SMTL ID : 5af9.1

Thrombin in complex with 4-Methoxy-N-(2-pyridinyl)benzamide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.18 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

NAG.1: 4 residues within 4Å: Chain A: L.46, P.48, N.53, W.92 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.46, A:P.48, A:W.92 Hydrogen bonds: A:N.53

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

NA.2: 4 residues within 4Å: Chain A: K.174, D.175, T.177, R.178 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.174 NA.3: 6 residues within 4Å: Chain A: D.232, R.233, D.234, G.235, K.236, Y.237 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.236, A:K.236 Water bridges: A:G.235, A:G.238

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

DMS.4: 7 residues within 4Å: Chain A: L.130, Q.131, A.132, I.167, V.168, R.170, F.186 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.170 DMS.5: 4 residues within 4Å: Chain A: E.124, T.125, F.215 Ligands: GOL.8 1 PLIP interactions: 1 interactions with chain A pi-Cation interactions: A:F.215

1 x SJR: 4-methoxy-N-(pyridin-2-yl)benzamide(Non-covalent)

SJR.6: 16 residues within 4Å: Chain A: E.146, 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, Y.240 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:A.200, A:V.225 Hydrogen bonds: A:S.226, A:G.230, A:G.230 Water bridges: A:G.203

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

PO4.7: 5 residues within 4Å: Chain A: R.89, N.91, D.97, R.98, R.180 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:R.89, A:N.91, A:D.97 Water bridges: A:R.89, A:R.98, A:R.98, A:R.180 Salt bridges: A:R.98, A:R.180

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 8 residues within 4Å: Chain A: D.122, E.124, T.125, S.213, F.215, N.216, Y.220 Ligands: DMS.5 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.220, A:Y.220 Water bridges: A:D.122, A:N.216 GOL.9: 6 residues within 4Å: Chain A: H.87, R.89, R.98, N.184, R.245, L.246 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:H.87, A:R.98, A:R.98, A:N.184, A:R.245, A:R.245, A:R.245 Water bridges: A:R.89, A:D.97, A:T.182 GOL.10: 4 residues within 4Å: Chain A: R.170, D.183, H.242, R.245 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.183, A:D.183 Water bridges: A:H.242

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.11: 4 residues within 4Å: Chain A: R.170, I.181, T.182, D.183 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.170, A:R.170 Water bridges: A:D.183

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

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