-((Furan-2-ylmethyl)(4-sulfamoylphenethyl)amino)-2-oxoethyl)(phenethyl)amino)propanoic acid (PDB entry 6WQ8)
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): 1.405
R work: 0.1462
R free: 0.1715
Average B factor: 18.0568
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.8
Crystallization temperature (K): 298
Crystal growth procedure: 1.6M sodium citrate and 50mM tris
Matthews coefficient: 2.1
Solvent content (%): 41.33
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: 2020-06-24
Fragment-Based Drug Discovery Targeting Inhibitor of Apoptosis Proteins: Compound 17 (PDB entry 5C7D)
Macromolecule: E3 ubiquitin-protein ligase XIAP
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 6.3.2
Sequence length: 110 residues
Sequence: GSHMNFPNSTNLPRNPSMADYEARIFTFGTWIYSVNKEQLARAGFYALGEGDKVKCFHCGGGLTDWKPSEDPWEQHAKWYPGCKYLLEQKGQEYINNIHLTHSLEECLVR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.25
R work: 0.20053
R free: 0.25123
Average B factor: 39.778
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.1M Hepes-NaOH 7.5, 3.9M NaCl
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: 2015-08-12
Crystal structure of JAK3 kinase domain in complex with compound 25 (PDB entry 7UYV)
Macromolecule: Tyrosine-protein kinase JAK3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 291 residues
Sequence: ACQDPTIFEERHLKYISQLGKGNFGSVELCRYDPLGDNTGALVAVKQLQHSGPDQQRDFQREIQILKALHSDFIVKYRGVSYGPGRQSLRLVMEYLPSGCLRDFLQRHRARLDASRLLLYSSQICKGMEYLGSRRCVHRDLAARNILVESEAHVKIADFGLAKLLPLDKDYYVVREPGQSPIFWYAPESLSDNIFSRQSDVWSFGVVLYELFTYCDKSCSPSAEFLRMMGSERDVPALSRLLELLEEGQRLPAPPACPAEVHELMKLCWAPSPQDRPSFSALGPQLDMLWS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.15
R work: 0.2206
R free: 0.2629
Average B factor: 39.447
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 298
Crystal growth procedure: Crystals of human JAK3 in complex with the ligand were prepared according to established protocols
Matthews coefficient: 2.7
Solvent content (%): 53.3
Ligand: 6-{[(2M)-2-(2-chloro-6-fluorophenyl)-5-oxo-5H-pyrrolo[3,4-b]pyridin-4-yl]amino}-N-ethylpyridine-3-carboxamide (OV5)
Ligand formula: C21 H15 Cl F N5 O2
Ligand molecular weight: 423.828
Ligand SMILES: CCNC(=O)c1ccc(nc1)Nc2cc(nc3c2C(=O)N=C3)c4c(cccc4Cl)F
Ligand InChI: InChI=1S/C21H15ClFN5O2/c1-2-24-20(29)11-6-7-17(25-9-11)28-15-8-14(18-12(22)4-3-5-13(18)23)27-16-10-26-21(30)19(15)16/h3-10H,2H2,1H3,(H,24,29)(H,25,27,28)
Release date: 2022-08-24
Human GAR transformylase in complex with GAR and N-{4-[4-(2-Amino-4-oxo-3,4-dihydrothieno[2,3-d]pyrimidin-6-yl)-butyl]benzoyl}-L-glutamic acid (AGF50) (PDB entry 4ZYU)
Macromolecule: Trifunctional purine biosynthetic protein adenosine-3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.2.2
Sequence length: 210 residues
