PDB Entry (5in4)

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Visualizer: MichelaNGLo

PDB ID: 5in4 Resolution: 1.6 Å Exp. Method: X-RAY DIFFRACTION
PMID: 27434622 DOI: 10.1021/acschembio.6b00460
Protein
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
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
Database Name Value
Binding MOAD Kd : 11000 nM