satarupa22/MacromolecularLigandDB huggingface dataset:
Structure of human DPP3 in complex with hemorphin like opioid peptide IVYPW (PDB entry 5E3C)
Macromolecule: Dipeptidyl peptidase 3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.14.4
Sequence length: 726 residues
Sequence: MADTQYILPNDIGVSSLDSREAFRLLSPTERLYAYHLSRAAWYGGLAVLLQTSPEAPYIYALLSRLFRAQDPDQLRQHALAEGLTEEEYQAFLVYAAGVYSNMGNYKSFGDTKFVPNLPKEKLERVILGSEAAQQHPEEVRGLWQTCGELMFSLEPRLRHLGLGKEGITTYFSGNCTMEDAKLAQDFLDSQNLSAYNTRLFKEVDGCGKPYYEVRLASVLGSEPSLDSEVTSKLKSYEFRGSPFQVTRGDYAPILQKVVEQLEKAKAYAANSHQGQMLAQYIESFTQGSIEAHKRGSRFWIQDKGPIVESYIGFIESYRDPFGSRGEFEGFVAVVNKAMSAKFERLVASAEQLLKELPWPPTFEKDKFLTPDFTSLDVLTFAGSGIPAGINIPNYDDLRQTEGFKNVSLGNVLAVAYATQREKLTFLEEDDKDLYILWKGPSFDVQVGLHALLGHGSGKLFVQDEKGAFNFDQETVINPETGEQIQSWYRCGETWDSKFSTIASSYEECRAESVGLYLSLHPQVLEIFGFEGADAEDVIYVNWLNMVRAGLLALEFYTPEAFNWRQAHMQARFVILRVLLEAGEGLVTITPTTGSDGRPDARVRLDRSKIRSVGKPALERFLRRLQVLKSTGDVAGGRALYEGYATVTDAPPESFLTLRDTVLLRKESRKLIVQPNTRLEGSDVQLLEYEASAAGLIRSFSERFPEDGPELEEILTQLATADARFW
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.765
R work: 0.204
R free: 0.2528
Average B factor: 56.3
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.2
Crystallization temperature (K): 293
Crystal growth procedure: 0.056 Sodium phosphate monobasic monohydrate, 1.344M Potassium phosphate dibasic
Matthews coefficient: 2.54
Solvent content (%): 51.65
Ligand: ZINC ION (ZN)
Ligand formula: Zn
Ligand molecular weight: 65.409
Ligand SMILES: [Zn+2]
Ligand InChI: InChI=1S/Zn/q+2
Release date: 2016-04-13
Specific covalent inhibitor(9) of ERK2 (PDB entry 8AO8)
Macromolecule: Mitogen-activated protein kinase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.24
Sequence length: 368 residues
Sequence: MAHHHHHHMAAAAAAGAGPEMVRGQVFDVGPRYTNLSYIGEGAYGMVCSAYDNVNKVRVAIKKISPFEHQTYCQRTLREIKILLRFRHENIIGINDIIRAPTIEQMKDVYIVQDLMETDLYKLLKTQHLSNDHICYFLYQILRGLKYIHSANVLHRDLKPSNLLLNTTCDLKICDFGLARVADPDHDHTGFLTEYVATRWYRAPEIMLNSKGYTKSIDIWSVGCILAEMLSNRPIFPGKHYLDQLNHILGILGSPSQEDLNCIINLKARNYLLSLPHKNKVPWNRLFPNADSKALDLLDKMLTFNPHKRIEVEQALAHPYLEQYYDPSDEPIAEAPFKFDMELDDLPKEKLKELIFEETARFQPGYRS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.697
R work: 0.1721
R free: 0.2114
Average B factor: 23.097
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.2
Crystallization temperature (K): 293
Crystal growth procedure: 0.25M (NH4)2SO4
33% MPEG 2000
0.02M Mercaptoethanol
0.1M pH=7.2 HEPES/NaOH
Matthews coefficient: 2.28
Solvent content (%): 46.17
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: 2022-09-28
FACTOR INHIBITING HIF-1 ALPHA IN COMPLEX WITH ZN(II) AND 3-methyl-2-oxoglutarate (PDB entry 7A1L)
Macromolecule: Hypoxia-inducible factor 1-alpha inhibitor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11.30
Sequence length: 349 residues
