satarupa22/MacromolecularLigandDB huggingface dataset:
CLK1 bound with GW807982X (Cpd 8) (PDB entry 6ZLN)
Macromolecule: Dual specificity protein kinase CLK1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.12.1
Sequence length: 339 residues
Sequence: SMHLICQSGDVLSARYEIVDTLGEGAFGKVVECIDHKAGGRHVAVKIVKNVDRYCEAARSEIQVLEHLNTTDPNSTFRCVQMLEWFEHHGHICIVFELLGLSTYDFIKENGFLPFRLDHIRKMAYQICKSVNFLHSNKLTHTDLKPENILFVQSDYTEAYNPKIKRDERTLINPDIKVVDFGSATYDDEHHSTLVSTRHYRAPEVILALGWSQPCDVWSIGCILIEYYLGFTVFPTHDSKEHLAMMERILGPLPKHMIQKTRKRKYFHHDRLDWDEHSSAGRYVSRACKPLKEFMLSQDVEHERLFDLIQKMLEYDPAKRITLREALKHPFFDLLKKSI
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.7
R work: 0.1695
R free: 0.1993
Average B factor: 22.264
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 9
Crystallization temperature (K): 277
Crystal growth procedure: 14% PEG 6k, 0.1M bicine
Matthews coefficient: 2.59
Solvent content (%): 52.54
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: 2020-08-26
Crystal structure of the Fyn SH3 domain in space group C21 at pH 7.5 (PDB entry 7A2J)
Macromolecule: Tyrosine-protein kinase Fyn
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 60 residues
Sequence: GVTLFVALYDYEARTEDDLSFHKGEKFQILNSSEGDWWEARSLTTGETGYIPSNYVAPVD
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.5
R work: 0.2121
R free: 0.2466
Average B factor: 46.7575
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 298
Crystal growth procedure: 4.5M sodium formate, 0.1M Hepes
Matthews coefficient: 2.66
Solvent content (%): 53.81
Ligand: SODIUM ION ()
Ligand formula: Na
Ligand molecular weight: 22.99
Ligand SMILES: [Na+]
Ligand InChI: InChI=1S/Na/q+1
Release date: 2021-08-25
Crystal Structure of human phosphodiesterase 10 in complex with 3-N-[2-(3-fluorophenyl)imidazo[1,2-a]pyrimidin-7-yl]-4-N,4-N,2-trimethylpyrazole-3,4-dicarboxamide (PDB entry 5SFE)
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): 1.86
R work: 0.1786
R free: 0.2206
Average B factor: 36.66
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 (%): 53.67
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: 2022-10-19
Crystal structure of CK2alpha bound to CAM4066 (PDB entry 5CU3)
Macromolecule: Casein kinase II subunit alpha
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 352 residues
Sequence: GSMDIEFDDDADDDGSGSGSGSGSSGPVPSRARVYTDVNTHRPSEYWDYESHVVEWGNQDDYQLVRKLGRGKYSEVFEAINITNNEKVVVKILKPVKKKKIKREIKILENLRGGPNIITLADIVKDPVSRTPALVFEHVNNTDFKQLYQTLTDYDIRFYMYEILKALDYCHSMGIMHRDVKPHNVMIDHEHRKLRLIDWGLAEFYHPGQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRKEPFFHGHDNYDQLVRIAKVLGTEDLYDYIDKYNIELDPRFNDILGRHSRKRWERFVHSENQHLVSPEALDFLDKLLRYDHQSRLTAREAMEHPYFYTVVK
Oligomeric state: Homo 2-mer
