3TU7 | pdb_00003tu7

Human alpha-thrombin complexed with N-(methylsulfonyl)-D-phenylalanyl-N-((1-carbamimidoyl-4-piperidinyl)methyl)-l-prolinamide (BMS-189664)

PDB DOI: https://doi.org/10.2210/pdb3TU7/pdb

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

Deposited: 2011-09-16 Released: 2011-10-12
Deposition Author(s): Malley, M., Sack, J.S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.49 Å
R-Value Free:
0.230 (Depositor), 0.262 (DCC)
R-Value Work:
0.159 (Depositor)
R-Value Observed:
0.163 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Molecular design and structure-activity relationships leading to the potent, selective, and orally active thrombin active site inhibitor BMS-189664.

Das, J., Kimball, S.D., Hall, S.E., Han, W.C., Iwanowicz, E., Lin, J., Moquin, R.V., Reid, J.A., Sack, J.S., Malley, M.F., Chang, C.Y., Chong, S., Wang-Iverson, D.B., Roberts, D.G., Seiler, S.M., Schumacher, W.A., Ogletree, M.L.

(2002) Bioorg Med Chem Lett 12: 45-49

PubMed: 11738570 Search on PubMed
DOI: https://doi.org/10.1016/s0960-894x(01)00667-9
Primary Citation Related Structures:
3TU7

PubMed Abstract:
A series of structurally novel small molecule inhibitors of human alpha-thrombin was prepared to elucidate their structure-activity relationships (SARs), selectivity and activity in vivo. BMS-189664 (3) is identified as a potent, selective, and orally active reversible inhibitor of human alpha-thrombin which is efficacious in vivo in a mouse lethality model, and at inhibiting both arterial and venous thrombosis in cynomolgus monkey models.

Organizational Affiliation

Bristol-Myers Squibb Pharmaceutical Research Institute, Princeton, NJ 08543-4000, USA. jagabandhu.das@bms.com

Macromolecule Content

Total Structure Weight: 35.9 kDa
Atom Count: 2,414
Modeled Residue Count: 292
Deposited Residue Count: 307
Unique protein chains: 3

Macromolecules

Find similar proteins by:

| 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% 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
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% 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-2	C [auth I]	12	Hirudo medicinalis	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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
0BM Query on 0BM 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]	N-(methylsulfonyl)-D-phenylalanyl-N-[(1-carbamimidoylpiperidin-4-yl)methyl]-L-prolinamide C₂₂ H₃₄ N₆ O₄ S UCVAQBJLJIKTFJ-MOPGFXCFSA-N		Interactions Focus chain D [auth H] Interactions & Density Focus chain D [auth H]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PTR Query on PTR	C [auth I]	L-PEPTIDE LINKING	C₉ H₁₂ N O₆ P		TYR

Biologically Interesting Molecules (External Reference)

1 Unique

Entity ID: 4
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000811 (0BM) Query on PRD_000811	D [auth H]	N-(METHYLSULFONYL)-D-PHENYLALANYL-N-[(1-CARBAMIMIDOYLPIPERIDIN-4-YL)METHYL]-L-PROLINAMIDE	Peptide-like / Thrombin inhibitor		Interactions Focus chain D [auth H] Interactions & Density Focus chain D [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.49 Å
R-Value Free: 0.230 (Depositor), 0.262 (DCC)
R-Value Work: 0.159 (Depositor)
R-Value Observed: 0.163 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 164.219	α = 90
b = 48.952	β = 90
c = 43.631	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2011-10-12

Deposition Author(s):

Malley, M.

Sack, J.S.

Revision History (Full details and data files)

Version 1.0: 2011-10-12
Type: Initial release
Version 1.1: 2012-12-12
Changes: Other
Version 1.2: 2024-11-20
Changes: Data collection, Database references, Derived calculations, Structure summary