Sequence: MARVAVLISGTGSNLQALIDSTREPNSSAQIDIVISNKAAVAGLDKAERAGIPTRVINHKLYKNRVEFDSAIDLVLEEFSIDIVCLAGFMRILSGPFVQKWNGKMLNIHPSLLPSFKGSNAHEQALETGVTVTGCTVHFVAEDVDAGQIILQEAVPVKRGDTVATLSERVKLAEHKIFPAALQLVASGTVQLGENGKICWVKEEHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.95
R work: 0.1789
R free: 0.2071
Average B factor: 33.3889
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 18 % PEG4000, 2 % PEG400, 0.33 M NaCl
Matthews coefficient: 3.88
Solvent content (%): 68.32
Ligand: GLYCINAMIDE RIBONUCLEOTIDE (GAR)
Ligand formula: C7 H13 N2 O8 P
Ligand molecular weight: 284.16
Ligand SMILES: C(C1C(C(C(O1)NC(=O)CN)O)O)OP(=O)([O-])[O-]
Ligand InChI: InChI=1S/C7H15N2O8P/c8-1-4(10)9-7-6(12)5(11)3(17-7)2-16-18(13,14)15/h3,5-7,11-12H,1-2,8H2,(H,9,10)(H2,13,14,15)/p-2/t3-,5-,6-,7-/m1/s1
Release date: 2016-04-20
Crystal structure of caspase-1 in complex with VX-765 (PDB entry 6PZP)
Macromolecule: Caspase-1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.22.36
Sequence length: 178 residues
Sequence: NPAMPTSSGSEGNVKLCSLEEAQRIWKQKSAEIYPIMDKSSRTRLALIICNEEFDSIPRRTGAEVDITGMTMLLQNLGYSVDVKKNLTASDMTTELEAFAHRPEHKTSDSTFLVFMSHGIREGICGKKHSEQVPDILQLNAIFNMLNTKNCPSLKDKPKVIIIQACRGDSPGVVWFKD
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.94
R work: 0.1671
R free: 0.2079
Average B factor: 47.2287
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 0.2 M sodium formate, 20% w/v PEG3350
Matthews coefficient: 2.76
Solvent content (%): 55.42
Ligand: N-(4-amino-3-chlorobenzene-1-carbonyl)-3-methyl-L-valyl-N-[(2S)-1-carboxy-3-oxopropan-2-yl]-L-prolinamide (P7S)
Ligand formula: C22 H29 Cl N4 O6
Ligand molecular weight: 480.942
Ligand SMILES: CC(C)(C)C(C(=O)N1CCCC1C(=O)NC(CC(=O)O)C=O)NC(=O)c2ccc(c(c2)Cl)N
Ligand InChI: InChI=1S/C22H29ClN4O6/c1-22(2,3)18(26-19(31)12-6-7-15(24)14(23)9-12)21(33)27-8-4-5-16(27)20(32)25-13(11-28)10-17(29)30/h6-7,9,11,13,16,18H,4-5,8,10,24H2,1-3H3,(H,25,32)(H,26,31)(H,29,30)/t13-,16-,18+/m0/s1
Release date: 2020-08-05
Crystal Structure of human phosphodiesterase 10 in complex with 2,3,5-trimethyl-6-[2-(1-methyl-4-phenylimidazol-2-yl)ethyl]imidazo[1,2-a]pyridine (PDB entry 5SHI)
Macromolecule: cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.4.17
Sequence length: 343 residues
Sequence: GSSICTSEEWQGLMQFTLPVRLCKEIELFHFDIGPFENMWPGIFVYMVHRSCGTSCFELEKLCRFIMSVKKNYRRVPYHNWKHAVTVAHCMYAILQNNHTLFTDLERKGLLIACLCHDLDHRGFSNSYLQKFDHPLAALYSTSTMEQHHFSQTVSILQLEGHNIFSTLSSSEYEQVLEIIRKAIIATDLALYFGNRKQLEEMYQTGSLNLNNQSHRDRVIGLMMTACDLCSVTKLWPVTKLTANDIYAEFWAEGDEMKKLGIQPIPMMDRDKKDEVPQGQLGFYNAVAIPCYTTLTQILPPTEPLLKACRDNLSQWEKVIRGEETATWISSPSVAQKAAASED
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.1
R work: 0.1736
R free: 0.2233
Average B factor: 45.929
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 295