Stoichiometry: A2
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.787
R work: 0.1835
R free: 0.2018
Average B factor: 41.94
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 298
Crystal growth procedure: 107mM Mes pH 6.5, 29% glycerol ethoxylate, 1 M ammonium acetate
Matthews coefficient: 2.18
Solvent content (%): 43.51
Ligand: ACETATE ION (ACT)
Ligand formula: C2 H3 O2
Ligand molecular weight: 59.044
Ligand SMILES: CC(=O)[O-]
Ligand InChI: InChI=1S/C2H4O2/c1-2(3)4/h1H3,(H,3,4)/p-1
Release date: 2016-07-27
Crystal structure of TTK kinase domain in complex with a pyrazolopyrimidine inhibitor (PDB entry 4ZEG)
Macromolecule: Dual specificity protein kinase TTK
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.12.1
Sequence length: 281 residues
Sequence: NECISVKGRIYSILKQIGSGGSSKVFQVLNEKKQIYAIKYVNLEEADNQTLDSYRNEIAYLNKLQQHSDKIIRLYDYEITDQYIYMVMECGNIDLNSWLKKKKSIDPWERKSYWKNMLEAVHTIHQHGIVHSDLKPANFLIVDGMLKLIDFGIANQMQPDTTSVVKDSQVGTVNYMPPEAIKDMSSSRENGKSKSKISPKSDVWSLGCILYYMTYGKTPFQQIINQISKLHAIIDPNHEIEFPDIPEKDLQDVLKCCLKRDPKQRISIPELLAHPYVQIQT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.33
R work: 0.20935
R free: 0.26289
Average B factor: 66.242
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.2 M MgCl2, 0.1M Tris pH 8.5, 25% PEG 3500
Matthews coefficient: 3.23
Solvent content (%): 61.94
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: 2016-04-27
Structure of human PARG complexed with JA2131 (PDB entry 6OAK)
Macromolecule: Poly(ADP-ribose) glycohydrolase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.2.1.143
Sequence length: 529 residues
Sequence: SPDKKWLGTPIEEMRRMPRCGIRLPLLRPSANHTVTIRVDLLRAGEVPKPFPTHYKDLWDNKHVKMPCSEQNLYPVEDENGERTAGSRWELIQTALLNKFTRPQNLKDAILKYNVAYSKKWDFTALIDFWDKVLEEAEAQHLYQSILPDMVKIALCLPNICTQPIPLLKQKMNHSITMSQEQIASLLANAFFCTFPRRNAKMKSEYSSYPDINFNRLFEGRSSRKPEKLKTLFCYFRRVTEKKPTGLVTFTRQSLEDFPEWERCEKPLTRLHVTYEGTIEENGQGMLQVDFANRFVGGGVTSAGLVQEEIRFLINPELIISRLFTEVLDHNECLIITGTEQYSEYTGYAETYRWSRSHEDGSERDDWQRRCTEIVAIDALHFRRYLDQFVPEKMRRELNKAYCGFLRPGVSSENLSAVATGNWGCGAFGGDARLKALIQILAAAAAERDVVYFTFGDSELMRDIYSMHIFLTERKLTVGDVYKLLLRYYNEECRNCSTPGPDIKLYPFIYHAVESCAETADHSGQRTGT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.7
R work: 0.1821
R free: 0.2088
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 295
Crystal growth procedure: 0.1 M PCTP, pH 7.5, 0.2 M (NH3)2SO4, 17%  PEG3350
Matthews coefficient: 2.43
Solvent content (%): 49.28
Ligand: (8S)-1,3-dimethyl-8-{[2-(morpholin-4-yl)ethyl]sulfanyl}-6-sulfanylidene-1,3,6,7,8,9-hexahydro-2H-purin-2-one (M0M)
Ligand formula: C13 H21 N5 O2 S2
Ligand molecular weight: 343.468
Ligand SMILES: CN1C2=C(C(=S)N(C1=O)C)NC(N2)SCCN3CCOCC3
