PDB Entry (5in5)

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Visualizer: MichelaNGLo

PDB ID: 5in5 Resolution: 1.9 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: 1173.06 Depth: 45.6979
Hydrophobicity: 0.642393 Drug Score: 0.913437
Pocket Similarity: Calculate
Ligand
Ligand Name:   GUANOSINE-5'-DIPHOSPHATE-BETA-L-FUCOPYRANOSE
HET ID:   GFB PubChem:   10918995, 135398655
DrugBank:   - ChEMBL:   CHEMBL1229250
Canonical SMILES:   O[C@@H]1[C@@H](CO[P@](=O)(O[P@](=O)(O[C@H]2O[C@@H](C)[C@H]([C@H]([C@@H]2O)O)O)O)O)O[C@H]([C@@H]1O)n1cnc2c1nc(N)[nH]c2=O
Standard InChI:   InChI=1S/C16H25N5O15P2/c1-4-7(22)9(24)11(26)15(33-4)35-38(30,31)36-37(28,29)32-2-5-8(23)10(25)14(34-5)21-3-18-6-12(21)19-16(17)20-13(6)27/h3-5,7-11,14-15,22-26H,2H2,1H3,(H,28,29)(H,30,31)(H3,17,19,20,27)/t4-,5+,7+,8+,9+,10+,11-,14+,15+/m0/s1
Molecular Formula:   C16H25N5O15P2 Mol. Weight:   589.34174 Heavy Atoms:   38
Charge:   0 Is Chiral:   True logP:   -3.0197
HBD:   9 HBA:   19 TPSA:   331.11
#Bonds:   51 #Rotatable Bonds:   8 Shape Complexity:   0.6875
Stereocomplexity:   0.6875 Ligand Type:   Small Molecule
Binding Affinity
Database Name Value
Binding MOAD Kd : 35000 nM