PDB Entry (5in4) Download |
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Visualizer: MichelaNGLo |
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PDB ID: 5in4 | Resolution: 1.6 Å | Exp. Method: X-RAY DIFFRACTION |
PMID: 27434622 | DOI: 10.1021/acschembio.6b00460 | |
Protein |
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Protein Name: GDP-mannose 4,6 dehydratase | |
Protein Class: TRANSCRIPTION REGULATOR | |
Uniprot ID/ACC: O60547 (GMDS_HUMAN) | Organism: Homo sapiens |
Gene Symbol: GMDS | Gene ID: 2762 |
Pocket Descriptors | |
Volume: 1040.83 | Depth: 51.7705 |
Hydrophobicity: 0.657264 | Drug Score: 0.950528 |
Pocket Similarity: Calculate |
Ligand |
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Ligand Name: [(2R,3S,4R,5R)-5-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3S,4R,5S,6R)-3,4,5-trihydroxy-6-(trifluoromethyl)tetrahydro-2H-pyran-2-yl dihydrogen diphosphate (non-preferred name) | ||
HET ID: 6CK | PubChem: 135567155 | |
DrugBank: - | ChEMBL: - | |
Canonical SMILES: O[C@@H]1[C@@H](CO[P@@](=O)(O[P@](=O)(O[C@H]2O[C@H]([C@H]([C@H]([C@@H]2O)O)O)C(F)(F)F)O)O)O[C@H]([C@@H]1O)n1cnc2c1nc(N)[nH]c2=O | ||
Standard InChI: InChI=1S/C16H22F3N5O15P2/c17-16(18,19)10-7(27)6(26)9(29)14(37-10)38-41(33,34)39-40(31,32)35-1-3-5(25)8(28)13(36-3)24-2-21-4-11(24)22-15(20)23-12(4)30/h2-3,5-10,13-14,25-29H,1H2,(H,31,32)(H,33,34)(H3,20,22,23,30)/t3-,5-,6-,7+,8-,9+,10-,13-,14-/m1/s1 | ||
Molecular Formula: C16H22F3N5O15P2 | Mol. Weight: 643.3131 | Heavy Atoms: 41 |
Charge: 0 | Is Chiral: True | logP: -2.4773 |
HBD: 9 | HBA: 19 | TPSA: 331.11 |
#Bonds: 54 | #Rotatable Bonds: 9 | Shape Complexity: 0.6875 |
Stereocomplexity: 0.6875 | Ligand Type: Small Molecule |
Binding Affinity |
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Database Name | Value |
Binding MOAD | Kd : 11000 nM |