Structure of PDB 5hmy Chain A

Receptor sequence

>5hmyA (length=591) Species: 11069 (dengue virus type 3)

NMDVIGERIKRIKEEHNSTWHYDDENPYKTWAYHGSYEVKATGSASSMIN
GVVKLLTKPWDVVPMVTQMAMTDTTPFGQQRVFKEKVDTRTPRPLPGTRK
VMEITAEWLWRTLGRNKRPRLCTREEFTKKVRTNAADSAKAAVEDEEFWK
LVDRERELHKLGKCGSCVYNMSRAIWYMWLGVRYLEFEALGFLNEDHWFS
RENSYSGVEGEGLHKLGYILRDISKIPGGAMYADDTAGWDTRITEDDLHN
EEKIIQQMDPEHRQLANAIFKLTYQNKVVKVQRPTPTGTVMDIISRKDQR
GSGQVGTYGLNTFTNMEAQLVRQMEGEGVLTKADLENPHLLEKKITQWLE
TKGVERLKRMAISGDDCVVKPIDDRFANALLALNDMGKVRKDIPQWQPSK
GWHDWQQVPFCSHHFHELIMKDGRKLVVPCRPQDELIGRARISQGAGWSL
RETACLGKAYAQMWSLMYFHRRDLRLASNAICSAVPVHWVPTSRTTWSIH
AHHQWMTTEDMLTVWNRVWIEENPWMEDKTPVTTWENVPYLGKREDQWCG
SLIGLTSRATWAQNIPTAIQQVRSLIGNEEFLDYMPSMKRF

3D structure

• PDB: 5hmy Discovery of Potent Non-Nucleoside Inhibitors of Dengue Viral RNA-Dependent RNA Polymerase from a Fragment Hit Using Structure-Based Drug Design.
• Chain: A
• Resolution: 2.1 Å

Enzymatic activity

• Enzyme Commision number: 2.1.1.56: mRNA (guanine-N(7))-methyltransferase.
  2.1.1.57: methyltransferase cap1.
  2.7.7.48: RNA-directed RNA polymerase.
  3.4.21.91: flavivirin.
  3.6.1.15: nucleoside-triphosphate phosphatase.
  3.6.4.13: RNA helicase.

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	ZN	A	H712 H714 C728 C847	H414 H416 C430 C549
BS02	ZN	A	E437 H441 C446 C449	E155 H159 C164 C167
BS03	LNY	A	L511 C709 R729 M761 M765 T794 S796 H798 A799 H800 Q802 W803	L213 C411 R431 M463 M467 T496 S498 H500 A501 H502 Q504 W505	MOAD: ic50=0.5uM PDBbind-CN: -logKd/Ki=6.30,IC50=0.5uM

Gene Ontology

Molecular Function

• GO:0003968 RNA-dependent RNA polymerase activity
• GO:0005524 ATP binding

Biological Process

• GO:0039694 viral RNA genome replication

External links

• PDB: RCSB:5hmy, PDBe:5hmy, PDBj:5hmy
• PDBsum: 5hmy
• PubMed: 26984786
• UniProt: Q6YMS4|POLG_DEN3S Genome polyprotein (Gene Name=pol)