SMTL ID : 4crd.1

Creating novel F1 inhibitors through fragment based lead generation and structure aided drug design

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-trimer

Ligands

3 x OTJ: Methyl N-[4-[5-chloro-2-[[3-[5-chloro-2-(tetrazol-1-yl)phenyl]propanoylamino]methyl]-1H-imidazol-4-yl]phenyl]carbamate(Non-covalent)

OTJ.1: 22 residues within 4Å: Chain A: R.26, H.27, L.28, H.44, Y.134, I.141, D.182, A.183, C.184, K.185, G.186, D.187, S.188, T.206, S.207, W.208, G.209, G.211, C.212, G.219, V.220, Y.221 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:T.206 Hydrogen bonds: A:R.26, A:H.27, A:K.185, A:G.186, A:D.187, A:S.188, A:S.188 Water bridges: A:H.44, A:S.207, A:G.209 OTJ.5: 22 residues within 4Å: Chain B: R.26, H.27, L.28, H.44, Y.134, I.141, D.182, A.183, C.184, K.185, G.186, D.187, S.188, T.206, S.207, W.208, G.209, G.211, C.212, G.219, V.220, Y.221 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:T.206 Hydrogen bonds: B:R.26, B:H.27, B:K.185, B:G.186, B:D.187, B:S.188, B:S.188 Water bridges: B:H.44, B:S.207, B:G.209 OTJ.9: 22 residues within 4Å: Chain C: R.26, H.27, L.28, H.44, Y.134, I.141, D.182, A.183, C.184, K.185, G.186, D.187, S.188, T.206, S.207, W.208, G.209, G.211, C.212, G.219, V.220, Y.221 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:T.206 Hydrogen bonds: C:R.26, C:H.27, C:K.185, C:G.186, C:D.187, C:S.188, C:S.188 Water bridges: C:H.44, C:S.207, C:G.209

9 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 8 residues within 4Å: Chain A: K.117, R.120 Chain B: K.117, R.120 Chain C: K.117, R.120 Ligands: SO4.6, SO4.10 6 PLIP interactions: 2 interactions with chain C, 2 interactions with chain A, 2 interactions with chain B Salt bridges: C:K.117, C:R.120, A:K.117, A:R.120, B:K.117, B:R.120 SO4.3: 4 residues within 4Å: Chain A: G.175, Y.176, R.177, E.178 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.177, A:E.178 SO4.4: 5 residues within 4Å: Chain A: N.121 Chain B: N.121 Chain C: N.121 Ligands: SO4.8, SO4.12 4 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C, 1 interactions with chain B Hydrogen bonds: A:N.121, A:N.121, C:N.121, B:N.121 SO4.6: 8 residues within 4Å: Chain A: K.117, R.120 Chain B: K.117, R.120 Chain C: K.117, R.120 Ligands: SO4.2, SO4.10 6 PLIP interactions: 2 interactions with chain C, 2 interactions with chain A, 2 interactions with chain B Salt bridges: C:K.117, C:R.120, A:K.117, A:R.120, B:K.117, B:R.120 SO4.7: 4 residues within 4Å: Chain B: G.175, Y.176, R.177, E.178 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.177, B:E.178 SO4.8: 5 residues within 4Å: Chain A: N.121 Chain B: N.121 Chain C: N.121 Ligands: SO4.4, SO4.12 4 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C, 2 interactions with chain B Hydrogen bonds: A:N.121, C:N.121, B:N.121, B:N.121 SO4.10: 8 residues within 4Å: Chain A: K.117, R.120 Chain B: K.117, R.120 Chain C: K.117, R.120 Ligands: SO4.2, SO4.6 6 PLIP interactions: 2 interactions with chain C, 2 interactions with chain A, 2 interactions with chain B Salt bridges: C:K.117, C:R.120, A:K.117, A:R.120, B:K.117, B:R.120 SO4.11: 4 residues within 4Å: Chain C: G.175, Y.176, R.177, E.178 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.177, C:E.178 SO4.12: 5 residues within 4Å: Chain A: N.121 Chain B: N.121 Chain C: N.121 Ligands: SO4.4, SO4.8 4 PLIP interactions: 1 interactions with chain A, 2 interactions with chain C, 1 interactions with chain B Hydrogen bonds: A:N.121, C:N.121, C:N.121, B:N.121

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fjellstrom, O. et al., Creating Novel Activated Factor Xi Inhibitors Through Fragment Based Lead Generation and Structure Aided Drug Design. Plos One (2015)

Release Date

2015-02-11

Peptides

COAGULATION FACTOR XI: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

COAGULATION FACTOR XI

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