SMTL ID : 5afz.1

Thrombin in complex with (2R)-2-(benzylsulfonylamino)-N-(2-((4- carbamimidoylphenyl)methylamino)-2-oxo-propyl)-3-phenyl-propanamide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.53 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

NA.1: 2 residues within 4Å: Chain A: R.233, K.236 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.236, A:K.236 Water bridges: A:G.235, A:G.238 NA.2: 2 residues within 4Å: Chain A: K.174, T.177 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.177

1 x UET: N-(BENZYLSULFONYL)-D-PHENYLALANYL-N-(4-CARBAMIMIDOYLBENZYL)GLYCINAMIDE(Non-covalent)

UET.3: 18 residues within 4Å: Chain A: H.43, Y.47, W.50, E.94, N.95, L.96, D.199, A.200, E.202, S.205, V.225, S.226, W.227, G.228, E.229, G.230, C.231, G.238 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:L.96, A:E.202, A:V.225, A:W.227 Hydrogen bonds: A:D.199, A:A.200, A:S.205, A:S.226, A:G.228, A:G.230, A:G.230 Water bridges: A:F.239

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.4: 4 residues within 4Å: Chain A: N.91, D.97, R.98, R.180 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.91, A:D.97, A:D.97 Water bridges: A:R.180, A:R.180 Salt bridges: A:R.98, A:R.180

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

NAG.5: 2 residues within 4Å: Chain A: L.46, N.53 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.46

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ruehmann, E. et al., Fragments Can Bind Either More Enthalpy or Entropy-Driven: Crystal Structures and Residual Hydration Pattern Suggest Why. J.Med.Chem. (2015)

Release Date

2015-08-26

Peptides

Prothrombin: A
Hirudin-2: B
Prothrombin: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
I

C
L

Prothrombin

Hirudin-2

Prothrombin

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