satarupa22/MacromolecularLigandDB huggingface dataset:
Crystal structure of Tdp1 catalytic domain in complex with compound XZ577 (PDB entry 6N17)
Macromolecule: Tyrosyl-DNA phosphodiesterase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.4
Sequence length: 461 residues
Sequence: SGEGQDIWDMLDKGNPFQFYLTRVSGVKPKYNSGALHIKDILSPLFGTLVSSAQFNYCFDVDWLVKQYPPEFRKKPILLVHGDKREAKAHLHAQAKPYENISLCQAKLDIAFGTHHTKMMLLLYEEGLRVVIHTSNLIHADWHQKTQGIWLSPLYPRIADGTHKSGESPTHFKADLISYLMAYNAPSLKEWIDVIHKHDLSETNVYLIGSTPGRFQGSQKDNWGHFRLKKLLKDHASSMPNAESWPVVGQFSSVGSLGADESKWLCSEFKESMLTLGKESKTPGKSSVPLYLIYPSVENVRTSLEGYPAGGSLPYSIQTAEKQNWLHSYFHKWSAETSGRSNAMPHIKTYMRPSPDFSKIAWFLVTSANLSKAAWGALEKNGTQLMIRSYELGVLFLPSAFGLDSFKVKQKFFAGSQEPMATFPVPYDLPPELYGSKDRPWIWNIPYVKAPDTHGNMWVPS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.639
R work: 0.1838
R free: 0.2112
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 291
Crystal growth procedure: 0.1M MOPS/HEPES-Na pH 7.5, 10% (w/v) PEG 8000, 20% (v/v) ethylene glycol, 0.03 M sodium fluoride, 0.03 M sodium bromide, 0.03 M sodium iodide
Matthews coefficient: 2.46
Solvent content (%): 49.91
Ligand: 4-[(3-carboxypropanoyl)amino]benzene-1,2-dicarboxylic acid (K8Y)
Ligand formula: C12 H11 N O7
Ligand molecular weight: 281.218
Ligand SMILES: c1cc(c(cc1NC(=O)CCC(=O)O)C(=O)O)C(=O)O
Ligand InChI: InChI=1S/C12H11NO7/c14-9(3-4-10(15)16)13-6-1-2-7(11(17)18)8(5-6)12(19)20/h1-2,5H,3-4H2,(H,13,14)(H,15,16)(H,17,18)(H,19,20)
Release date: 2019-07-03
Crystal structure of human carbonic anhydrase isozyme XIII with 2-chloro-4-{[(4-methyl-6-oxo-1,6-dihydropyrimidin-2-yl)thio]acetyl}benzenesulfonamide (PDB entry 4QSJ)
Macromolecule: Carbonic anhydrase 13
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 263 residues
Sequence: MMSRLSWGYREHNGPIHWKEFFPIADGDQQSPIEIKTKEVKYDSSLRPLSIKYDPSSAKIISNSGHSFNVDFDDTENKSVLRGGPLTGSYRLRQVHLHWGSADDHGSEHIVDGVSYAAELHVVHWNSDKYPSFVEAAHEPDGLAVLGVFLQIGEPNSQLQKITDTLDSIKEKGKQTRFTNFDLLSLLPPSWDYWTYPGSLTVPPLLESVTWIVLKQPINISSQQLAKFRSLLCTAEGEAAAFLVSNHRPPQPLKGRKVRASFH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.7
R work: 0.1637
R free: 0.20422
Average B factor: 17.402
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5
Crystallization temperature (K): 291
Crystal growth procedure: 0.1M sodium citrate (pH 5.5), 0.2M sodium acetate (pH 4.5), 28% PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Matthews coefficient: 2.21
Solvent content (%): 44.4
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: 2015-01-21
Identification of a New Zinc Binding Chemotype by Fragment Screening (PDB entry 5U0D)
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): 1.59
R work: 0.11848
R free: 0.15449
Average B factor: 15.669
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 281