Ligand InChI: InChI=1S/C13H21N5O2S2/c1-16-10-9(11(21)17(2)13(16)19)14-12(15-10)22-8-5-18-3-6-20-7-4-18/h12,14-15H,3-8H2,1-2H3/t12-/m0/s1
Release date: 2020-03-18
CFF-Notum complex (PDB entry 6TV4)
Macromolecule: Palmitoleoyl-protein carboxylesterase NOTUM
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.1.98
Sequence length: 383 residues
Sequence: ETGSAQQLNEDLRLHLLLNTSVTCNDGSPAGYYLKESRGSRRWLLFLEGGWYCFNRENCDSRYDTMRRLMSSRDWPRTRTGTGILSSQPEENPYWWNANMVFIPYCSSDVWSGASSKSEKNEYAFMGALIIQEVVRELLGRGLSGAKVLLLAGSSAGGTGVLLNVDRVAEQLEKLGYPAIQVRGLADSGWFLDNKQYRHTDCVDTITCAPTEAIRRGIRYWNGVVPERCRRQFQEGEEWNCFFGYKVYPTLRSPVFVVQWLFDEAQLTVDNVHLTGQPVQEGLRLYIQNLGRELRHTLKDVPASFAPACLSHEIIIRSHWTDVQVKGTSLPRALHCWDRSLHDSHKASKTPLKGCPVHLVDSCPWPHCNPSCPTGTKHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.53
R work: 0.1704
R free: 0.2142
Average B factor: 22.657
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 4.2
Crystallization temperature (K): 300
Crystal growth procedure: 1.5 M Ammonium Sulphate
0.1 M Sodium citrate pH 4.2
Matthews coefficient: 1.93
Solvent content (%): 36.25
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: 2020-10-28
ARHGEF2 PanDDA analysis group deposition -- ARHGEF2 and RhoA in complex with Z1416193393 (PDB entry 7G8W)
Macromolecule: Transforming protein RhoA
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.5.2
Sequence length: 185 residues
Sequence: SMAAIRKKLVIVGDGACGKTCLLIVFSKDQFPEVYVPTVFENYVADIEVDGKQVELALWDTAGQEDYDRLRPLSYPDTDVILMCFSIDSPDSLENIPEKWTPEVKHFCPNVPIILVGNKKDLRNDEHTRRELAKMKQEPVKPEEGRDMANRIGAFGYMECSAKTKDGVREVFEMATRAALQARRG
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.939
R work: 0.2082
R free: 0.2504
Average B factor: 34.05
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: 2.53
Solvent content (%): 51.31
Ligand: DIMETHYL SULFOXIDE (DMS)
Ligand formula: C2 H6 O S
Ligand molecular weight: 78.133
Ligand SMILES: CS(=O)C
Ligand InChI: InChI=1S/C2H6OS/c1-4(2)3/h1-2H3
Release date: 2023-07-12
Selenols: a new class of Carbonic Anhydrase inhibitors (PDB entry 6HX5)
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): 1.44
R work: 0.18821
R free: 0.20979
Average B factor: 14.848
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 8
Crystallization temperature (K): 296
Crystal growth procedure: 1.5 M sodium citrate, Tris 50 mM
Matthews coefficient: 2.1
Solvent content (%): 41.29
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: 2018-12-26
Cocrystal structure of cAMP-dependent Protein Kinase (PKA) in complex with a R-methyl-piperazine substituted Fasudil-derivative (Ligand 02) (PDB entry 5LCT)
Macromolecule: cAMP-dependent protein kinase catalytic subunit alpha
Type: Protein, polypeptide(L)
