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SMTL ID : 6rot.1

Thrombin in complex with MI2105

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.34 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x KDQ: (2~{S})-~{N}-[[5-chloranyl-2-(hydroxymethyl)phenyl]methyl]-1-[2-[(phenylmethyl)sulfonylamino]ethanoyl]pyrrolidine-2-carboxamide(Non-covalent)

KDQ.1:

21 residues within 4Å:

Chain B: H.43, Y.47, W.50, E.94, N.95, L.96, I.173, D.193, A.194, C.195, E.196, S.199, V.219, S.220, W.221, G.222, E.223, G.224, C.225, G.232, F.233

11 PLIP interactions:

11 interactions with chain B

Hydrophobic interactions: B:Y.47, B:W.50, B:L.96, B:I.173, B:V.219, B:W.221, B:W.221
Hydrogen bonds: B:S.220, B:G.222, B:G.222
Water bridges: B:G.224

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

NAG.2:

4 residues within 4Å:

Chain B: L.46, P.48, N.53, W.92

2 PLIP interactions:

2 interactions with chain B

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

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

PO4.3:

6 residues within 4Å:

Chain B: R.89, N.91, D.97, R.98, R.174, T.176

12 PLIP interactions:

12 interactions with chain B

Hydrogen bonds: B:N.91, B:D.97, B:D.97, B:D.97
Water bridges: B:R.89, B:R.89, B:E.94, B:R.174, B:R.174, B:R.174
Salt bridges: B:R.98, B:R.174

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

DMS.4:	7 residues within 4Å: Chain B: L.130, Q.131, A.132, I.161, V.162, R.164, F.180 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.164
DMS.7:	4 residues within 4Å: Chain B: E.124, T.125, S.128, F.209 2 PLIP interactions: 2 interactions with chain B Water bridges: B:S.128 pi-Cation interactions: B:F.209
DMS.8:	1 residues within 4Å: Chain B: R.172 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.172

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

NA.5:	1 residues within 4Å: Chain B: F.209 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:F.209
NA.6:	6 residues within 4Å: Chain B: D.226, R.227, D.228, G.229, K.230, Y.231 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.230, B:K.230 Water bridges: B:G.229, B:G.232

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

2019-11-27

Peptides

Prothrombin: A
Prothrombin: B
Hirudin variant-2: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
L

B
H

C
A

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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Background

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