4E7R

Thrombin in complex with 3-amidinophenylalanine inhibitor

PDB DOI: https://doi.org/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
Deposition Author(s): Ruehmann, E., Heine, A., Klebe, G.

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

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

DOI: https://doi.org/10.1039/C2MD20074K

Macromolecule Content

Total Structure Weight: 72.94 kDa
Atom Count: 5,034
Modelled Residue Count: 578
Deposited Residue Count: 612
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D 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 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 Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00734
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Thrombin heavy chain	C [auth H], D [auth G]	259	Homo sapiens	Mutation(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 Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00734
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain C [auth H] Focus chain D [auth G]	Go to GlyGen: P00734-1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D 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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P09945
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
0NW Query on 0NW Download Ideal Coordinates CCD File SDF format, chain H SDF format, chain O [auth G] MOL2 format, chain H MOL2 format, chain O [auth G] mmCIF format, chain H mmCIF format, chain O [auth G]	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		Interactions Focus chain H Focus chain O [auth G] Interactions & Density Focus chain H Focus chain O [auth G]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain G [auth H] SDF format, chain N [auth G] MOL2 format, chain G [auth H] MOL2 format, chain N [auth G] mmCIF format, chain G [auth H] mmCIF format, chain N [auth G]	G [auth H], N [auth G]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain G [auth H] Focus chain N [auth G] Interactions & Density Focus chain G [auth H] Focus chain N [auth G]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain K [auth H] SDF format, chain R [auth G] MOL2 format, chain K [auth H] MOL2 format, chain R [auth G] mmCIF format, chain K [auth H] mmCIF format, chain R [auth G]	K [auth H], R [auth G]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain K [auth H] Focus chain R [auth G] Interactions & Density Focus chain K [auth H] Focus chain R [auth G]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain L [auth H] SDF format, chain M [auth H] SDF format, chain S [auth G] MOL2 format, chain L [auth H] MOL2 format, chain M [auth H] MOL2 format, chain S [auth G] mmCIF format, chain L [auth H] mmCIF format, chain M [auth H] mmCIF format, chain S [auth G]	L [auth H], M [auth H], S [auth G]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain L [auth H] Focus chain M [auth H] Focus chain S [auth G] Interactions & Density Focus chain L [auth H] Focus chain M [auth H] Focus chain S [auth G]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain I [auth H] SDF format, chain J [auth H] SDF format, chain P [auth G] SDF format, chain Q [auth G] MOL2 format, chain I [auth H] MOL2 format, chain J [auth H] MOL2 format, chain P [auth G] MOL2 format, chain Q [auth G] mmCIF format, chain I [auth H] mmCIF format, chain J [auth H] mmCIF format, chain P [auth G] mmCIF format, chain Q [auth G]	I [auth H], J [auth H], P [auth G], Q [auth G]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain I [auth H] Focus chain J [auth H] Focus chain P [auth G] Focus chain Q [auth G] Interactions & Density Focus chain I [auth H] Focus chain J [auth H] Focus chain P [auth G] Focus chain Q [auth G]

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

Binding Affinity Annotations
ID	Source	Binding Affinity
ONW	PDBBind: 4E7R	Ki: 20 (nM) from 1 assay(s)

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 Package:

Software Name	Purpose
MAR345dtb	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

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
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

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Help and Resources

4E7R

Thrombin in complex with 3-amidinophenylalanine inhibitor

New 3-amidinophenylalanine-derived inhibitors of matriptase

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Entity ID: 2

UniProt & NIH Common Fund Data Resources

Entity Groups

Glycosylation

Sequence Annotations

Expand

Entity ID: 3

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)