Crystal growth procedure: the reservoir condition consisted of 2.9 M ammonium sulfate with 0.1 M Tris buffer at pH 8.3; concentrated CA II at ~10 mg mL-1 was set up with seeding; dry compound was added to crystals several days before harvesting and data collection
Matthews coefficient: 2.1
Solvent content (%): 41.35
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: 2017-08-30
KDM4C bound to pyrazolo-pyrimidine scaffold (PDB entry 5KR7)
Macromolecule: Lysine-specific demethylase 4C
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11
Sequence length: 367 residues
Sequence: GSHMASMTGGQQMGRGSMEVAEVESPLNPSCKIMTFRPSMEEFREFNKYLAYMESKGAHRAGLAKVIPPKEWKPRQCYDDIDNLLIPAPIQQMVTGQSGLFTQYNIQKKAMTVKEFRQLANSGKYCTPRYLDYEDLERKYWKNLTFVAPIYGADINGSIYDEGVDEWNIARLNTVLDVVEEECGISIEGVNTPYLYFGMWKTTFAWHTEDMDLYSINYLHFGEPKSWYAIPPEHGKRLERLAQGFFPSSSQGCDAFLRHKMTLISPSVLKKYGIPFDKITQEAGEFMITFPYGYHAGFNHGFNCAESTNFATVRWIDYGKVAKLCTCRKDMVKISMDIFVRKFQPDRYQLWKQGKDIYTIDHTKPTP
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.9
R work: 0.1924
R free: 0.2339
Average B factor: 26.056
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 10-15% PEG 3350
0.2 magnesium chloride
0.1 HEPES pH 7.5
Matthews coefficient: 2.55
Solvent content (%): 51.73
Ligand: FE (II) ION (FE2)
Ligand formula: Fe
Ligand molecular weight: 55.845
Ligand SMILES: [Fe+2]
Ligand InChI: InChI=1S/Fe/q+2
Release date: 2016-08-17
Structure of human SHP2 without N-SH2 domain (PDB entry 6CMQ)
Macromolecule: Tyrosine-protein phosphatase non-receptor type 11
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 427 residues
Sequence: GSGDPTSERWFHGHLSGKEAEKLLTEKGKHGSFLVRESQSHPGDFVLSVRTGDDKGESNDGKSKVTHVMIRCQELKYDVGGGERFDSLTDLVEHYKKNPMVETLGTVLQLKQPLNTTRINAAEIESRVRELSKLAETTDKVKQGFWEEFETLQQQECKLLYSRKEGQRQENKNKNRYKNILPFDHTRVVLHDGDPNEPVSDYINANIIMPEFETKCNNSKPKKSYIATQGCLQNTVNDFWRMVFQENSRVIVMTTKEVERGKSKCVKYWPDEYALKEYGVMRVRNVKESAAHDYTLRELKLSKVGQGNTERTVWQYHFRTWPDHGVPSDPGGVLDFLEEVHHKQESIMDAGPVVVHCSAGIGRTGTFIVIDILIDIIREKGVDCDIDVPKTIQMVRSQRSGMVQTEAQYRFIYMAVQHYIETLQRRI
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.9
R work: 0.2491
R free: 0.2764
Average B factor: 48.8
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 100 mM ammonium formate, 22% PEG 3,350 and 1.5% xylitol
Matthews coefficient: 2.64
Solvent content (%): 53.48
Release date: 2018-11-14
Protein Kinase A in complex with an Inhibitor (PDB entry 4UJ9)
Macromolecule: cAMP-dependent protein kinase catalytic subunit alpha
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.11
Sequence length: 351 residues
Sequence: MGNAAAAKKGSEQESVKEFLAKAKEDFLKKWESPAQNTAHLDQFERIKTLGTGSFGRVMLVKHKETGNHYAMKILDKQKVVKLKQIEHTLNEKRILQAVNFPFLVKLEFSFKDNSNLYMVMEYVPGGEMFSHLRRIGRFSEPHARFYAAQIVLTFEYLHSLDLIYRDLKPENLLIDQQGYIQVTDFGFAKRVKGRTWTLCGTPEYLAPEIILSKGYNKAVDWWALGVLIYEMAAGYPPFFADQPIQIYEKIVSGKVRFPSHFSSDLKDLLRNLLQVDLTKRFGNLKNGVNDIKNHKWFATTDWIAIYQRKVEAPFIPKFKGPGDTSNFDDYEEEEIRVSINEKCGKEFSEF