Source organism: Cricetulus griseus
EC number: 2.7.11.11
Sequence length: 353 residues
Sequence: GHMGNAAAAKKGSEQESVKEFLAKAKEEFLKKWESPSQNTAQLDHFDRIKTLGTGSFGRVMLVKHKETGNHYAMKILDKQKVVKLKQIEHTLNEKRILQAVNFPFLVKLEFSFKDNSNLYMVMEYVPGGEMFSHLRRIGRFSEPHARFYAAQIVLTFEYLHSLDLIYRDLKPENLLIDQQGYIQVTDFGFAKRVKGRTWTLCGTPEYLAPEIILSKGYNKAVDWWALGVLIYEMAAGYPPFFADQPIQIYEKIVSGKVRFPSHFSSDLKDLLRNLLQVDLTKRFGNLKNGVNDIKNHKWFATTDWIAIYQRKVEAPFIPKFKGPGDTSNFDDYEEEEIRVSINEKCGKEFTEF
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.615
R work: 0.1427
R free: 0.1742
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.9
Crystallization temperature (K): 277.15
Crystal growth procedure: Drop:
10 mg/ml PKA (0.240 mM)
30 mM MBT (MES/Bis-Tris Puffer pH 6.9)
1 mM DTT
0.1 mM EDTA
75 mM LiCl
0.03 mM Mega 8
0.07mM PKI (Sigma: P7739)
1.2 mM ligand solved in DMSO (50 mM Stock)

Reservoir: 19% Methanol

0.003 mL drop volume, 0.4 mL reservoir volume
Matthews coefficient: 2.15
Solvent content (%): 55.36
Ligand: 5-[(2~{R})-2-methylpiperazin-1-yl]sulfonylisoquinoline (6TY)
Ligand formula: C14 H17 N3 O2 S
Ligand molecular weight: 291.369
Ligand SMILES: CC1CNCCN1S(=O)(=O)c2cccc3c2ccnc3
Ligand InChI: InChI=1S/C14H17N3O2S/c1-11-9-16-7-8-17(11)20(18,19)14-4-2-3-12-10-15-6-5-13(12)14/h2-6,10-11,16H,7-9H2,1H3/t11-/m1/s1
Release date: 2018-01-17
Crystal structural of MacroD1-ADPr complex (PDB entry 6LH4)
Macromolecule: ADP-ribose glycohydrolase MACROD1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.1.106
Sequence length: 235 residues
Sequence: TSTDWKEAKSFLKGLSDKQREEHYFCKDFVRLKKIPTWKEMAKGVAVKVEEPRYKKDKQLNEKISLLRSDITKLEVDAIVNAANSSLLGGGGVDGCIHRAAGPLLTDECRTLQSCKTGKAKITGGYRLPAKYVIHTVGPIAYGEPSASQAAELRSCYLSSLDLLLEHRLRSVAFPCISTGVFGYPCEAAAEIVLATLREWLEQHKDKVDRLIICVFLEKDEDIYRSRLPHYFPVA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.999
R work: 0.2401
R free: 0.2848
Average B factor: 47.8011
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291.1
Crystal growth procedure: 0.2M Sodium thiocyanate, 20% PEG 3350
Matthews coefficient: 2.78
Solvent content (%): 55.82
Ligand: [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL
[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE (AR6)
Ligand formula: C15 H23 N5 O14 P2
Ligand molecular weight: 559.316
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)O)O)O)O)O)N
Ligand InChI: InChI=1S/C15H23N5O14P2/c16-12-7-13(18-3-17-12)20(4-19-7)14-10(23)8(21)5(32-14)1-30-35(26,27)34-36(28,29)31-2-6-9(22)11(24)15(25)33-6/h3-6,8-11,14-15,21-25H,1-2H2,(H,26,27)(H,28,29)(H2,16,17,18)/t5-,6-,8-,9-,10-,11-,14-,15+/m1/s1
Release date: 2020-12-09
Fragment-based screening of HSP70 sheds light on the functional role of ATP-binding site residues (PDB entry 5AQT)
