5LCT

Cocrystal structure of cAMP-dependent Protein Kinase (PKA) in complex with a R-methyl-piperazine substituted Fasudil-derivative (Ligand 02)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.61 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.143 
  • R-Value Observed: 0.144 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Cocrystal structure of cAMP-dependent Protein Kinase (PKA) in complex with different Fasudil-derivatives

Wienen-Schmidt, B.Jonker, H.R.A.Wulsdorf, T.Gerber, H.-D.Saxena, K.Kudlinzki, D.Sreeramulu, S.Parigi, G.Luchinat, C.Heine, A.Schwalbe, H.Klebe, G.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
cAMP-dependent protein kinase catalytic subunit alphaA353Cricetulus griseusMutation(s): 0 
Gene Names: PRKACA
EC: 2.7.11.11
UniProt
Find proteins for P25321 (Cricetulus griseus)
Explore P25321 
Go to UniProtKB:  P25321
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP25321
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
cAMP-dependent protein kinase inhibitor alphaB20Homo sapiensMutation(s): 0 
Gene Names: PKIAPRKACN1
UniProt & NIH Common Fund Data Resources
Find proteins for P61925 (Homo sapiens)
Explore P61925 
Go to UniProtKB:  P61925
PHAROS:  P61925
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP61925
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
6TY
Query on 6TY

Download Ideal Coordinates CCD File 
C [auth A]5-[(2~{R})-2-methylpiperazin-1-yl]sulfonylisoquinoline
C14 H17 N3 O2 S
BDVFVCGFMNCYPV-LLVKDONJSA-N
 Ligand Interaction
MPD
Query on MPD

Download Ideal Coordinates CCD File 
D [auth A](4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
MOH
Query on MOH

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A]
METHANOL
C H4 O
OKKJLVBELUTLKV-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
A L-PEPTIDE LINKINGC3 H8 N O6 PSER
TPO
Query on TPO
A L-PEPTIDE LINKINGC4 H10 N O6 PTHR
Binding Affinity Annotations 
IDSourceBinding Affinity
IQP BindingDB:  5LCT IC50: 6641 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.61 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.143 
  • R-Value Observed: 0.144 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.014α = 90
b = 73.7β = 90
c = 109.837γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research CouncilBelgium268145 - Project Acronym: DrugProfilBind

Revision History  (Full details and data files)

  • Version 1.0: 2018-01-17
    Type: Initial release