Sequence: MAATAAEAVASGSGEPREEAGALGPAWDESQLRSYSFPTRPIPRLSQSDPRAEELIENEEPVVLTDTNLVYPALKWDLEYLQENIGNGDFSVYSASTHKFLYYDEKKMANFQNFKPRSNREEMKFHEFVEKLQDIQQRGGEERLYLQQTLNDTVGRKIVMDFLGFNWNWINKQQGKRGWGQLTSNLLLIGMEGNVTPAHYDEQQNFFAQIKGYKRCILFPPDQFECLYPYPVHHPCDRQSQVDFDNPDYERFPNFQNVVGYETVVGPGDVLYIPMYWWHHIESLLNGGITITVNFWYKGAPTPKRIEYPLKAHQKVAIMRNIEKMLGEALGNPQEVGPLLNTMIKGRYN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.29
R work: 0.2078
R free: 0.2215
Average B factor: 83.48
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 1.6M AMMONIUM SULPHATE, 6% PEG 400, 0.1M HEPES PH 7.5
Matthews coefficient: 3.44
Solvent content (%): 64.23
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: 2021-08-25
ARHGEF2 PanDDA analysis group deposition -- ARHGEF2 and RhoA in complex with Z1565771450 (PDB entry 7G93)
Macromolecule: Rho guanine nucleotide exchange factor 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 245 residues
Sequence: SMEMDEKDFAADSWSLAVDSSFLQQHKKEVMKQQDVIYELIQTELHHVRTLKIMTRLFRTGMLEELHLEPGVVQGLFPCVDELSDIHTRFLSQLLERRRQALCPGSTRNFVIHRLGDLLISQFSGPSAEQMCKTYSEFCSRHSKALKLYKELYARDKRFQQFIRKVTRPAVLKRHGVQECILLVTQRITKYPLLISRILQHSHGIEEERQDLTTALGLVKELLSNVDEGIYQLEKGARLQEIYNR
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.693
R work: 0.1981
R free: 0.2254
Average B factor: 29.21
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 293
Crystal growth procedure: 100 mM Tris, 2.6M sodium formate
Matthews coefficient: 2.52
Solvent content (%): 51.22
Ligand: N-(8-methyl-1,2,3,4-tetrahydroquinolin-5-yl)acetamide (VW7)
Ligand formula: C12 H16 N2 O
Ligand molecular weight: 204.268
Ligand SMILES: Cc1ccc(c2c1NCCC2)NC(=O)C
Ligand InChI: InChI=1S/C12H16N2O/c1-8-5-6-11(14-9(2)15)10-4-3-7-13-12(8)10/h5-6,13H,3-4,7H2,1-2H3,(H,14,15)
Release date: 2023-07-12
Human ERK2 in complex with an inhibitor (PDB entry 4ZZN)
Macromolecule: MITOGEN-ACTIVATED PROTEIN KINASE 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.24
Sequence length: 350 residues
Sequence: PEMVRGQVFDVGPRYTNLSYIGEGAYGMVCSAYDNLNKVRVAIKKISPFEHQTYCQRTLREIKILLRFRHENIIGINDIIRAPTIEQMKDVYIVQDLMETDLYKLLKTQHLSNDHICYFLYQILRGLKYIHSANVLHRDLKPSNLLLNTTCDLKICDFGLARVADPDHDHTGFLTEYVATRWYRAPEIMLNSKGYTKSIDIWSVGCILAEMLSNRPIFPGKHYLDQLNHILGILGSPSQEDLNCIINLKARNYLLSLPHKNKVPWNRLFPNADSKALDLLDKMLTFNPHKRIEVEQALAHPYLEQYYDPSDEPIAEAPFKFDMELDDLPKEKLKELIFEETARFQPGYRS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.33
R work: 0.1703
R free: 0.2023
Average B factor: 23.28
Matthews coefficient: 2.36
Solvent content (%): 47.97
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: 2015-05-27
Crystal structure of FXR in complex with agonist XJ034 (PDB entry 6ITM)
Macromolecule: Bile acid receptor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 240 residues
Sequence: MGHHHHHHGSTELTPDQQTLLHFIMDSYNKQRMPQEITNKILKEAFSAEENFLILTEMATNHVQVLVEFTKKLPGFQTLDHEDQIALLKGSAVEAMFLRSAEIFNKKLPSGHSDLLEARIRNSGISDEYITPMFSFYKSIGELKMTQEEYALLTAIVILSPDRQYIKDREAVEKLQEPLLDVLQKLCKIHQPENPQHFACLLGRLTELRTFNHHHAEMLMSWRVNDHKFTPLLCEIWDVQ
