4E7R

Thrombin in complex with 3-amidinophenylalanine inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 
    0.223 (Depositor), 0.210 (DCC) 
  • R-Value Work: 
    0.171 (Depositor), 0.160 (DCC) 
  • R-Value Observed: 
    0.174 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 0NWClick on this verticalbar to view detailsBest fitted NAGClick on this verticalbar to view details

This is version 1.7 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
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Thrombin light chainA [auth L],
B [auth M]
36Homo sapiensMutation(s): 0 
EC: 3.4.21.5
UniProt & NIH Common Fund Data Resources
Find proteins for P00734 (Homo sapiens)
Explore P00734 
Go to UniProtKB:  P00734
PHAROS:  P00734
GTEx:  ENSG00000180210 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00734
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Thrombin heavy chainC [auth H],
D [auth G]
259Homo sapiensMutation(s): 0 
EC: 3.4.21.5
UniProt & NIH Common Fund Data Resources
Find proteins for P00734 (Homo sapiens)
Explore P00734 
Go to UniProtKB:  P00734
PHAROS:  P00734
GTEx:  ENSG00000180210 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00734
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P00734-1
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Hirudin variant-2E [auth I],
F [auth J]
11Hirudo medicinalisMutation(s): 0 
UniProt
Find proteins for P09945 (Hirudo medicinalis)
Explore P09945 
Go to UniProtKB:  P09945
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP09945
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
0NW
Query on 0NW

Download Ideal Coordinates CCD File 
H,
O [auth G]
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
NAG
Query on NAG

Download Ideal Coordinates CCD File 
G [auth H],
N [auth G]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
K [auth H],
R [auth G]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL
Query on GOL

Download Ideal Coordinates CCD File 
L [auth H],
M [auth H],
S [auth G]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
I [auth H],
J [auth H],
P [auth G],
Q [auth G]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
TYS
Query on TYS
E [auth I],
F [auth J]
L-PEPTIDE LINKINGC9 H11 N O6 STYR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free:  0.223 (Depositor), 0.210 (DCC) 
  • R-Value Work:  0.171 (Depositor), 0.160 (DCC) 
  • R-Value Observed: 0.174 (Depositor) 
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
MAR345dtbdata collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 0NWClick on this verticalbar to view detailsBest fitted NAGClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-06-20
    Type: Initial release
  • Version 1.1: 2012-12-12
    Changes: Other
  • Version 1.2: 2013-03-13
    Changes: Other
  • Version 1.3: 2016-08-17
    Changes: Database references
  • Version 1.4: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.5: 2023-09-13
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 1.6: 2023-12-06
    Changes: Data collection
  • Version 1.7: 2024-10-09
    Changes: Structure summary