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.87
R work: 0.1647
R free: 0.2065
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 10MG/ML PROTEIN, 25MM BISTRIS/MES PH6.9, 50MM KCL, 1.5MM OCTANOYL-N-METHYLGLUCAMIDE, 1MM PROTEIN KINASE INHIBITOR PEPTIDE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K
Matthews coefficient: 2.55
Solvent content (%): 51.79
Ligand: 7-[(3S,4R)-4-[4-(trifluoromethyl)phenyl]carbonylpyrrolidin-3-yl]-3H-quinazolin-4-one (S3N)
Ligand formula: C20 H16 F3 N3 O2
Ligand molecular weight: 387.355
Ligand SMILES: c1cc(ccc1C(=O)C2CNCC2c3ccc4c(c3)N=CNC4=O)C(F)(F)F
Ligand InChI: InChI=1S/C20H16F3N3O2/c21-20(22,23)13-4-1-11(2-5-13)18(27)16-9-24-8-15(16)12-3-6-14-17(7-12)25-10-26-19(14)28/h1-7,10,15-16,24H,8-9H2,(H,25,26,28)/t15-,16+/m1/s1
Release date: 2016-04-13
Crystal Structure of Lysophospholipase A2 Conjugated with Phenylmethylsulfonyl Fluoride (PDB entry 6BJE)
Macromolecule: Acyl-protein thioesterase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.2
Sequence length: 222 residues
Sequence: LLTDAATVSGAERETAAVIFLHGLGDTGHSWADALSTIRLPHVKYICPHAPRIPVTLNMKMVMPSWFDLMGLSPDAPEDEAGIKKAAENIKALIEHEMKNGIPANRIVLGGFSQGGALSLYTALTCPHPLAGIVALSCWLPLHRAFPQAANGSAKDLAILQCHGELDPMVPVRFGALTAEKLRSVVTPARVQFKTYPGVMHSSCPQEMAAVKEFLEKLLPPV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.7
R work: 0.2213
R free: 0.2641
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M NaCitric pH 5.6, 15% PEG-3350
Matthews coefficient: 2.2
Solvent content (%): 44.05
Ligand: phenylmethanesulfonic acid (PMS)
Ligand formula: C7 H8 O3 S
Ligand molecular weight: 172.202
Ligand SMILES: c1ccc(cc1)CS(=O)(=O)O
Ligand InChI: InChI=1S/C7H8O3S/c8-11(9,10)6-7-4-2-1-3-5-7/h1-5H,6H2,(H,8,9,10)
Release date: 2018-11-14
Crystal structure of human MDM2-G443T RING domain homodimer bound to UbcH5B-Ub (Crystal form 1) (PDB entry 7AI0)
Macromolecule: E3 ubiquitin-protein ligase Mdm2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2.27
Sequence length: 75 residues
Sequence: GSTQDKEESVESSLPLNAIEPCVICQTRPKNGCIVHGKTGHLMACFTCAKKLKKRNKPCPVCRQPIQMIVLTYFP
Oligomeric state: Homo 2-mer
Stoichiometry: A2
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.559
R work: 0.1335
R free: 0.1848
Average B factor: 20.479
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8
Crystallization temperature (K): 292
Crystal growth procedure: 0.1 M Tris, 0.075 M NaOAc, 0.1 M NaCl, 15 % w/v PEG Smear Medium
Matthews coefficient: 2.65
Solvent content (%): 53.56
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: 2021-01-20
Structure of Calcineurin mutant in complex with NHE1 peptide (PDB entry 6NUU)
Macromolecule: Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.16
Sequence length: 372 residues
