6T53

Thrombin in Complex with a D-Phe-Pro-p-benzylamine derivative

PDB DOI: https://doi.org/10.2210/pdb6T53/pdb

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

Deposited: 2019-10-15 Released: 2020-11-18
Deposition Author(s): Ngo, K., Abazi, N., Heine, A., Klebe, G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.35 Å
R-Value Free: 0.151
R-Value Work: 0.129
R-Value Observed: 0.131

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Thrombin in Complex with a D-Phe-Pro-p-benzylamine derivative

Ngo, K., Abazi, N., Heine, A., Klebe, G.

To be published.

Macromolecule Content

Total Structure Weight: 36.82 kDa
Atom Count: 2,823
Modelled Residue Count: 290
Deposited Residue Count: 306
Unique protein chains: 3

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Prothrombin	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00734
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Prothrombin	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% Identity50% Identity70% Identity90% Identity95% Identity100% 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
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 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
K73 (Subject of Investigation/LOI) Query on K73 Download Ideal Coordinates CCD File SDF format, chain H MOL2 format, chain H mmCIF format, chain H	H	(2~{S})-~{N}-[[4-(aminomethyl)phenyl]methyl]-1-[(2~{R})-2-azanyl-3-phenyl-propanoyl]pyrrolidine-2-carboxamide C₂₂ H₂₈ N₄ O₂ MTUGEKUGFKKRIV-UXHICEINSA-N		Interactions Focus chain H Interactions & Density Focus chain H
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain P [auth H] MOL2 format, chain P [auth H] mmCIF 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]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain O [auth H] MOL2 format, chain O [auth H] mmCIF format, chain O [auth H]	O [auth H]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain O [auth H] Interactions & Density Focus chain O [auth H]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain I [auth H] SDF format, chain J [auth H] SDF format, chain K [auth H] SDF format, chain M [auth H] SDF format, chain N [auth H] SDF format, chain L [auth H] MOL2 format, chain I [auth H] MOL2 format, chain J [auth H] MOL2 format, chain K [auth H] MOL2 format, chain M [auth H] MOL2 format, chain N [auth H] MOL2 format, chain L [auth H] mmCIF format, chain I [auth H] mmCIF format, chain J [auth H] mmCIF format, chain K [auth H] mmCIF format, chain M [auth H] mmCIF format, chain N [auth H] mmCIF format, chain L [auth H]	I [auth H] J [auth H] K [auth H] L [auth H] M [auth H] I [auth H], J [auth H], K [auth H], L [auth H], M [auth H], N [auth H]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth H] Focus chain J [auth H] Focus chain K [auth H] Focus chain L [auth H] Focus chain M [auth H] Focus chain N [auth H] Interactions & Density Focus chain I [auth H] Focus chain J [auth H] Focus chain K [auth H] Focus chain L [auth H] Focus chain M [auth H] Focus chain N [auth H]
DMS Query on DMS Download Ideal Coordinates CCD File SDF format, chain F [auth H] SDF format, chain G [auth H] MOL2 format, chain F [auth H] MOL2 format, chain G [auth H] mmCIF format, chain F [auth H] mmCIF format, chain G [auth H]	F [auth H], G [auth H]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain F [auth H] Focus chain G [auth H] Interactions & Density Focus chain F [auth H] Focus chain G [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]