3ZDU Chain A
Cyclin-dependent kinase-like 3 (CDKL3)
Inactive — 27.3%DFG-inαC-inType1 · 38R
Resolution
2.2 Å
R-value
0.217
Predicted activity confidence27.3%
Structure info
Alternate conformation—
Missing atoms15
Missing residues0
Salt bridge (KinCore)Saltbr-in
Sequence info
PDB sequence
MEMYETLGKVGEGSYGTVMKCKHKNTGQIVAIKIFYNKIAMREIKFLKQFHHENLVNLIEVFRQKKKIHLVFEFIDHTVLDELQHYCHGLESKRLRKYLFQILRAIDYLHSNNIIHRDIKPENILVSQSGITKLCDFGFARTDIYDDEVATRWYRAPELVLKDTSYGKPVDIWALGCMIIEMATGNPYLPSSSDLDLLHKIVLKVGNLSPHLQNIFSKSPIFAGVVLPQVQHPKNARKKYPKLNGLLADIVHACLQIDPADRISSSDLLHHEYFTRDGFIEKFMPELKAKLLQEAKV
UniProt reference sequence
YETLGKVGEGSYGTVMKCKHKNTGQIVAIKIFYERPEQSVNKIAMREIKFLKQFHHENLVNLIEVFRQKKKIHLVFEFIDHTVLDELQHYCHGLESKRLRKYLFQILRAIDYLHSNNIIHRDIKPENILVSQSGITKLCDFGFARTLAAPGDIYTDYVATRWYRAPELVLKDTSYGKPVDIWALGCMIIEMATGNPYLPSSSDLDLLHKIVLKVGNLSPHLQNIFSKSPIFAGVVLPQVQHPKNARKKYPKLNGLLADIVHACLQIDPADRISSSDLLHHEYF
Aligned reference sequence
YETL----------------GKVGEGS----------------YGTVMKCKH--KN------------------------------------TGQIVAIKIFY--ERPEQSV---------------------------NKIAMREIKFLKQF--------------------------HHENLVNLIEVFRQKK--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------KIHLVFEFID---------------HTVLDELQH--YCH------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GLESKRLRKYLFQILRAIDYLHSN---------------------------------------------NIIHRDI-----KPENILVSQ--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SGITKLCDFGFARTLAAPGDI--Y---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TDYVATRWYRAPELVLK--D-----------------------------TSYG-KPVDIWALGCMIIEMATG-----------------NPYLPS--------------------------------------------------SSDLDLLHKIVLK--VGNLSPHLQNIFSKSPIFAGVVLPQVQHPKNARKKYPKLN-----------------------------------------------------------------------GLLADIVHACLQIDPADRIS--------------SSDLLHHEYF
Shaded segments mark residues present in the UniProt reference but not resolved in this structure.
Projected alignment
YETL----------------GKVGEGS----------------YGTVMKCKH--KN------------------------------------TGQIVAIKIFY------------------------------------NKIAMREIKFLKQF--------------------------HHENLVNLIEVFRQKK--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------KIHLVFEFID---------------HTVLDELQH--YCH------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GLESKRLRKYLFQILRAIDYLHSN---------------------------------------------NIIHRDI-----KPENILVSQ--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SGITKLCDFGFART-----DI--Y---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DDEVATRWYRAPELVLK--D-----------------------------TSYG-KPVDIWALGCMIIEMATG-----------------NPYLPS--------------------------------------------------SSDLDLLHKIVLK--VGNLSPHLQNIFSKSPIFAGVVLPQVQHPKNARKKYPKLN-----------------------------------------------------------------------GLLADIVHACLQIDPADRIS--------------SSDLLHHEYF
Activation segment
DFGFART-----DI--Y---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DDEVATRWYRAPE
Binding pocket
GKVGEGSYGTVMKVAIKIFIAMREIKFLKQFHENLVNLIEVHLVFEFID_HTVLDELQHYLHSNNIIHRDIKPENILVLCDFGFA
Ligand info
Orthosteric ligand
38R
Allosteric ligand
None
Ligand typeType1
Consensus conformation
DFG conformationin
αC-helix conformationin
Predicted activityinactive
KinaDB — structure detail · data from Browse_each_pdb_structure.csv · PDB 3ZDU, Chain A