Sequence: GHMSEPKAIDPKLSTTDRVVKAVPFPPSHRLTAKEVFDNDGKPRVDILKAHLMKEGRLEESVALRIITEGASILRQEKNLLDIDAPVTVCGDIHGQFFDLMKLFEVGGSPANTRYLFLGDYVDRGYFSIECVLYLWALKILYPKTLFLLRGNHECRALTEAFTFKQECKIKYSERVYDACMDAFDCLPLAALMNQQFLCVHGGLSPEINTLDDIRKLDRFKEPPAYGPMCDILWSDPLEDFGNEKTQEHFTHNTVRGCSYFYSYPAVCEFLQHNNLLSILRAHEAQDAGYRMYRKSQTTGFPSLITIFSAPNYLDVYNNKAAVLKYENNVMNIRQFNCSPHPYWLPNFMDVFTWSLPFVGEKVTEMLVNVLN
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.3
R work: 0.195
R free: 0.243
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 9.5
Crystallization temperature (K): 298
Crystal growth procedure: 40% (v/v) PEG 600, 100 mM CHES/ Sodium hydroxide pH 9.5, 0.2 M MgCl2
Matthews coefficient: 2.49
Solvent content (%): 50.6
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: 2019-07-03
Crystal Structure of Human BACE-1 in Complex with CNP520 (PDB entry 6EQM)
Macromolecule: Beta-secretase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.23.46
Sequence length: 402 residues
Sequence: GPDEEPEEPGRRGSFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHPFLHRYYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTVRANIAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTHVPNLFSLQLCGAGFPLNQSEVLASVGGSMIIGGIDHSLYTGSLWYTPIRREWYYEVIIVRVEINGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVKSIKAASSTEKFPDGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRITILPQQYLRPVEDVATSQDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSACHVHDEFRTAAVEGPFVTLDMEDCGYNI
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.35
R work: 0.1836
R free: 0.2001
Average B factor: 24.78
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 292
Crystal growth procedure: 15% PEG 1,500 in water
Matthews coefficient: 2.13
Solvent content (%): 42.31
Ligand: ~{N}-[6-[(3~{R},6~{R})-5-azanyl-3,6-dimethyl-6-(trifluoromethyl)-2~{H}-1,4-oxazin-3-yl]-5-fluoranyl-pyridin-2-yl]-3-chloranyl-5-(trifluoromethyl)pyridine-2-carboxamide (BUH)
Ligand formula: C19 H15 Cl F7 N5 O2
Ligand molecular weight: 513.797
Ligand SMILES: CC1(COC(C(=N1)N)(C)C(F)(F)F)c2c(ccc(n2)NC(=O)c3c(cc(cn3)C(F)(F)F)Cl)F
Ligand InChI: InChI=1S/C19H15ClF7N5O2/c1-16(7-34-17(2,15(28)32-16)19(25,26)27)13-10(21)3-4-11(30-13)31-14(33)12-9(20)5-8(6-29-12)18(22,23)24/h3-6H,7H2,1-2H3,(H2,28,32)(H,30,31,33)/t16-,17+/m0/s1
Release date: 2018-09-19
Structure of human Uracil DNA Glycosylase (UDG) bound to Aurintricarboxylic acid (ATA) (PDB entry 6VBA)
Macromolecule: Uracil-DNA glycosylase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.2.2.27
Sequence length: 223 residues
Sequence: MEFFGESWKKHLSGEFGKPYFIKLMGFVAEERKHYTVYPPPHQVFTWTQMCDIKDVKVVILGQDPYHGPNQAHGLCFSVQRPVPPPPSLENIYKELSTDIEDFVHPGHGDLSGWAKQGVLLLNAVLTVRAHQANSHKERGWEQFTDAVVSWLNQNSNGLVFLLWGSYAQKKGSAIDRKRHHVLQTAHPSPLSVYRGFFGCRHFSKTNELLQKSGKKPIDWKEL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.1792
R free: 0.2336
Average B factor: 26.05
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 291
