4UE7

Thrombin in complex with 1-amidinopiperidine

PDB DOI: https://doi.org/10.2210/pdb4UE7/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens, Hirudo medicinalis
Mutation(s): No

Deposited: 2014-12-16 Released: 2015-08-26
Deposition Author(s): Ruehmann, E., Heine, A., Klebe, G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.13 Å
R-Value Free: 0.139
R-Value Work: 0.123
R-Value Observed: 0.124

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.2 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 35.71 kDa
Atom Count: 2,814
Modelled Residue Count: 291
Deposited Residue Count: 298
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 HEAVY CHAIN	A [auth H]	258	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

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HIRUDIN VARIANT-2	B [auth I]	12	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

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
THROMBIN LIGHT CHAIN	C [auth L]	28	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

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain P [auth H] MOL2 format, chain P [auth H]	P [auth H]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain P [auth H] Interactions & Density Focus chain P [auth H]
MRZ Query on MRZ Download Ideal Coordinates CCD File SDF format, chain O [auth H] MOL2 format, chain O [auth H]	O [auth H]	piperidine-1-carboximidamide C₆ H₁₃ N₃ QUUYRYYUKNNNNS-UHFFFAOYSA-N		Interactions Focus chain O [auth H] Interactions & Density Focus chain O [auth H]
IOD Query on IOD Download Ideal Coordinates CCD File SDF format, chain D [auth H] MOL2 format, chain D [auth H]	D [auth H]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M		Interactions Focus chain D [auth H] Interactions & Density Focus chain D [auth H]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain J [auth H] MOL2 format, chain J [auth H]	J [auth H]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain J [auth H] Interactions & Density Focus chain J [auth H]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain F [auth H] SDF format, chain G [auth H] SDF format, chain E [auth H] MOL2 format, chain F [auth H] MOL2 format, chain G [auth H] MOL2 format, chain E [auth H]	E [auth H], F [auth H], G [auth H]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth H] Focus chain F [auth H] Focus chain G [auth H] Interactions & Density Focus chain E [auth H] Focus chain F [auth H] Focus chain G [auth H]
DMS Query on DMS Download Ideal Coordinates CCD File SDF format, chain L [auth H] SDF format, chain N [auth H] SDF format, chain K [auth H] MOL2 format, chain L [auth H] MOL2 format, chain N [auth H] MOL2 format, chain K [auth H]	K [auth H], L [auth H], N [auth H]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain K [auth H] Focus chain L [auth H] Focus chain N [auth H] Interactions & Density Focus chain K [auth H] Focus chain L [auth H] Focus chain N [auth H]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain M [auth H] MOL2 format, chain M [auth H]	M [auth H]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain M [auth H] Interactions & Density Focus chain M [auth H]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain H SDF format, chain I [auth H] MOL2 format, chain H MOL2 format, chain I [auth H]	H, I [auth H]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain H Focus chain I [auth H] Interactions & Density Focus chain H Focus chain I [auth H]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TYS Query on TYS	B [auth I]	L-PEPTIDE LINKING	C₉ H₁₁ N O₆ S		TYR

Binding Affinity Annotations
ID	Source	Binding Affinity
MRZ	BindingDB: 4UE7	Ki: min: 150, max: 1.11e+5 (nM) from 2 assay(s)
	BindingDB: 4UE7	Kd: min: 1.07e+5, max: 1.97e+5 (nM) from 2 assay(s)
	Binding MOAD: 4UE7	Kd: 1.07e+5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.13 Å
R-Value Free: 0.139
R-Value Work: 0.123
R-Value Observed: 0.124
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.262	α = 90
b = 71.483	β = 100.3
c = 72.44	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2015-08-26

Deposition Author(s):

Ruehmann, E.

Heine, A.

Klebe, G.

Revision History (Full details and data files)

Version 1.0: 2015-08-26
Type: Initial release
Version 1.1: 2015-09-23
Changes: Database references
Version 2.0: 2019-10-23
Changes: Atomic model, Data collection, Derived calculations, Other
Version 2.1: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 2.2: 2023-12-20
Changes: Data collection, Database references, Refinement description, Structure summary

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Help and Resources

4UE7

Thrombin in complex with 1-amidinopiperidine

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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Entity ID: 2

UniProt

Entity Groups

Sequence Annotations

Expand

Entity ID: 3

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)