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.5
R work: 0.1918
R free: 0.2418
Average B factor: 45.246
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 291
Crystal growth procedure: 0.2M Ammonium acetate, 0.1M Bis-Tris pH 6.5, 25% w/v Polyethylene glycol 3350
Matthews coefficient: 2.09
Solvent content (%): 41.18
Ligand: 1-adamantyl-[4-(5-chloranyl-2-methyl-phenyl)piperazin-1-yl]methanone (AWL)
Ligand formula: C22 H29 Cl N2 O
Ligand molecular weight: 372.931
Ligand SMILES: Cc1ccc(cc1N2CCN(CC2)C(=O)C34CC5CC(C3)CC(C5)C4)Cl
Ligand InChI: InChI=1S/C22H29ClN2O/c1-15-2-3-19(23)11-20(15)24-4-6-25(7-5-24)21(26)22-12-16-8-17(13-22)10-18(9-16)14-22/h2-3,11,16-18H,4-10,12-14H2,1H3/t16-,17+,18-,22-
Release date: 2019-11-27
Structure of human RNase 6 in complex with sulphate anions (PDB entry 4X09)
Macromolecule: Ribonuclease K6
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.27.5
Sequence length: 128 residues
Sequence: MWPKRLTKAHWFEIQHIQPSPLQCNRAMSGINNYTQHCKHQNTFLHDSFQNVAAVCDLLSIVCKNRRHNCHQSSKPVNMTDCRLTSGKYPQCRYSAAAQYKFFIVACDPPQKSDPPYKLVPVHLDSIL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.722
R work: 0.1928
R free: 0.2267
Average B factor: 31.98
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 2M AMMONIUM SULPHATE, 0.1M SODIUM, CACODYLATE, 0.05M SODIUM CHLORIDE, PH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293 K
Matthews coefficient: 1.79
Solvent content (%): 31.27
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: 2016-04-06
Structure of BACE1 complex with a HEA-type inhibitor (PDB entry 4TRY)
Macromolecule: Beta-secretase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.23.46
Sequence length: 388 residues
Sequence: FVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHPFLHRYYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTVRANIAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTHVPNLFSLQLCGAGFPLNQSEVLASVGGSMIIGGIDHSLYTGSLWYTPIRREWYYEVIIVRVEINGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVKSIKAASSTEKFPDGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRITILPQQYLRPVEDVATSQDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSACHVHDEFRTAAVEGPFVTLDMEDCGYNI
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.75
R work: 0.1795
R free: 0.2517
Average B factor: 54.999
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5
Crystallization temperature (K): 293
Crystal growth procedure: 100mM Sodium citrate pH5.0, 200mM Ammonium sulfate, 22% v/v PEG 10000
Matthews coefficient: 3.2
Solvent content (%): 61.61
Release date: 2015-07-29
Crystal structure of human heparanase, in complex with glucuronic acid configured aziridine probe JJB355 (PDB entry 5L9Y)
Macromolecule: Heparanase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.2.1.166