Macromolecule: HEAT SHOCK COGNATE 71 KDA PROTEIN
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.3.51
Sequence length: 386 residues
Sequence: GPLGSMSKGPAVGIDLGTTYSCVGVFQHGKVEIIANDQGNRTTPSYVAFTDTERLIGDAAKNQVAMNPTNTVFDAKRLIGRRFDDAVVQSDMKHWPFMVVNDAGRPKVQVEYKGETKSFYPEEVSSMVLTKMKEIAEAYLGKTVTNAVVTVPAYFNDSQRQATKDAGTIAGLNVLRIINEPTAAAIAYGLDKKVGAERNVLIFDLGGGTFDVSILTIEDGIFEVKSTAGDTHLGGEDFDNRMVNHFIAEFKRKHKKDISENKRAVRRLRTACERAKRTLSSSTQASIEIDSLYEGIDFYTSITRARFEELNADLFRGTLDPVEKALRDAKLDKSQIHDIVLVGGSTRIPKIQKLLQDFFNGKELNKSINPDEAVAYGAAVQAAILS
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.9
R work: 0.1803
R free: 0.2224
Average B factor: 40.54
Crystallization pH: 8.5
Crystal growth procedure: 16-26% (W/V) PEG3350, 0.1 M K-NA TARTRATE, 0.1 M TRIS.HCL PH 8.5 AND 25% (V/V) GLYCEROL
Matthews coefficient: 2.45
Solvent content (%): 49.83
Ligand: (1S,2R,3R,5R)-3-(hydroxymethyl)-5-(quinazolin-4-ylamino)cyclopentane-1,2-diol (5P7)
Ligand formula: C14 H17 N3 O3
Ligand molecular weight: 275.303
Ligand SMILES: c1ccc2c(c1)c(ncn2)NC3CC(C(C3O)O)CO
Ligand InChI: InChI=1S/C14H17N3O3/c18-6-8-5-11(13(20)12(8)19)17-14-9-3-1-2-4-10(9)15-7-16-14/h1-4,7-8,11-13,18-20H,5-6H2,(H,15,16,17)/t8-,11-,12-,13+/m1/s1
Release date: 2016-10-05
Thrombin in complex with diphenyl ((4-carbamimidoylphenyl)((S)-1-((R)-3-cyclohexyl 2-((phenylmethyl)sulfonamido)propanoyl)pyrrolidine-2-carboxamido)methyl)phosphonate (MI-492) (PDB entry 6T8A)
Macromolecule: Prothrombin
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.5
Sequence length: 36 residues
Sequence: TFGSGEADCGLRPLFEKKSLEDKTERELLESYIDGR
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.62
R work: 0.1596
R free: 0.1853
Average B factor: 26.721
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7
Crystallization temperature (K): 277
Crystal growth procedure: 20 mM sodium dihydrogen phosphate ph 7.5
350 mM NaCl
27 % PEG 8000
Matthews coefficient: 2.87
Solvent content (%): 57.11
Ligand: PHOSPHATE ION (PO4)
Ligand formula: O4 P
Ligand molecular weight: 94.971
Ligand SMILES: [O-]P(=O)([O-])[O-]
Ligand InChI: InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4)/p-3
Release date: 2020-11-18
Crystal structure of cIAP1-BIR3 in complex with a covalently bound SM (PDB entry 6EXW)
Macromolecule: Baculoviral IAP repeat-containing protein 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2.27
Sequence length: 122 residues
Sequence: MENSLETLRFSISNLSMQTHAARMRTFMYWPSSVPVQPEQLASAGFYYVGRNDDVKCFCCDGGLRCWESGDDPWVEHAKWFPRCEFLIRMKGQEFVDEIQGRYPHLLEQLLSTSLEHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.2
R work: 0.191
R free: 0.2514
Average B factor: 35.787
Crystallization method: EVAPORATION
Crystallization pH: 5.9
