6FJT | pdb_00006fjt

4-chloro-benzamidine in complex with thrombin

PDB DOI: https://doi.org/10.2210/pdb6FJT/pdb

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

Deposited: 2018-01-23 Released: 2019-02-06
Deposition Author(s): Abazi, N., Heine, A., Klebe, G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.27 Å
R-Value Free:
0.151 (Depositor), 0.153 (DCC)
R-Value Work:
0.133 (Depositor), 0.136 (DCC)
R-Value Observed:
0.134 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

4-chloro-benzamidine in complex with thrombin

Abazi, A., Heine, A., Klebe, G.

To be published.

Macromolecule Content

Total Structure Weight: 34.55 kDa
Atom Count: 2,749
Modeled Residue Count: 290
Deposited Residue Count: 290
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Prothrombin	A [auth L]	28	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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00734
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Prothrombin	B [auth H]	251	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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00734
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain B [auth H]	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	C [auth I]	11	Hirudo medicinalis	Mutation(s): 0

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG (Subject of Investigation/LOI) Query on NAG Download:Ideal Coordinates CCD File SDF format, chain L [auth H] MOL2 format, chain L [auth H] mmCIF format, chain L [auth H]	L [auth H]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain L [auth H] Interactions & Density Focus chain L [auth H]
DKQ (Subject of Investigation/LOI) Query on DKQ Download:Ideal Coordinates CCD File SDF format, chain F [auth H] MOL2 format, chain F [auth H] mmCIF format, chain F [auth H]	F [auth H]	4-chloranylbenzenecarboximidamide C₇ H₇ Cl N₂ LFCUMSZYMJRUHD-UHFFFAOYSA-N		Interactions Focus chain F [auth H] Interactions & Density Focus chain F [auth H]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain J [auth H] MOL2 format, chain J [auth H] mmCIF 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 K [auth H] MOL2 format, chain K [auth H] mmCIF format, chain K [auth H]	K [auth H]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain K [auth H] Interactions & Density Focus chain K [auth H]
DMS Query on DMS Download:Ideal Coordinates CCD File SDF format, chain G [auth H] SDF format, chain H SDF format, chain I [auth H] MOL2 format, chain G [auth H] MOL2 format, chain H MOL2 format, chain I [auth H] mmCIF format, chain G [auth H] mmCIF format, chain H mmCIF format, chain I [auth H]	G [auth H], H, I [auth H]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain G [auth H] Focus chain H Focus chain I [auth H] Interactions & Density Focus chain G [auth H] Focus chain H Focus chain I [auth H]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain D [auth H] SDF format, chain E [auth H] MOL2 format, chain D [auth H] MOL2 format, chain E [auth H] mmCIF format, chain D [auth H] mmCIF format, chain E [auth H]	D [auth H], E [auth H]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain D [auth H] Focus chain E [auth H] Interactions & Density Focus chain D [auth H] Focus chain E [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: 1.27 Å
R-Value Free: 0.151 (Depositor), 0.153 (DCC)
R-Value Work: 0.133 (Depositor), 0.136 (DCC)
R-Value Observed: 0.134 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.2	α = 90
b = 71.319	β = 100.31
c = 72.435	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing
Coot	model building

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2019-02-06

Deposition Author(s):

Abazi, N.

Heine, A.

Klebe, G.

Revision History (Full details and data files)

Version 1.0: 2019-02-06
Type: Initial release
Version 1.1: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 1.2: 2024-01-17
Changes: Data collection, Database references, Refinement description, Structure summary
Version 1.3: 2024-10-16
Changes: Structure summary