Sequence length: 389 residues
Sequence: DPGKKFKNSTYSRSSVDVLYTFANCSGLDLIFGLNALLRTADLQWNSSNAQLLLDYCSSKGYNISWELGNEPNSFLKKADIFINGSQLGEDFIQLHKLLRKSTFKNAKLYGPDVGQPRRKTAKMLKSFLKAGGEVIDSVTWHHYYLNGRTATREDFLNPDVLDIFISSVQKVFQVVESTRPGKKVWLGETSSAYGGGAPLLSDTFAAGFMWLDKLGLSARMGIEVVMRQVFFGAGNYHLVDENFDPLPDYWLSLLFKKLVGTKVLMASVQGSKRRKLRVYLHCTNTDNPRYKEGDLTLYAINLHNVTKYLRLPYPFSNKQVDKYLLRPLGPHGLLSKSVQLNGLTLKMVDDQTLPPLMEKPLRPGSSLGLPAFSYSFFVIRNAKVAACI
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.88
R work: 0.17925
R free: 0.2217
Average B factor: 40.063
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M MES pH 5.5, 0.1 M MgCl2, 17% PEG3350, 200:500 nl protein:well ratio
Matthews coefficient: 2.49
Solvent content (%): 50.56
Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose (NAG)
Ligand formula: C8 H15 N O6
Ligand molecular weight: 221.208
Ligand SMILES: CC(=O)NC1C(C(C(OC1O)CO)O)O
Ligand InChI: InChI=1S/C8H15NO6/c1-3(11)9-5-7(13)6(12)4(2-10)15-8(5)14/h4-8,10,12-14H,2H2,1H3,(H,9,11)/t4-,5-,6-,7-,8-/m1/s1
Release date: 2017-05-31
Crystal structure of the TgGalNAc-T3 in complex with UDP, manganese and FGF23c (PDB entry 6S22)
Macromolecule: Polypeptide N-acetylgalactosaminyltransferase
Type: Protein, polypeptide(L)
Source organism: Taeniopygia guttata
EC number: 2.4.1
Sequence length: 631 residues
Sequence: MALKKAPKLFKTFFHWKLWKFSIIVFVFLVFLFLLQREVGVQDFKDEAGIEPVVGKKSHVLGLVLNAMNNIKGAKPKMQIKAPIRQTKVPGERHCLPGHYTPVELKPFLDRPLQDPNAPGASGKAFKTINLNSEEQKEKQAGEEKHCFNAFASDRISLHRDLGPDTRPPECIEQKFKRCPPLPTTSIIIVFHNEAWSTLLRTVHSVMYTSPAILLKEIILVDDASVDEYLHDKLDEYVKQFQIVKVVRQKERKGLITARLLGASVATGETLTFLDAHCECFYGWLEPLLARIAENPVAVVSPDIASIDLNTFEFSKPSPYGHSHNRGNFDWSLSFGWESLPKHENKRRKDETYPIRTPTFAGGLFSISKDYFEYIGSYDEEMEIWGGENIEMSFRVWQCGGQLEIMPCSVVGHVFRSKSPHTFPKGTQVITRNQVRLAEVWMDEYKEIFYRRNTEAAKIVKQKTFGDISKRIDLRQRLQCKNFTWYLSNVYPEAYVPDLNPLFSGYLKNIGNRMCLDVGENNHGGKPLIMYSCHGLGGNQYFEYSAHHEIRHNIQKELCLHASKGPVQLRECTYKGQKTFAVGEEQWLHQKDQTLYNEALHMCLTGNGEHPSLASCNPSDPFQKWIFGQND
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.96
R work: 0.17902
R free: 0.21589
Average B factor: 35.312
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: Morpheus precipitant mix 4, nitrate phosphate buffer and Morpheus buffer System 1
Matthews coefficient: 2.57
Solvent content (%): 52.21
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: 2019-12-25
EphA2 LBD in complex with bA-WLA-YSKbio peptide (PDB entry 6NKP)
Macromolecule: Ephrin type-A receptor 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 187 residues
Sequence: MASQGPGEVVLLDFAAAGGELGWLTHPYGKGWDLMQNIMNDMPIYMYSVCNVMSGDQDNWLRTNWVYRGEAERIFIELKFTVRDCNSFPGGASSCKETFNLYYAESDLDYGTNFQKRLFTKIDTIAPDEITVSSDFEARHVKLNVEERSVGPLTRKGFYLAFQDIGACVALLSVRVYYKKAHHHHHH
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.033
R work: 0.1675
R free: 0.2132
