6SJU | pdb_00006sju

Human kallikrein 7 with aromatic coumarinic ester compound 3 covalently bound to H57


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 
    0.221 (Depositor), 0.213 (DCC) 
  • R-Value Work: 
    0.174 (Depositor), 0.172 (DCC) 
  • R-Value Observed: 
    0.175 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 6SJU

Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Structural Studies on the Inhibitory Binding Mode of Aromatic Coumarinic Esters to Human Kallikrein-Related Peptidase 7.

Hanke, S.Tindall, C.A.Pippel, J.Ulbricht, D.Pirotte, B.Reboud-Ravaux, M.Heiker, J.T.Strater, N.

(2020) J Med Chem 63: 5723-5733

  • DOI: https://doi.org/10.1021/acs.jmedchem.9b01806
  • Primary Citation Related Structures: 
    6SHH, 6SHI, 6SJU, 6Y4S

  • PubMed Abstract: 

    The serine protease kallikrein-related peptidase 7 (KLK7) is a member of the human tissue kallikreins. Its dysregulation leads to pathophysiological inflammatory processes in the skin. Furthermore, it plays a role in several types of cancer. For the treatment of KLK7-associated diseases, coumarinic esters have been developed as small-molecule enzyme inhibitors. To characterize the inhibition mode of these inhibitors, we analyzed structures of the inhibited protease by X-ray crystallography. Electron density shows the inhibitors covalently attached to His57 of the catalytic triad. This confirms the irreversible character of the inhibition process. Upon inhibitor binding, His57 undergoes an outward rotation; thus, the catalytic triad of the protease is disrupted. Besides, the halophenyl moiety of the inhibitor was absent in the final enzyme-inhibitor complex due to the hydrolysis of the ester linkage. With these results, we analyze the structural basis of KLK7 inhibition by the covalent attachment of aromatic coumarinic esters.


  • Organizational Affiliation
    • Institute of Bioanalytical Chemistry, Center for Biotechnology and Biomedicine, Leipzig University, Deutscher Platz 5, 04103 Leipzig, Germany.

Macromolecule Content 

  • Total Structure Weight: 209.12 kDa 
  • Atom Count: 15,842 
  • Modeled Residue Count: 1,792 
  • Deposited Residue Count: 1,792 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Kallikrein-7
A, B, C, D, E
A, B, C, D, E, F, G, H
224Homo sapiensMutation(s): 0 
Gene Names: KLK7PRSS6SCCE
EC: 3.4.21.117
UniProt & NIH Common Fund Data Resources
Find proteins for P49862 (Homo sapiens)
Explore P49862 
Go to UniProtKB:  P49862
PHAROS:  P49862
GTEx:  ENSG00000169035 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49862
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
LFW

Query on LFW



Download:Ideal Coordinates CCD File
HA [auth B]
JC [auth F]
JD [auth H]
LB [auth D]
T [auth A]
HA [auth B],
JC [auth F],
JD [auth H],
LB [auth D],
T [auth A],
UC [auth G],
WB [auth E],
XA [auth C]
(3-iodanylphenyl) 6-methyl-2-oxidanylidene-chromene-3-carboxylate
C17 H11 I O4
OUKFXYLCMXELAC-UHFFFAOYSA-N
EPE

Query on EPE



Download:Ideal Coordinates CCD File
VC [auth H],
WC [auth H]
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
PGE

Query on PGE



Download:Ideal Coordinates CCD File
I [auth A]
J [auth A]
MB [auth E]
U [auth B]
XB [auth F]
I [auth A],
J [auth A],
MB [auth E],
U [auth B],
XB [auth F],
YA [auth D]
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
AA [auth B]
AB [auth D]
AC [auth F]
AD [auth H]
BA [auth B]
AA [auth B],
AB [auth D],
AC [auth F],
AD [auth H],
BA [auth B],
BB [auth D],
BC [auth F],
BD [auth H],
CA [auth B],
CB [auth D],
CC [auth F],
CD [auth H],
DA [auth B],
DB [auth D],
DC [auth F],
DD [auth H],
EA [auth B],
EB [auth D],
EC [auth F],
ED [auth H],
FA [auth B],
FB [auth D],
FC [auth F],
FD [auth H],
GA [auth B],
GB [auth D],
GC [auth F],
GD [auth H],
HB [auth D],
HC [auth F],
HD [auth H],
IA [auth C],
IB [auth D],
IC [auth F],
ID [auth H],
JA [auth C],
JB [auth D],
K [auth A],
KA [auth C],
KB [auth D],
KC [auth G],
L [auth A],
LA [auth C],
LC [auth G],
M [auth A],
MA [auth C],
MC [auth G],
N [auth A],
NA [auth C],
NB [auth E],
NC [auth G],
O [auth A],
OA [auth C],
OB [auth E],
OC [auth G],
P [auth A],
PA [auth C],
PB [auth E],
PC [auth G],
Q [auth A],
QA [auth C],
QB [auth E],
QC [auth G],
R [auth A],
RA [auth C],
RB [auth E],
RC [auth G],
S [auth A],
SA [auth C],
SB [auth E],
SC [auth G],
TA [auth C],
TB [auth E],
TC [auth G],
UA [auth C],
UB [auth E],
V [auth B],
VA [auth C],
VB [auth E],
W [auth B],
WA [auth C],
X [auth B],
XC [auth H],
Y [auth B],
YB [auth F],
YC [auth H],
Z [auth B],
ZA [auth D],
ZB [auth F],
ZC [auth H]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free:  0.221 (Depositor), 0.213 (DCC) 
  • R-Value Work:  0.174 (Depositor), 0.172 (DCC) 
  • R-Value Observed: 0.175 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.65α = 90
b = 116.95β = 90
c = 291.19γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
BUSTERrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanyCRC 1052 - project C4

Revision History  (Full details and data files)

  • Version 1.0: 2020-05-20
    Type: Initial release
  • Version 1.1: 2020-06-24
    Changes: Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Refinement description
  • Version 1.3: 2024-11-20
    Changes: Structure summary