SMTL ID : 4udw.1

Thrombin in complex with 1-(2R)-2-amino-3-phenyl-propanoyl-N-(2, 5dichlorophenyl)methylpyrrolidine-2-carboxamide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.16 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

NA.1: 6 residues within 4Å: Chain A: D.232, R.233, D.234, G.235, K.236, Y.237 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.233, A:K.236 Water bridges: A:G.235 NA.2: 4 residues within 4Å: Chain A: K.174, D.175, T.177, R.178 No protein-ligand interaction detected (PLIP)

1 x N6L: D-phenylalanyl-N-(2,5-dichlorobenzyl)-L-prolinamide(Non-covalent)

N6L.3: 21 residues within 4Å: Chain A: H.43, Y.47, W.50, E.94, N.95, 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, G.238, F.239 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:Y.47, A:W.50, A:L.96, A:I.179, A:A.200, A:V.225, A:W.227 Hydrogen bonds: A:S.226, A:G.228, A:G.228

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

PO4.4: 6 residues within 4Å: Chain A: R.89, N.91, N.95, 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:D.97, A:R.180 Salt bridges: A:R.98, A:R.180

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 4 residues within 4Å: Chain A: R.170, I.181, T.182, D.183 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.170, A:R.170 Water bridges: A:R.170, A:D.183, A:D.183

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

NAG.6: 4 residues within 4Å: Chain A: L.46, P.48, N.53, W.92 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

THROMBIN HEAVY CHAIN: A
HIRUDIN VARIANT-2: B
THROMBIN LIGHT CHAIN: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
I

C
L

THROMBIN HEAVY CHAIN

HIRUDIN VARIANT-2

THROMBIN LIGHT CHAIN

Related Entries With Identical Sequence