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.09 M BIS-TRIS pH 5.5, 22.5% w/v PEG 3,350, 3% w/v 6-aminohexanoic acid
Matthews coefficient: 2.21
Solvent content (%): 44.3
Ligand: BIOTIN (BTN)
Ligand formula: C10 H16 N2 O3 S
Ligand molecular weight: 244.311
Ligand SMILES: C1C2C(C(S1)CCCCC(=O)O)NC(=O)N2
Ligand InChI: InChI=1S/C10H16N2O3S/c13-8(14)4-2-1-3-7-9-6(5-16-7)11-10(15)12-9/h6-7,9H,1-5H2,(H,13,14)(H2,11,12,15)/t6-,7-,9-/m0/s1
Release date: 2019-05-01
Small Molecule inhibitors of IAP (PDB entry 5M6N)
Macromolecule: Baculoviral IAP repeat-containing protein 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 6.3.2
Sequence length: 118 residues
Sequence: MGSSHHHHHHSSGLVPRGSHMQTHAARMRTFMYWPSSVPVQPEQLASAGFYYVGRNDDVKCFCCDGGLRCWESGDDPWVEHAKWFPRCEFLIRMKGQEFVDEIQGRYPHLLEQLLSTS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.166
R free: 0.203
Average B factor: 32.137
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.6
Crystallization temperature (K): 291
Crystal growth procedure: .65M (NH4)2SO4
10% Glycerol
.4M Li2SO4
.005M TCEP
.1M pH=5.6 Na3 citrate/HCl
Matthews coefficient: 2.35
Solvent content (%): 47.6
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: 2017-05-24
JAK2 JH2 IN COMPLEX WITH JAK292 (PDB entry 7T1T)
Macromolecule: Tyrosine-protein kinase JAK2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 289 residues
Sequence: VFHKIRNEDLIFNESLGQGTFTKIFKGVRREVGDYGQLHETEVLLKVLDKAHRNYSESFFEAASMMSKLSHKHLVLNYGVCVCGDENILVQEFVKFGSLDTYLKKNKNCINILWKLEVAKQLAAAMHFLEENTLIHGNVCAKNILLIREEDRKTGNPPFIKLSDPGISITVLPKDILQERIPWVPPECIENPKNLNLATDKWSFGTTLWEICSGGDKPLSALDSQRKLQFYEDRHQLPAPKAAELANLINNCMDYEPDHRPSFRAIIRDLNSLFTPDLVPRGSHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.08
R work: 0.181
R free: 0.2282
Average B factor: 23.2314
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 0.1M TRIS, PH 8.0 0.2M SODIUM ACETATE, 0.001 M TCEP, 12-24% PEG 4,000
Matthews coefficient: 2.21
Solvent content (%): 44.27
Ligand: (2S)-2-[({4-[(2-amino-7H-pyrrolo[2,3-d]pyrimidin-4-yl)oxy]phenyl}carbamoyl)amino]-4-phenylbutanoic acid (E8I)
Ligand formula: C23 H22 N6 O4
Ligand molecular weight: 446.459
Ligand SMILES: c1ccc(cc1)CCC(C(=O)O)NC(=O)Nc2ccc(cc2)Oc3c4cc[nH]c4nc(n3)N
Ligand InChI: InChI=1S/C23H22N6O4/c24-22-28-19-17(12-13-25-19)20(29-22)33-16-9-7-15(8-10-16)26-23(32)27-18(21(30)31)11-6-14-4-2-1-3-5-14/h1-5,7-10,12-13,18H,6,11H2,(H,30,31)(H2,26,27,32)(H3,24,25,28,29)/t18-/m0/s1
Release date: 2022-05-25
Native state mass spectrometry, surface plasmon resonance and X-ray crystallography correlate strongly as a fragment screening combination (PDB entry 5FNH)
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): 1.66
R work: 0.13707
R free: 0.17965
Average B factor: 14.283
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystal growth procedure: 15 MG/ML PROTEIN WITH 2.7 M AMMONIUM SULFATE, 100 MM TRIS PH 8.5 AT 8 C IN SITTING DROPS.
