1Y6B Chain A
Vascular endothelial growth factor receptor 2 (KDR)
Inactive — 0.0%DFG-outαC-inType1 · AAX
Resolution
2.1 Å
R-value
0.194
Predicted activity confidence0.0%
Structure info
Alternate conformation—
Missing atoms0
Missing residues5
Salt bridge (KinCore)Saltbr-in
Sequence info
PDB sequence
RLPYDASKWEFPRDRLKLGKPLGRGGQVIEADAFGIDKTATCRTVAVKMLKATHSEHRALMSELKILIHIGHHLNVVNLLGACTKPGGPLMVIVEFCKFGNLSTYLRSKRNEFVPYFLTLEHLICYSFQVAKGMEFLASRKCIHRDLAARNILLSEKNVVKICDFPLKWMAPETIFDRVYTIQSDVWSFGVLLWEIFSLGASPYPGVKIDEEFCRRLKEGTRMRAPDYTTPEMYQTMLDCWHGEPSQRPTFSELVEHLGNLLQANA
UniProt reference sequence
LKLGKPLGRGAFGQVIEADAFGIDKTATCRTVAVKMLKEGATHSEHRALMSELKILIHIGHHLNVVNLLGACTKPGGPLMVIVEFCKFGNLSTYLRSKRNEFVPYKTKGARFRQGKDYVGAIPVDLKRRLDSITSSQSSASSGFVEEKSLSDVEEEEAPEDLYKDFLTLEHLICYSFQVAKGMEFLASRKCIHRDLAARNILLSEKNVVKICDFGLARDIYKDPDYVRKGDARLPLKWMAPETIFDRVYTIQSDVWSFGVLLWEIFSLGASPYPGVKIDEEFCRRLKEGTRMRAPDYTTPEMYQTMLDCWHGEPSQRPTFSELVEHLGN
Aligned reference sequence
LKLG----------------KPLGRGA----------------FGQVIEADA--FGIDKTA-------------------------------TCRTVAVKMLK--EGATHSE---------------------------HRALMSELKILIHI--G-----------------------HHLNVVNLLGACTKPG--G-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PLMVIVEFCKF--------------GNLSTYLRS--KRNEFVPYKTKGARFRQGKDYVGAIPVDLKRRLDSITSSQSSASSGFVEEKSLSDVEEEEAPEDLYKD-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------FLTLEHLICYSFQVAKGMEFLASR---------------------------------------------KCIHRDL-----AARNILLSE--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------KNVVKICDFGLARDIYKDPDY--VRK-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GDARLPLKWMAPETIFD--------------------------------RVYT-IQSDVWSFGVLLWEIFSL--G--------------ASPYPG--V-----------------------------------------------KIDEEFCRRLKEG--TRMRAPDYTT-----------------------------------------------------------------------------------------------------PEMYQTMLDCWHGEPSQRPT--------------FSELVEHLGN
Shaded segments mark residues present in the UniProt reference but not resolved in this structure.
Projected alignment
LKLG----------------KPLGRG------------------GQVIEADA--FGIDKTA-------------------------------TCRTVAVKMLK----ATHSE---------------------------HRALMSELKILIHI--G-----------------------HHLNVVNLLGACTKPG--G-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PLMVIVEFCKF--------------GNLSTYLRS--KRNEFVPY-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------FLTLEHLICYSFQVAKGMEFLASR---------------------------------------------KCIHRDL-----AARNILLSE--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------KNVVKICDF-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PLKWMAPETIFD--------------------------------RVYT-IQSDVWSFGVLLWEIFSL--G--------------ASPYPG--V-----------------------------------------------KIDEEFCRRLKEG--TRMRAPDYTT-----------------------------------------------------------------------------------------------------PEMYQTMLDCWHGEPSQRPT--------------FSELVEHLGN
Activation segment
DF-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PLKWMAPE
Binding pocket
KPLGRG__GQVIEVAVKMLALMSELKILIHIGLNVVNLLGAMVIVEFCKFGNLSTYLRSFLASRKCIHRDLAARNILLICDF___
Ligand info
Orthosteric ligand
AAX
Allosteric ligand
None
Ligand typeType1
Consensus conformation
DFG conformationout
αC-helix conformationin
Predicted activityinactive
KinaDB — structure detail · data from Browse_each_pdb_structure.csv · PDB 1Y6B, Chain A