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SMTL ID : 6gwe.1 (1 other biounit)

Crystal structure of Thrombin bound to P2 macrocycle

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

hetero-1-1-mer

Ligands

1 x ODB: (10S,14S,17R)-14-(3-carbamimidamidopropyl)-3-[[2-(hydroxymethyl)phenyl]methyl]-5,12,15-tris(oxidanylidene)-19-thia-3,6,13,16-tetrazatricyclo[19.4.0.0^{6,10}]pentacosa-1(21),22,24-triene-17-carboxamide(Non-covalent)

ODB.1:

21 residues within 4Å:

Chain A: H.43, Y.47, W.50, W.92, R.93, E.94, N.95, L.96, I.179, D.199, A.200, C.201, E.202, V.225, S.226, W.227, G.228, E.229, G.230, C.231, G.238

14 PLIP interactions:

14 interactions with chain A

Hydrophobic interactions: A:Y.47, A:W.50, A:L.96, A:I.179, A:W.227, A:W.227, A:E.229
Hydrogen bonds: A:E.202, A:W.227, A:W.227, A:G.228, A:G.228, A:G.230
Salt bridges: A:D.199

1 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG.2:

2 residues within 4Å:

Chain A: L.46, N.53

2 PLIP interactions:

2 interactions with chain A

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

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

EDO.3:	6 residues within 4Å: Chain A: I.167, V.168, R.170, C.173, F.186, C.187 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.170, A:C.187
EDO.4:	8 residues within 4Å: Chain A: S.176, T.177, W.227, G.228, E.229, K.236, Y.237, F.239 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.176, A:S.176, A:E.229, A:Y.237
EDO.5:	2 residues within 4Å: Chain A: E.124, A.127 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.124 Water bridges: A:E.124

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

NA.6:

3 residues within 4Å:

Chain A: D.232, R.233, K.236

3 PLIP interactions:

3 interactions with chain A

Hydrogen bonds: A:Y.190, A:K.236
Water bridges: A:Y.190

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Kale, S.S. et al., Thiol-to-amine cyclization reaction enables screening of large libraries of macrocyclic compounds and the generation of sub-kilodalton ligands. Sci Adv (2019)

Release Date

2019-09-25

Peptides

Thrombin heavy chain: A
Thrombin light chain: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Export Alignment

Secondary Structure
NoneDSSPPSIPREDSSpro

Colour Scheme

Fade MismatchesEnhance Mismatches

ChainUnique ChainRainbow2° StructureBfactorBfactor RangeSOAEntropyClustalHydrophobicSizeChargedPolarProlineSer/ThrCysteineAliphaticAromaticNo Colour

Background

3D Viewer
NGLPV2D

Thrombin heavy chain

Thrombin light chain

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