Matthews coefficient: 2.1
Solvent content (%): 41.8
Ligand: ZINC ION (ZN)
Ligand formula: Zn
Ligand molecular weight: 65.409
Ligand SMILES: [Zn+2]
Ligand InChI: InChI=1S/Zn/q+2
Release date: 2016-03-02
Naturally Occurring Mutations in the MPS1 Gene Predispose Cells to Kinase Inhibitor Drug Resistance. (PDB entry 5AP0)
Macromolecule: DUAL SPECIFICITY PROTEIN KINASE TTK
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.12.1
Sequence length: 313 residues
Sequence: MHHHHHHSSGVDLGTENLYFQSMSVKGRIYSILKQIGSGGSSKVFQVLNEKKQIYAIKYVNLEEADNQTLDSYRNEIAYLNKLQQHSDKIIRLYDYEITDQYIYMVMECGNIDLNSWLKKKKSIDPWERKSYWKNMLEAVHTIHQHGIVHSDLKPANFLIVDGMLKLIDFGIANQMQPDTTSVVKDSQVGTVNYMPPEAIKDMSSSRENGKSKSKISPKSDVWSLGCILYYMTYGKTPFQQIINQISKLHAIIDPNHEIEFPDIPEKDLQDVLKCCLKRDPKQRISIPELLAHPYVQIQTHPVNQMAKGTTEE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.15
R work: 0.1842
R free: 0.2199
Average B factor: 74.03
Crystallization pH: 7.5
Crystal growth procedure: 30% (V/V) PEG300, PH 7.5
Matthews coefficient: 3.1
Solvent content (%): 60.34
Ligand: 9-CYCLOPENTYL-2-[[2-METHOXY-4-[(1-METHYLPIPERIDIN-4-YL)OXY]-PHENYL]AMINO]-7-METHYL-7,9-DIHYDRO-8H-PURIN-8-ONE (AU5)
Ligand formula: C24 H32 N6 O3
Ligand molecular weight: 452.549
Ligand SMILES: CN1CCC(CC1)Oc2ccc(c(c2)OC)Nc3ncc4c(n3)N(C(=O)N4C)C5CCCC5
Ligand InChI: InChI=1S/C24H32N6O3/c1-28-12-10-17(11-13-28)33-18-8-9-19(21(14-18)32-3)26-23-25-15-20-22(27-23)30(24(31)29(20)2)16-6-4-5-7-16/h8-9,14-17H,4-7,10-13H2,1-3H3,(H,25,26,27)
Release date: 2015-09-23
Structure of DHODH in Complex with Fragment 2 (PDB entry 8VHM)
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): 2.26
R work: 0.196
R free: 0.228
Average B factor: 10.775
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 4.8
Crystallization temperature (K): 293
Crystal growth procedure: 0.10 M NaAcetate pH 4.8, 2.30 M (NH4)2SO4, 30% Glycerol
Matthews coefficient: 3.6
Solvent content (%): 65.82
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: 2024-04-03
Chimeric titin Z1Z2 functionalized with a KLER exogenous peptide from decorin (PDB entry 6SDB)
Macromolecule: Titin,Decorin,Titin
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 197 residues
Sequence: GAMATQAPTFTQPLQSVVVLEGSTATFEAHISGFPVPEVSWFRDGQVKLERLPGVQISFSDGRAKLTIPAVTKANSGRYSLKATNGSGQATSTAELLVKAETAPPNFVQRLQSMTVRQGSQVRLQVRVTGIPTPVVKFYRDGAEIQSSLDFQISQEGDLYSLLIAEAYPEDSGTYSVNATNSVGRATSTAELLVQGE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.8
R work: 0.1914
R free: 0.2335
Average B factor: 67.11
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 295
Crystal growth procedure: 1 M NH4H2PO4 pH 4.6, 100 mM sodium acetate
