SMTL ID : 2va7.1

X-ray crystal structure of beta secretase complexed with compound 27

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

6 x IOD: IODIDE ION(Non-functional Binders)

IOD.1: 4 residues within 4Å: Chain A: H.108, T.166, E.167, S.168 Ligand excluded by PLIP IOD.2: 4 residues within 4Å: Chain A: H.108, D.169, K.170 Chain B: F.110 Ligand excluded by PLIP IOD.3: 1 residues within 4Å: Chain A: R.412 Ligand excluded by PLIP IOD.5: 4 residues within 4Å: Chain B: H.108, T.166, E.167, S.168 Ligand excluded by PLIP IOD.6: 4 residues within 4Å: Chain A: F.110 Chain B: H.108, D.169, K.170 Ligand excluded by PLIP IOD.7: 1 residues within 4Å: Chain B: R.412 Ligand excluded by PLIP

2 x C27: (6R)-2-amino-6-[2-(3'-methoxybiphenyl-3-yl)ethyl]-3,6-dimethyl-5,6-dihydropyrimidin-4(3H)-one(Non-covalent)

C27.4: 19 residues within 4Å: Chain A: S.73, G.74, Q.75, G.76, L.93, D.95, G.97, S.98, Y.134, F.171, I.173, W.178, D.291, S.292, G.293, T.294, T.295, A.398 Chain B: K.170 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:L.93, A:L.93, A:Y.134, A:Y.134, A:I.173, A:W.178 Water bridges: A:Y.77, A:G.97 Salt bridges: A:D.95, A:D.291 pi-Stacking: A:F.171 C27.8: 19 residues within 4Å: Chain A: K.170 Chain B: S.73, G.74, Q.75, G.76, L.93, D.95, G.97, S.98, Y.134, F.171, I.173, W.178, D.291, S.292, G.293, T.294, T.295, A.398 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:L.93, B:L.93, B:Y.134, B:Y.134, B:I.173, B:W.178 Water bridges: B:Y.77, B:G.97 Salt bridges: B:D.95, B:D.291 pi-Stacking: B:F.171

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Edwards, P.D. et al., Application of Fragment-Based Lead Generation to the Discovery of Novel, Cyclic Amidine Beta-Secretase Inhibitors with Nanomolar Potency, Cellular Activity, and High Ligand Efficiency. J.Med.Chem. (2007)

Release Date

2007-11-13

Peptides

BETA-SECRETASE 1 .: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

BETA-SECRETASE 1 .

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