Crystal growth procedure: 2mM TRIS pH 8.5, 20 mM Mgcl2, 21% PEG8000, ATA inhibitor was co-crystallized with the UDG protein with a concentration of circa 4mM in solution
Matthews coefficient: 2.37
Solvent content (%): 48.07
Ligand: 3,3'-[(3-carboxy-4-oxocyclohexa-2,5-dien-1-ylidene)methylene]bis(6-hydroxybenzoic acid) (QU4)
Ligand formula: C22 H14 O9
Ligand molecular weight: 422.341
Ligand SMILES: c1cc(c(cc1C(=C2C=CC(=O)C(=C2)C(=O)O)c3ccc(c(c3)C(=O)O)O)C(=O)O)O
Ligand InChI: InChI=1S/C22H14O9/c23-16-4-1-10(7-13(16)20(26)27)19(11-2-5-17(24)14(8-11)21(28)29)12-3-6-18(25)15(9-12)22(30)31/h1-9,23-24H,(H,26,27)(H,28,29)(H,30,31)
Release date: 2021-03-03
Human cyclophilin A at 100K, Data set 6 (PDB entry 5KUS)
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: 0.1721
R free: 0.213
Average B factor: 21.2644
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: 2.77
Solvent content (%): 55.67
Release date: 2016-08-10
MELK in complex with NVS-MELK1 (PDB entry 5IH8)
Macromolecule: Maternal embryonic leucine zipper kinase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 335 residues
Sequence: MDYDELLKYYELHETIGTGGFAKVKLACHILTGEMVAIKIMDKNTLGSDLPRIKTEIEALKNLRHQHICQLYHVLETANKIFMVLEYCPGGELFDYIISQDRLSEEETRVVFRQIVSAVAYVHSQGYAHRDLKPENLLFDEYHKLKLIDFGLCAKPKGNKDYHLQTCCGSLAYAAPELIQGKSYLGSEADVWSMGILLYVLMCGFLPFDDDNVMALYKKIMRGKYDVPKWLSPSSILLLQQMLQVDPKKRISMKNLLNHPWIMQDYNYPVEWQSKNPFIHLDDDCVTELSVHHRNNRQTMEDLISLWQYDHLTATYLLLLAKKARGKPVHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.85
R work: 0.1766
R free: 0.1995
Average B factor: 37.11
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 100mM Hepes pH 7.5, 0.2M sodium chloride, 25% PEG 3350
Matthews coefficient: 2.53
Solvent content (%): 51.37
Ligand: N-[(pyridin-2-yl)methyl]-4-[4-(pyridin-4-yl)-1H-pyrazol-1-yl]benzamide (6BJ)
Ligand formula: C21 H17 N5 O
Ligand molecular weight: 355.393
Ligand SMILES: c1ccnc(c1)CNC(=O)c2ccc(cc2)n3cc(cn3)c4ccncc4
Ligand InChI: InChI=1S/C21H17N5O/c27-21(24-14-19-3-1-2-10-23-19)17-4-6-20(7-5-17)26-15-18(13-25-26)16-8-11-22-12-9-16/h1-13,15H,14H2,(H,24,27)
Release date: 2016-06-01
Structure of human Cathepsin K with an ectosteric inhibitor at 1.85 Angstrom resolution (PDB entry 6PXF)
Macromolecule: Cathepsin K
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.22.38
Sequence length: 215 residues
Sequence: APDSVDYRKKGYVTPVKNQGQCGSCWAFSSVGALEGQLKKKTGKLLNLAPQNLVDCVSENDGCGGGYMTNAFQYVQKNRGIDSEDAYPYVGQEESCMYNPTGKAAKCRGYREIPEGNEKALKRAVARVGPVSVAIDASLTSFQFYSKGVYYDESCNSDNLNHAVLAVGYGIQKGNKHWIIKNSWGENWGNKGYILMARNKNNACGIANLASFPKM
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.85
R work: 0.1697
R free: 0.188
Average B factor: 23.96
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 295
Crystal growth procedure: 0.04 M Potassium phosphate monobasic, 16% w/v PEG8000, 20% v/v glycerol