Crystallization temperature (K): 293
Crystal growth procedure: 12% PEG 3350, 0.22 M MgCl2, 0.1M BISTris
Matthews coefficient: 3.23
Solvent content (%): 61.94
Ligand: (3~{S},6~{S},7~{R},9~{a}~{S})-6-[[(2~{S})-2-(methylamino)propanoyl]amino]-5-oxidanylidene-~{N}-(phenylmethyl)-7-[(propanoylamino)methyl]-3,6,7,8,9,9~{a}-hexahydropyrrolo[1,2-a]azepine-3-carboxamide (C3K)
Ligand formula: C25 H35 N5 O4
Ligand molecular weight: 469.577
Ligand SMILES: CCC(=O)NCC1CCC2C=CC(N2C(=O)C1NC(=O)C(C)NC)C(=O)NCc3ccccc3
Ligand InChI: InChI=1S/C25H35N5O4/c1-4-21(31)27-15-18-10-11-19-12-13-20(24(33)28-14-17-8-6-5-7-9-17)30(19)25(34)22(18)29-23(32)16(2)26-3/h5-9,12-13,16,18-20,22,26H,4,10-11,14-15H2,1-3H3,(H,27,31)(H,28,33)(H,29,32)/t16-,18+,19-,20-,22-/m0/s1
Release date: 2018-08-08
PanDDA analysis group deposition -- Crystal Structure of ATAD2 in complex with RZ201 (PDB entry 5R4E)
Macromolecule: ATPase family AAA domain-containing protein 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.1.3
Sequence length: 130 residues
Sequence: SMQEEDTFRELRIFLRNVTHRLAIDKRFRVFTKPVDPDEVPDYRTVIKEPMDLSSVISKIDLHKYLTVKDYLRDIDLICSNALEYNPDRDPGDRLIRHRACALRDTAYAIIKEELDEDFEQLCEEIQESR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.83
R work: 0.217
R free: 0.2637
Average B factor: 32.487
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 277
Crystal growth procedure: 1.6M Ammonium Sulfate, 0.1M bis-tris pH 5.5
Matthews coefficient: 4.08
Solvent content (%): 69.88
Ligand: (5R)-5-[(4-fluorophenyl)methyl]-5-(2-hydroxyethyl)-3-(2-methoxyethyl)imidazolidine-2,4-dione (RQP)
Ligand formula: C15 H19 F N2 O4
Ligand molecular weight: 310.321
Ligand SMILES: COCCN1C(=O)C(NC1=O)(CCO)Cc2ccc(cc2)F
Ligand InChI: InChI=1S/C15H19FN2O4/c1-22-9-7-18-13(20)15(6-8-19,17-14(18)21)10-11-2-4-12(16)5-3-11/h2-5,19H,6-10H2,1H3,(H,17,21)/t15-/m0/s1
Release date: 2020-04-08
HUMAN VH1-RELATED DUAL-SPECIFICITY PHOSPHATASE (VHR) in apo form (PDB entry 8TK6)
Macromolecule: Dual specificity protein phosphatase 3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.16
Sequence length: 183 residues
Sequence: GSFELSVQDLNDLLSDGSGCYSLPSQPCNEVTPRIYVGNASVAQDIPKLQKLGITHVLNAAEGRSFMHVNTNANFYKDSGITYLGIKANDTQEFNLSAYFERAADFIDQALAQKNGRVLVHCREGYSRSPTLVIAYLMMRQKMDVKSALSIVRQNREIGPNDGFLAQLCQLNDRLAKEGKLKP
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.65
R work: 0.14595
R free: 0.18336
Average B factor: 16.04
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 294
Crystal growth procedure: Protein in 50 mM TRIS-Cl pH 8.5, 1 mM TCEP, 0.5 mM EDTA was mixed with the precipitant solution (100 mM Bis-Tris pH 6.5, 50 mM NH4F, 28% (w/v) PEG-4000) and equilibrated against the precipitant solution.
