4E7R

Thrombin in complex with 3-amidinophenylalanine inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.171 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

New 3-amidinophenylalanine-derived inhibitors of matriptase

Hammami, M.Ruehmann, E.Mauerer, M.Heine, A.Guetschow, M.Klebe, G.Steinmetzer, T.

(2012) MEDCHEMCOMM 3: 807-813


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Thrombin light chain
L, M
36Homo sapiensMutation(s): 0 
Gene Names: F2
EC: 3.4.21.5
Find proteins for P00734 (Homo sapiens)
Go to Gene View: F2
Go to UniProtKB:  P00734
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Thrombin heavy chain
H, G
259Homo sapiensMutation(s): 0 
Gene Names: F2
EC: 3.4.21.5
Find proteins for P00734 (Homo sapiens)
Go to Gene View: F2
Go to UniProtKB:  P00734
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Hirudin variant-2
I, J
11Hirudo medicinalisMutation(s): 0 
Find proteins for P09945 (Hirudo medicinalis)
Go to UniProtKB:  P09945
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

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Download CCD File 
G, H
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
NA
Query on NA

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Download CCD File 
G, H
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

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G, H
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
0NW
Query on 0NW

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Download CCD File 
G, H
3-[(2S)-3-[4-(2-aminoethyl)piperidin-1-yl]-2-{[(2',4'-dichlorobiphenyl-3-yl)sulfonyl]amino}-3-oxopropyl]benzenecarboximidamide
C29 H33 Cl2 N5 O3 S
ZLCINVZAICQINL-MHZLTWQESA-N
 Ligand Interaction
NAG
Query on NAG

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Download CCD File 
G, H
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TYS
Query on TYS
I, J
L-PEPTIDE LINKINGC9 H11 N O6 STYR
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
ONWKi: 20 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.171 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 50.242α = 97.61
b = 50.284β = 96.61
c = 71.837γ = 90.57
Software Package:
Software NamePurpose
PHASERphasing
HKL-2000data scaling
HKL-2000data reduction
PHENIXrefinement
MAR345dtbdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-06-20
    Type: Initial release
  • Version 1.1: 2012-12-12
    Type: Other
  • Version 1.2: 2013-03-13
    Type: Other
  • Version 1.3: 2016-08-17
    Type: Database references