Matthews coefficient: 2.1
Solvent content (%): 41.51
Ligand: 1,6,6-trimethyl-10,11-dioxo-6,7,8,9,10,11-hexahydrophenanthro[1,2-b]furan-2-sulfonic acid (J0V)
Ligand formula: C19 H18 O6 S
Ligand molecular weight: 374.408
Ligand SMILES: Cc1c2c(oc1S(=O)(=O)O)-c3ccc4c(c3C(=O)C2=O)CCCC4(C)C
Ligand InChI: InChI=1S/C19H18O6S/c1-9-13-15(20)16(21)14-10-5-4-8-19(2,3)12(10)7-6-11(14)17(13)25-18(9)26(22,23)24/h6-7H,4-5,8H2,1-3H3,(H,22,23,24)
Release date: 2020-07-29
Crystal structure of the human soluble adenylyl cyclase in complex with the allosteric inhibitor LRE1 (PDB entry 5IV4)
Macromolecule: Adenylate cyclase type 10
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.6.1.1
Sequence length: 475 residues
Sequence: MNTPKEEFQDWPIVRIAAHLPDLIVYGHFSPERPFMDYFDGVLMFVDISGFTAMTEKFSSAMYMDRGAEQLVEILNYHISAIVEKVLIFGGDILKFAGDALLALWRVERKQLKNIITVVIKCSLEIHGLFETQEWEEGLDIRVKIGLAAGHISMLVFGDETHSHFLVIGQAVDDVRLAQNMAQMNDVILSPNCWQLCDRSMIEIESVPDQRAVKVNFLKPPPNFNFDEFFTKCTTFMHYYPSGEHKNLLRLACTLKPDPELEMSLQKYVMESILKQIDNKQLQGYLSELRPVTIVFVNLMFEDQDKAEEIGPAIQDAYMHITSVLKIFQGQINKVFMFDKGCSFLCVFGFPGEKVPDELTHALECAMDIFDFCSQVHKIQTVSIGVASGIVFCGIVGHTVRHEYTVIGQKVNLAARMMMYYPGIVTCDSVTYNGSNLPAYFFKELPKKVMKGVADSGPLYQYWGRTEKVHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.79
R work: 0.15972
R free: 0.20626
Average B factor: 30.704
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 277.15
Crystal growth procedure: 100 mM sodium acetate pH 4.8
200 mM tri-sodium-citrate
15% (w/v) PEG 4000
10% (v/v) glycerol
Matthews coefficient: 2.3
Solvent content (%): 47
Ligand: 6-chloro-N~4~-cyclopropyl-N~4~-[(thiophen-2-yl)methyl]pyrimidine-2,4-diamine (LRI)
Ligand formula: C12 H13 Cl N4 S
Ligand molecular weight: 280.776
Ligand SMILES: c1cc(sc1)CN(c2cc(nc(n2)N)Cl)C3CC3
Ligand InChI: InChI=1S/C12H13ClN4S/c13-10-6-11(16-12(14)15-10)17(8-3-4-8)7-9-2-1-5-18-9/h1-2,5-6,8H,3-4,7H2,(H2,14,15,16)
Release date: 2016-08-17
Crystal Structure of human phosphodiesterase 10 in complex with N-(12-methoxy-5-methyl-3-propyl-2,4,8,13-tetrazatricyclo[7.4.0.02,6]trideca-1(13),3,5,7,9,11-hexaen-7-yl)methanesulfonamide (PDB entry 5SI5)
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): 2.27
R work: 0.1796
R free: 0.2244
Average B factor: 45.186
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: 2.6
Solvent content (%): 52.76
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: 2022-10-12
Crystal structure of EGFR 696-1022 T790M in complex with Go6976 (PDB entry 5XGM)
Macromolecule: Epidermal growth factor receptor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 331 residues
Sequence: GAMGGEAPNQALLRILKETEFKKIKVLGSGAFGTVYKGLWIPEGEKVKIPVAIKELREATSPKANKEILDEAYVMASVDNPHVCRLLGICLTSTVQLIMQLMPFGCLLDYVREHKDNIGSQYLLNWCVQIAKGMNYLEDRRLVHRDLAARNVLVKTPQHVKITDFGLAKLLGAEEKEYHAEGGKVPIKWMALESILHRIYTHQSDVWSYGVTVWELMTFGSKPYDGIPASEISSILEKGERLPQPPICTIDVYMIMVKCWMIDADSRPKFRELIIEFSKMARDPQRYLVIQGDERMHLPSPTDSNFYRALMDEEDMDDVVDADEYLIPQQG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.952
