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SMTL ID : 5jzy.1

Thrombin in complex with (S)-1-((R)-2-amino-3-cyclohexylpropanoyl)-N-(4-carbamimidoylbenzyl)pyrrolidine-2-carboxamide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.27 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 B: L.46, P.48, N.53, W.92

3 PLIP interactions:

3 interactions with chain B

Hydrophobic interactions: B:L.46, B:P.48
Hydrogen bonds: B:N.53

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

DMS.2:	7 residues within 4Å: Chain B: L.130, Q.131, A.132, I.167, V.168, R.170, F.186 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.170
DMS.3:	7 residues within 4Å: Chain A: Y.32, I.33 Chain B: S.128, L.129, Y.134, P.214, F.215 No protein-ligand interaction detected (PLIP)
DMS.7:	3 residues within 4Å: Chain B: S.176, G.235, K.236 No protein-ligand interaction detected (PLIP)

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

PO4.4:

7 residues within 4Å:

Chain B: R.89, N.91, N.95, D.97, R.98, R.180, T.182

6 PLIP interactions:

6 interactions with chain B

Hydrogen bonds: B:N.91, B:D.97
Water bridges: B:E.94, B:R.180
Salt bridges: B:R.98, B:R.180

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

NA.5:	5 residues within 4Å: Chain B: D.232, R.233, D.234, G.235, K.236 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.236, B:K.236 Water bridges: B:G.235, B:G.238
NA.6:	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

1 x 6OV: 3-cyclohexyl-D-alanyl-N-[(4-carbamimidoylphenyl)methyl]-L-prolinamide(Non-covalent)

6OV.8:

20 residues within 4Å:

Chain B: 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

13 PLIP interactions:

13 interactions with chain B

Hydrophobic interactions: B:Y.47, B:W.50, B:V.225, B:W.227
Hydrogen bonds: B:D.199, B:D.199, B:A.200, B:S.226, B:G.228, B:G.228
Water bridges: B:E.202, B:E.202, B:F.239

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

2017-06-07

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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