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SMTL ID : 5jfd.1

Thrombin in complex with (S)-N-(2-(aminomethyl)-5-chlorobenzyl)-1-((benzylsulfonyl)-D-arginyl)pyrrolidine-2-carboxamide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.46 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x 2TS: (2S)-N-[[2-(aminomethyl)-5-chloro-phenyl]methyl]-1-[(2R)-5-carbamimidamido-2-(phenylmethylsulfonylamino)pentanoyl]pyrrolidine-2-carboxamide(Non-covalent)

2TS.1:

22 residues within 4Å:

Chain B: H.43, Y.47, W.50, L.96, I.179, D.199, A.200, C.201, E.202, S.205, V.225, S.226, W.227, G.228, E.229, G.230, C.231, R.233, G.238, F.239, Y.240
Ligands: GOL.7

15 PLIP interactions:

15 interactions with chain B

Hydrophobic interactions: B:Y.47, B:W.50, B:W.50, B:A.200, B:V.225, B:W.227, B:E.229
Hydrogen bonds: B:S.205, B:S.226, B:G.228, B:G.230, B:G.230
Water bridges: B:T.177, B:E.229
Salt bridges: B:E.229

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

NAG.2:

4 residues within 4Å:

Chain B: L.46, P.48, N.53, W.92

2 PLIP interactions:

2 interactions with chain B

Hydrophobic interactions: B:L.46
Hydrogen bonds: B:N.53

2 x NA: SODIUM ION(Non-functional Binders)

NA.3:	4 residues within 4Å: Chain B: K.174, D.175, T.177, R.178 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.174
NA.4:	6 residues within 4Å: Chain B: D.232, R.233, D.234, G.235, K.236, Y.237 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.236, B:K.236 Water bridges: B:G.235, B:G.238

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5:	5 residues within 4Å: Chain B: R.89, N.91, D.97, R.98, R.180 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:R.89, B:R.89, B:N.91, B:D.97, B:R.98, B:R.98, B:R.180 Water bridges: B:D.97, B:D.97
GOL.7:	9 residues within 4Å: Chain B: L.27, C.28, H.43, W.50, K.52, E.202, G.203, S.205 Ligands: 2TS.1 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.27, B:K.52, B:G.203

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

DMS.6:

6 residues within 4Å:

Chain B: L.130, Q.131, A.132, I.167, R.170, F.186

1 PLIP interactions:

1 interactions with chain B

Hydrogen bonds: B:R.170

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Sandner, A. et al., Strategies for Late-Stage Optimization: Profiling Thermodynamics by Preorganization and Salt Bridge Shielding. J.Med.Chem. (2019)

Release Date

2017-05-24

Peptides

Prothrombin: A
Prothrombin: B
Hirudin variant-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 variant-2

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