R work: 0.2026
R free: 0.2318
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 9.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M NaCl,0.05M Glycine pH 9.5, 39% PEG 300
Matthews coefficient: 3.47
Solvent content (%): 64.51
Ligand: 12-(2-Cyanoethyl)-6,7,12,13-tetrahydro-13-methyl-5-oxo-5H-indolo[2,3-a]pyrrolo[3,4-c]carbazole (85X)
Ligand formula: C24 H18 N4 O
Ligand molecular weight: 378.426
Ligand SMILES: Cn1c2ccccc2c3c1c4c(c5ccccc5n4CCC#N)c6c3C(=O)NC6
Ligand InChI: InChI=1S/C24H18N4O/c1-27-17-9-4-2-7-14(17)20-21-16(13-26-24(21)29)19-15-8-3-5-10-18(15)28(12-6-11-25)23(19)22(20)27/h2-5,7-10H,6,12-13H2,1H3,(H,26,29)
Release date: 2017-10-11
PI3K-gamma K802T in complex with Cpd 8 10-((1-(tert-butyl)piperidin-4-yl)sulfinyl)-2-(1-isopropyl-1H-1,2,4-triazol-5-yl)-5,6-dihydrobenzo[f]imidazo[1,2-d][1,4]oxazepine (PDB entry 6AUD)
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: MSEESQAFQRQLTALIGYDVTDVSNVHDDELEFTRRGLVTPRMAEVASRDPKLYAMHPWVTSKPLPEYLWKKIANNCIFIVIHRSTTSQTIKVSPDDTPGAILQSFFTKMAKKKSLMDIPESQSEQDFVLRVCGRDEYLVGETPIKNFQWVRHCLKNGEEIHVVLDTPPDPALDEVRKEEWPLVDDCTGVTGYHEQLTIHGKDHESVFTVSLWDCDRKFRVKIRGIDIPVLPRNTDLTVFVEANIQHGQQVLCQRRTSPKPFTEEVLWNVWLEFSIKIKDLPKGALLNLQIYCGKAPALSSKASAESPSSESKGKVQLLYYVNLLLIDHRFLLRRGEYVLHMWQISGKGEDQGSFNADKLTSATNPDKENSMSISILLDNYCHPIALPKHQPTPDPEGDRVRAEMPNQLRKQLEAIIATDPLNPLTAEDKELLWHFRYESLKHPKAYPKLFSSVKWGQQEIVAKTYQLLARREVWDQSALDVGLTMQLLDCNFSDENVRAIAVQKLESLEDDDVLHYLLQLVQAVKFEPYHDSALARFLLKRGLRNKRIGHFLFWFLRSEIAQSRHYQQRFAVILEAYLRGCGTAMLHDFTQQVQVIEMLQKVTLDIKSLSAEKYDVSSQVISQLKQKLENLQNSQLPESFRVPYDPGLKAGALAIEKCTVMASKKKPLWLEFKCADPTALSNETIGIIFKHGDDLRQDMLILQILRIMESIWETESLDLCLLPYGCISTGDKIGMIEIVKDATTIAKIQQSTVGNTGAFKDEVLNHWLKEKSPTEEKFQAAVERFVYSCAGYCVATFVLGIGDRHNDNIMITETGNLFHIDFGHILGNYKSFLGINKERVPFVLTPDFLFVMGTSGKKTSPHFQKFQDICVKAYLALRHHTNLLIILFSMMLMTGMPQLTSKEDIEYIRDALTVGKNEEDAKKYFLDQIEVCRDKGWTVQFNWFLHLVLGIKQGEKHSAHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.015
R work: 0.2027
R free: 0.2331
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 8.5
Crystallization temperature (K): 289
Crystal growth procedure: PEG 3350, 0.2M NH4SO4, 0.1M Tris-HCl 8.5
Matthews coefficient: 2.41
Solvent content (%): 48.89
Ligand: 10-[(S)-(1-tert-butylpiperidin-4-yl)sulfinyl]-2-[1-(propan-2-yl)-1H-1,2,4-triazol-5-yl]-5,6-dihydroimidazo[1,2-d][1,4]benzoxazepine (BWY)
Ligand formula: C25 H34 N6 O2 S
Ligand molecular weight: 482.641
Ligand SMILES: CC(C)n1c(ncn1)c2cn3c(n2)-c4cc(ccc4OCC3)S(=O)C5CCN(CC5)C(C)(C)C
Ligand InChI: InChI=1S/C25H34N6O2S/c1-17(2)31-24(26-16-27-31)21-15-29-12-13-33-22-7-6-19(14-20(22)23(29)28-21)34(32)18-8-10-30(11-9-18)25(3,4)5/h6-7,14-18H,8-13H2,1-5H3/t34-/m0/s1
Release date: 2017-11-15