Download MendeleyNew 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
- DOI: 10.1039/C2MD20074K
4E7R
Thrombin in complex with 3-amidinophenylalanine inhibitor
- DOI: 10.2210/pdb4E7R/pdb
- Classification: HYDROLASE/HYDROLASE INHIBITOR
- Organism(s): Homo sapiens, Hirudo medicinalis
- Mutation(s): No
- Deposited: 2012-03-19 Released: 2012-06-20
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.25 Å
- R-Value Free: 0.223
- R-Value Work: 0.171
- R-Value Observed: 0.174
wwPDB Validation 3D Report Full Report
This is version 1.4 of the entry. See complete history.
Literature
Macromolecules
Find similar proteins by:
(by identity cutoff) | Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Thrombin light chain | A [auth L], B [auth M] | 36 | Homo sapiens | Mutation(s): 0 Gene Names: F2 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 | |||||
Protein Feature ViewExpand | |||||
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Find similar proteins by:
(by identity cutoff) | Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Thrombin heavy chain | D [auth G], C [auth H] | 259 | Homo sapiens | Mutation(s): 0 Gene Names: F2 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 | |||||
Protein Feature ViewExpand | |||||
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- Find similar proteins by: Sequence | Structure
Entity ID: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Hirudin variant-2 | E [auth I], F [auth J] | 11 | Hirudo medicinalis | Mutation(s): 0 |  |
UniProt | |||||
Find proteins for P09945 (Hirudo medicinalis) Explore P09945 Go to UniProtKB: P09945 | |||||
Protein Feature ViewExpand | |||||
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Small Molecules
| Ligands 5 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| 0NW Query on 0NW | 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 |  | Ligand Interaction | |
| NAG Query on NAG | G [auth H], N [auth G] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |  | Ligand Interaction | |
| PO4 Query on PO4 | K [auth H], R [auth G] | PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K |  | Ligand Interaction | |
| GOL Query on GOL | L [auth H], M [auth H], S [auth G] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | Ligand Interaction | |
| NA Query on NA | I [auth H], J [auth H], P [auth G], Q [auth G] | SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N |  | Ligand Interaction | |
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| TYS Query on TYS | E [auth I], F [auth J] | L-PEPTIDE LINKING | C9 H11 N O6 S |  | TYR |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.25 Å
- R-Value Free: 0.223
- R-Value Work: 0.171
- R-Value Observed: 0.174
- Space Group: P 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 50.242 | α = 97.61 |
| b = 50.284 | β = 96.61 |
| c = 71.837 | γ = 90.57 |
| Software Name | Purpose |
|---|---|
| MAR345dtb | data collection |
| PHASER | phasing |
| PHENIX | refinement |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
Entry History
Deposition Data
- Deposited Date: 2012-03-19
- Released Date: 2012-06-20 Deposition Author(s): Ruehmann, E., Heine, A., Klebe, G.
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
