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SMTL ID : 6t8a.1

Thrombin in complex with diphenyl ((4-carbamimidoylphenyl)((S)-1-((R)-3-cyclohexyl 2-((phenylmethyl)sulfonamido)propanoyl)pyrrolidine-2-carboxamido)methyl)phosphonate (MI-492)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.62 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x MUZ: [(~{R})-(4-carbamimidoylphenyl)-[[(2~{S})-1-[(2~{R})-3-cyclohexyl-2-[(phenylmethyl)sulfonylamino]propanoyl]pyrrolidin-2-yl]carbonylamino]methyl]-phenoxy-phosphinous acid(Covalent)

MUZ.1:

22 residues within 4Å:

Chain B: L.27, H.43, Y.47, W.50, E.94, N.95, L.96, D.199, A.200, C.201, E.202, G.203, D.204, S.205, V.225, S.226, W.227, G.228, E.229, G.230, C.231, G.238

20 PLIP interactions:

20 interactions with chain B

Hydrophobic interactions: B:Y.47, B:W.50, B:W.50, B:L.96, B:E.202, B:E.202, B:V.225, B:W.227
Hydrogen bonds: B:D.199, B:A.200, B:G.203, B:D.204, B:S.205, B:S.226, B:G.228, B:G.228, B:G.230, B:G.230
Water bridges: B:F.239
pi-Cation interactions: B:K.52

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

NAG.2:

2 residues within 4Å:

Chain B: P.48, N.53

2 PLIP interactions:

2 interactions with chain B

Hydrophobic interactions: B:P.48
Hydrogen bonds: B:N.53

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.5:	2 residues within 4Å: Chain B: R.233, 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

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

PO4.4:

4 residues within 4Å:

Chain B: N.91, D.97, R.98, R.180

9 PLIP interactions:

9 interactions with chain B

Hydrogen bonds: B:N.91, B:D.97, B:D.97
Water bridges: B:R.89, B:R.89, B:R.180, B:R.180
Salt bridges: B:R.98, B:R.180

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

DMS.6:	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
DMS.7:	3 residues within 4Å: Chain B: E.124, T.125, F.215 1 PLIP interactions: 1 interactions with chain B pi-Cation interactions: B:F.215

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Ngaha, S.A. et al., Thrombin in complex with diphenyl ((4-carbamimidoylphenyl)((S)-1-((R)-3-cyclohexyl-2-((phenylmethyl)sulfonamido)propanoyl)pyrrolidine-2-carboxamido)methyl)phosphonate (MI-492). to be published

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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