Matthews coefficient: 5.77
Solvent content (%): 78.67
Ligand: ACETATE ION (ACT)
Ligand formula: C2 H3 O2
Ligand molecular weight: 59.044
Ligand SMILES: CC(=O)[O-]
Ligand InChI: InChI=1S/C2H4O2/c1-2(3)4/h1H3,(H,3,4)/p-1
Release date: 2019-09-18
PanDDA analysis group deposition -- Crystal Structure of human NUDT22 in complex with N13960a (PDB entry 5R5K)
Macromolecule: Uridine diphosphate glucose pyrophosphatase NUDT22
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.1.45
Sequence length: 304 residues
Sequence: SMDPEVTLLLQCPGGGLPQEQIQAELSPAHDRRPLPGGDEAITAIWETRLKAQPWLFDAPKFRLHSATLAPIGSRGPQLLLRLGLTSYRDFLGTNWSSSAAWLRQQGATDWGDTQAYLADPLGVGAALATADDFLVFLRRSRQVAEAPGLVDVPGGHPEPQALCPGGSPQHQDLAGQLVVHELFSSVLQEICDEVNLPLLTLSQPLLLGIARNETSAGRASAEFYVQCSLTSEQVRKHYLSGGPEAHESTGIFFVETQNVRRLPETEMWAELCPSAKGAIILYNRVQGSPTGAALGSPALLPPL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.6
R work: 0.1897
R free: 0.229
Average B factor: 25.667
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.1M HEPES pH 7.5, 0.3M sodium/potassium phosphate, 15% PEG Smear High, 20% ethylene glycol
Matthews coefficient: 2.01
Solvent content (%): 38.82
Ligand: methyl 2-[(2~{R})-1-(ethylcarbamoyl)-3-oxidanylidene-piperazin-2-yl]ethanoate (S2J)
Ligand formula: C10 H17 N3 O4
Ligand molecular weight: 243.26
Ligand SMILES: CCNC(=O)N1CCNC(=O)C1CC(=O)OC
Ligand InChI: InChI=1S/C10H17N3O4/c1-3-11-10(16)13-5-4-12-9(15)7(13)6-8(14)17-2/h7H,3-6H2,1-2H3,(H,11,16)(H,12,15)/t7-/m1/s1
Release date: 2020-07-01
CRYSTAL STRUCTURE OF HUMAN METHIONINE AMINOPEPTIDASE-2 IN COMPLEX WITH AN INHIBITOR (S)-3-Hydroxy-2-oxo-1-phenyl-pyrrolidine-3-carboxylic acid 3-chloro-5-fluoro-benzylamide (PDB entry 6QEF)
Macromolecule: Methionine aminopeptidase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.11.18
Sequence length: 378 residues
Sequence: MGPKVQTDPPSVPICDLYPNGVFPKGQECEYPPTQDGRTAAWRTTSEEKKALDQASEEIWNDFREAAEAHRQVRKYVMSWIKPGMTMIEICEKLEDCSRKLIKENGLNAGLAFPTGCSLNNCAAHYTPNAGDTTVLQYDDICKIDFGTHISGRIIDCAFTVTFNPKYDTLLKAVKDATNTGIKCAGIDVRLCDVGEAIQEVMESYEVEIDGKTYQVKPIRNLNGHSIGQYRIHAGKTVPIVKGGEATRMEEGEVYAIETFGSTGKGVVHDDMECSHYMKNFDVGHVPIRLPRTKHLLNVINENFGTLAFCRRWLDRLGESKYLMALKNLCDLGIVDPYPPLCDIKGSYTAQFEHTILLRPTCKEVVSRGDDYHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.79
R work: 0.175
R free: 0.195
Average B factor: 38.52
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6
Crystallization temperature (K): 277
Crystal growth procedure: 20% METHANOL, 0.1 M CITRATE, PH 6.0
Matthews coefficient: 2.6
Solvent content (%): 52.7
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: 2019-05-01