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SMTL ID : 6t89.1

Thrombin in complex with (S)-N-(tert-butyl)-4-(3-(3-carbamimidoylphenyl)-2-((2',4'-dimethoxy-[1,1'-biphenyl])-3-sulfonamido)propanoyl)piperazine-1-carboxamide (MI-498)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x MUQ: 4-[(2~{S})-3-(3-carbamimidoylphenyl)-2-[[3-(4-methoxy-2-oxidanyl-phenyl)phenyl]sulfonylamino]propanoyl]-~{N}-methyl-piperazine-1-carboxamide(Non-covalent)

MUQ.1:

19 residues within 4Å:

Chain B: H.43, Y.47, W.50, 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

11 PLIP interactions:

11 interactions with chain B

Hydrophobic interactions: B:W.50, B:V.225, B:W.227, B:W.227
Hydrogen bonds: B:D.199, B:A.200, B:G.228, B:G.230, B:G.230, B:G.230
Water bridges: B:D.232

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

NAG.2:

2 residues within 4Å:

Chain B: L.46, N.53

1 PLIP interactions:

1 interactions with chain B

Hydrophobic interactions: B:L.46

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

NA.3:	2 residues within 4Å: Chain B: K.174, T.177 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.177
NA.4:	2 residues within 4Å: Chain B: R.233, K.236 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.236, B:K.236 Water bridges: B:G.235

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

DMS.5:

5 residues within 4Å:

Chain B: L.130, I.167, V.168, R.170, F.186

1 PLIP interactions:

1 interactions with chain B

Hydrogen bonds: B:R.170

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Pilgram, O. et al., Improving the selectivity of 3-amidinophenylalanine-derived matriptase inhibitors. Eur.J.Med.Chem. (2022)

Release Date

2020-11-18

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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