Matthews coefficient: 2.02
Solvent content (%): 39.25
Release date: 2024-08-14
Crystal structure of hEphB1 bound with chlortetracycline (PDB entry 6UMW)
Macromolecule: Ephrin type-B receptor 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 301 residues
Sequence: HHHHHHDPNEAVREFAKEIDVSFVKIEEVIGAGEFGEVYKGRLKLPGKREIYVAIKTLKAGYSEKQRRDFLSEASIMGQFDHPNIIRLEGVVTKSRPVMIITEFMENGALDSFLRQNDGQFTVIQLVGMLRGIAAGMKYLAEMNYVHRDLAARNILVNSNLVCKVSDFGLSRYLQDDTSDPTYTSSLGGKIPVRWTAPEAIAYRKFTSASDVWSYGIVMWEVMSFGERPYWDMSNQDVINAIEQDYRLPPPMDCPAALHQLMLDCWQKDRNSRPRFAEIVNTLDKMIRNPASLKTVATITA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.982
R work: 0.1815
R free: 0.2212
Average B factor: 22.0974
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 0.1 M sodium malonate, pH 4.6, 14% PEG3350
Matthews coefficient: 2.12
Solvent content (%): 41.88
Ligand: 7-CHLOROTETRACYCLINE (CTC)
Ligand formula: C22 H23 Cl N2 O8
Ligand molecular weight: 478.88
Ligand SMILES: CC1(c2c(ccc(c2C(=O)C3=C(C4(C(CC31)C(C(=C(C4=O)C(=O)N)O)N(C)C)O)O)O)Cl)O
Ligand InChI: InChI=1S/C22H23ClN2O8/c1-21(32)7-6-8-15(25(2)3)17(28)13(20(24)31)19(30)22(8,33)18(29)11(7)16(27)12-10(26)5-4-9(23)14(12)21/h4-5,7-8,15,26,28-29,32-33H,6H2,1-3H3,(H2,24,31)/t7-,8-,15-,21-,22-/m0/s1
Release date: 2020-10-14
Structure of MavC in complex with its substrate in R3 spacegroup (PDB entry 6ULH)
Macromolecule: LPG2147 (MavC)
Type: Protein, polypeptide(L)
Source organism: Legionella pneumophila
Sequence length: 389 residues
Sequence: GPLGSMTTSKLEKTGLHVHEKIKHMVKNYGTMITGIPAEILGQNEAEISVGYVKKMGNMKENIAEVVRKSEMTQPTNSAGKASNEVCDLLLGTEGASEFEKSSYQVLSGDGSNLKGSLPNKNLLVRVEMDRFNAPQKYQKIKREEFNPETAEKNKIYLLEDQLVYLDIFGKVIDLGQTSDTCHRLFNAITTPFYQNYILYDEYIDPEESAEEAAMFEMGEIVKAKMKNIDCWTATHSFTIFVPESDSEDTRTLYPYQAYWTSHTLQQWFSGDKDEKLSRLGIDGYIEKLALLGTTTDSKIRSSIYGELFSPPGKEHVFCTGMNEKFSPLRVKFKVTEVNPEIALQNLEEVQEFIDTNYPGENAKDQCELYKIKAQEAMTKQLEMRLLIE
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.968
R work: 0.1829
R free: 0.2265
Average B factor: 39.8601
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 4.6
Crystallization temperature (K): 294
Crystal growth procedure: 0.1 M Sodium Acetate: HCl, pH 4.6
3.5 M Sodium Formate
Matthews coefficient: 2.4
Solvent content (%): 48.83
Release date: 2020-05-27
THE CRYSTAL STRUCTURE OF THE COMPLEX OF HCAII WITH CAFFEIC ACID (PDB entry 6YRI)
Macromolecule: Carbonic anhydrase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 262 residues
Sequence: MGMSHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHAFNVEFDDSQDKAVLKGGPLDGTYRLIQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDFGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTKGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLLECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.6
R work: 0.159
R free: 0.1925
Average B factor: 12.2197
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 1.3 M sodium citrate, 0.1 M Tris-HCl, pH 8.5
Matthews coefficient: 2.07
Solvent content (%): 40.6
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: 2021-03-31