Crystal growth procedure: 5-20 mg/mL protein in 25mM HEPES/NaOH pH7.5, 150mM NaCl, 50mM BME mixed 1:1 with reservoir 0.1M HEPES/NaOH pH7.5, 30% PEG550MME, 50mM MgCl2
Matthews coefficient: 2.65
Solvent content (%): 53.58
Ligand: (4R)-2,3,5-trimethyl-6-[2-(1-methyl-4-phenyl-1H-imidazol-2-yl)ethyl]imidazo[1,2-a]pyridine (JG9)
Ligand formula: C22 H24 N4
Ligand molecular weight: 344.453
Ligand SMILES: Cc1c(n2c(c(ccc2n1)CCc3nc(cn3C)c4ccccc4)C)C
Ligand InChI: InChI=1S/C22H24N4/c1-15-16(2)26-17(3)18(11-13-22(26)23-15)10-12-21-24-20(14-25(21)4)19-8-6-5-7-9-19/h5-9,11,13-14H,10,12H2,1-4H3
Release date: 2022-10-12
Oxidation-Mediated Inhibition of the Peptidyl-Prolyl Isomerase Pin1 (PDB entry 4QIB)
Macromolecule: Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 5.2.1.8
Sequence length: 159 residues
Sequence: GALPPGWEKAMSRSSGRVYYFNHITNASQWERPSGNSSSGGKNGQGEPARVRCSHLLVKHSQSRRPSSWRQEKITRTKEEALELINGYIQKIKSGEEDFESLASQFSDCSSAKARGDLGAFSRGQMQKPFEDASFALRTGEMSGPVFTDSGIHIILRTE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.865
R work: 0.1528
R free: 0.1851
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.4
Crystallization temperature (K): 277
Crystal growth procedure: 20 mg/mL protein, 2.0 to 2.4 M ammonium sulfate, 1% poly(ethylene glycol) 400, 100 mM Hepes, 10 mM H2O2, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Matthews coefficient: 2.95
Solvent content (%): 58.3
Ligand: 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL (PE4)
Ligand formula: C16 H34 O8
Ligand molecular weight: 354.436
Ligand SMILES: CCOCCOCCOCCOCCOCCOCCOCCO
Ligand InChI: InChI=1S/C16H34O8/c1-2-18-5-6-20-9-10-22-13-14-24-16-15-23-12-11-21-8-7-19-4-3-17/h17H,2-16H2,1H3
Release date: 2015-02-04
Crystal Structure of WHSC1L1 in Complex with Inhibitor PEP21 (PDB entry 6CEN)
Macromolecule: Histone-lysine N-methyltransferase NSD3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1.43
Sequence length: 228 residues
Sequence: KEALEIEKNSRKPPPYKHIKANKVIGKVQIQVADLSEIPRCNCKPADENPCGLESECLNRMLQYECHPQVCPAGDRCQNQCFTKRLYPDAEIIKTERRGWGLRTKRSIKKGEFVNEYVGELIDEEECRLRIKRAHENSVTNFYMLTVTKDRIIDAGPKGNYSRFMNHSCNPNCETQKWTVNGDVRVGLFALCDIPAGMELTFNYNLDCLGNGRTECHCGADNCSGFLG
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.61
R work: 0.1789
R free: 0.2151
Average B factor: 25.933
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 291
Crystal growth procedure: 0.1 M Bis-Tris pH 6.5, 20% w/v PEG5000MME
Matthews coefficient: 2.34
Solvent content (%): 47.48
Ligand: S-ADENOSYLMETHIONINE (SAM)
Ligand formula: C15 H22 N6 O5 S
Ligand molecular weight: 398.437
Ligand SMILES: C[S+](CCC(C(=O)[O-])N)CC1C(C(C(O1)n2cnc3c2ncnc3N)O)O
Ligand InChI: InChI=1S/C15H22N6O5S/c1-27(3-2-7(16)15(24)25)4-8-10(22)11(23)14(26-8)21-6-20-9-12(17)18-5-19-13(9)21/h5-8,10-11,14,22-23H,2-4,16H2,1H3,(H2-,17,18,19,24,25)/t7-,8+,10+,11+,14+,27-/m0/s1
Release date: 2018-05-09