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SMTL ID : 9r8q.1

Structure of thrombin bound to BAY 3389934

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x 01: 2-(1-methylimidazol-2-yl)ethyl (2~{S})-3-[(5-chloranylthiophen-2-yl)carbonylamino]-2-[[2-ethyl-3-[(3~{S})-3-oxidanyl-2-oxidanylidene-pyrrolidin-1-yl]phenyl]sulfonylamino]propanoate

01.1:

22 residues within 4Å:

Chain B: H.43, Y.47, W.50, E.94, N.95, L.96, D.199, A.200, C.201, E.202, V.225, S.226, W.227, G.228, E.229, G.230, C.231, G.238, F.239, Y.240
Ligands: GOL.3, GOL.7

11 PLIP interactions:

11 interactions with chain B

Hydrophobic interactions: B:W.50, B:W.227
Hydrogen bonds: B:E.94, B:G.228, B:G.230, B:G.230, B:G.230
Water bridges: B:Y.47, B:Y.47, B:S.205
pi-Stacking: B:Y.47

1 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.2:

3 residues within 4Å:

Chain B: L.46, P.48, N.53

3 PLIP interactions:

3 interactions with chain B

Hydrophobic interactions: B:L.46, B:P.48
Hydrogen bonds: B:N.53

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.3:	4 residues within 4Å: Chain B: E.229, G.230, R.233 Ligands: 01.1 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.229, B:E.229, B:R.233, B:R.233
GOL.4:	4 residues within 4Å: Chain B: D.122, T.125, F.215, N.216 1 PLIP interactions: 1 interactions with chain B Water bridges: B:Y.220
GOL.7:	6 residues within 4Å: Chain B: N.143, E.146, C.201, E.202, G.230 Ligands: 01.1 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.143, B:G.230 Water bridges: B:E.146

4 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.5:	5 residues within 4Å: Chain B: R.89, N.91, D.97, R.98, R.180 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.91, B:R.98, B:R.180 Salt bridges: B:D.97
DMS.6:	6 residues within 4Å: Chain A: Y.27 Chain B: S.128, L.129, Q.131, Y.134, F.215 No protein-ligand interaction detected (PLIP)
DMS.8:	4 residues within 4Å: Chain B: L.130, I.167, R.170, F.186 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.170
DMS.9:	3 residues within 4Å: Chain B: D.175, S.176, K.236 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.236

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Beck, H. et al., Discovery of BAY 3389934 Hydrochloride: A Potent and Selective Small-Molecule Dual Factor IIa/Xa Inhibitor with Short Half-Life for the Acute Treatment of Sepsis-Induced Coagulopathy. J.Med.Chem. (2025)

Release Date

2025-06-18

Peptides

Prothrombin: A
Prothrombin: B
Hirudin-2: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
L

B
H

C
I

Export Alignment

Secondary Structure
NoneDSSPPSIPREDSSpro

Colour Scheme

Fade MismatchesEnhance Mismatches

ChainUnique ChainRainbow2° StructureBfactorBfactor RangeSOAEntropyClustalHydrophobicSizeChargedPolarProlineSer/ThrCysteineAliphaticAromaticNo Colour

Background

3D Viewer
NGLPV2D

Prothrombin

Prothrombin

Hirudin-2

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