SMTL ID : 3bjm.1

Crystal structure of human DPP-IV in complex with (1S,3S, 5S)-2-[(2S)-2-AMINO-2-(3-HYDROXYTRICYCLO[3.3.1.13,7]DEC-1- YL)ACETYL]-2-AZABICYCLO[3.1.0]HEXANE-3-CARBONITRILE (CAS), (1S,3S,5S)-2-((2S)-2-AMINO-2-(3-HYDROXYADAMANTAN-1- YL)ACETYL)-2-AZABICYCLO[3.1.0]HEXANE-3-CARBONITRILE (IUPAC), OR BMS-477118

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

homo-dimer

Ligands

8 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG.1: 4 residues within 4Å: Chain A: V.40, N.47, S.48, S.49 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.47 NAG.2: 3 residues within 4Å: Chain A: R.109, I.110, N.112 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:R.109 Hydrogen bonds: A:R.109, A:N.112 NAG.3: 5 residues within 4Å: Chain A: I.156, N.191, T.193, E.194, K.229 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.156 Hydrogen bonds: A:N.191, A:E.194, A:K.229 NAG.4: 3 residues within 4Å: Chain A: W.149, V.241, N.243 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.243 NAG.5: 3 residues within 4Å: Chain A: N.482, R.543, D.567 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.482, A:R.543, A:R.543, A:E.566, A:D.567 NAG.7: 6 residues within 4Å: Chain B: E.29, V.40, N.42, N.47, S.48, S.49 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.47 Water bridges: B:N.42 NAG.8: 5 residues within 4Å: Chain B: Y.80, R.109, I.110, P.111, N.112 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:R.109 Hydrogen bonds: B:N.112, B:N.112 NAG.9: 4 residues within 4Å: Chain B: I.156, N.191, T.193, E.194 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:I.156 Hydrogen bonds: B:N.191, B:T.193, B:E.194, B:E.194 Water bridges: B:Q.189

2 x BJM: (2~{S})-2-azanyl-1-[(1~{S},3~{S},5~{S})-3-(iminomethyl)-2-azabicyclo[3.1.0]hexan-2-yl]-2-[(5~{R},7~{S})-3-oxidanyl-1-ad amantyl]ethanone(Covalent)

BJM.6: 13 residues within 4Å: Chain A: R.87, E.167, E.168, F.319, Y.509, S.592, Y.593, V.618, Y.624, Y.628, N.672, V.673, H.702 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:F.319, A:Y.593, A:V.618, A:Y.624, A:Y.624, A:Y.628, A:V.673 Hydrogen bonds: A:R.87, A:E.167, A:E.167, A:Y.509, A:Y.593, A:Y.624, A:N.672 BJM.10: 13 residues within 4Å: Chain B: R.87, E.167, E.168, F.319, Y.509, S.592, Y.593, V.618, Y.624, Y.628, N.672, V.673, H.702 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:F.319, B:Y.593, B:Y.593, B:V.618, B:Y.628, B:Y.628, B:V.673 Hydrogen bonds: B:R.87, B:E.167, B:Y.509, B:N.672 Water bridges: B:Y.509

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Metzler, W.J. et al., Involvement of DPP-IV catalytic residues in enzyme-saxagliptin complex formation. Protein Sci. (2008)

Release Date

2008-04-22

Peptides

Dipeptidyl peptidase 4: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Dipeptidyl peptidase 4

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