3EGK | pdb_00003egk

KNOBLE Inhibitor

PDB DOI: https://doi.org/10.2210/pdb3EGK/pdb

Classification: Blood Clotting/Hydrolase Inhibitor
Organism(s): Homo sapiens, Hirudo medicinalis
Mutation(s): No

Deposited: 2008-09-10 Released: 2008-09-30
Deposition Author(s): Baum, B., Heine, A., Klebe, G., Muenzel, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.312 (Depositor), 0.242 (DCC)
R-Value Work:
0.202 (Depositor), 0.204 (DCC)
R-Value Observed:
0.205 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.6 of the entry. See complete history.

Literature

KNOBLE: a knowledge-based approach for the design and synthesis of readily accessible small-molecule chemical probes to test protein binding

Gerlach, C., Munzel, M., Baum, B., Gerber, H.-D., Craan, T., Diederich, W.E., Klebe, G.

(2007) Angew Chem Int Ed Engl 46: 9105-9109

PubMed: 17955562 Search on PubMed
DOI: https://doi.org/10.1002/anie.200703323
Primary Citation Related Structures:
3EGK

Organizational Affiliation

Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032 Marburg, Germany.

Macromolecule Content

Total Structure Weight: 35.75 kDa
Atom Count: 2,411
Modeled Residue Count: 285
Deposited Residue Count: 306
Unique protein chains: 3

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thrombin light chain	A [auth L]	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00734
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Thrombin heavy chain	B [auth H]	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00734
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Hirudin variant-1	C [auth I]	11	N/A	Mutation(s): 0
UniProt
Find proteins for P01050 (Hirudo medicinalis) Explore P01050 Go to UniProtKB: P01050
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P01050
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
M18 Query on M18 Download:Ideal Coordinates CCD File SDF format, chain D [auth H] MOL2 format, chain D [auth H] mmCIF format, chain D [auth H]	D [auth H]	{(2S)-1-[N-(tert-butoxycarbonyl)glycyl]pyrrolidin-2-yl}methyl (3-chlorophenyl)acetate C₂₀ H₂₇ Cl N₂ O₅ ONXGIEJBNQLITK-INIZCTEOSA-N		Interactions Focus chain D [auth H] Interactions & Density Focus chain D [auth H]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain F [auth H] SDF format, chain E [auth H] MOL2 format, chain F [auth H] MOL2 format, chain E [auth H] mmCIF format, chain F [auth H] mmCIF format, chain E [auth H]	E [auth H], F [auth H]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain E [auth H] Focus chain F [auth H] Interactions & Density Focus chain E [auth H] Focus chain F [auth H]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.312 (Depositor), 0.242 (DCC)
R-Value Work: 0.202 (Depositor), 0.204 (DCC)
R-Value Observed: 0.205 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.2	α = 90
b = 71.43	β = 100.52
c = 72.58	γ = 90

Software Package:

Software Name	Purpose
MAR345	data collection
CNS	refinement
SHELXL-97	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2008-09-30

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2008-09-30
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2013-10-09
Changes: Derived calculations
Version 1.3: 2017-10-25
Changes: Refinement description
Version 1.4: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.5: 2023-11-15
Changes: Data collection
Version 1.6: 2024-10-30
Changes: Structure summary