SMTL ID : 8hu6.1

AMP deaminase 2 in complex with AMP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.33 Å

Oligo State

homo-tetramer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.217, H.219, H.486, H.508, D.563 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.217, A:H.219, A:H.486, A:D.563, H2O.5 ZN.3: 5 residues within 4Å: Chain B: H.217, H.219, H.486, H.508, D.563 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.217, B:H.219, B:H.486, B:D.563, H2O.9 ZN.5: 5 residues within 4Å: Chain C: H.217, H.219, H.486, H.508, D.563 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.217, C:H.219, C:H.486, C:D.563, H2O.19 ZN.7: 6 residues within 4Å: Chain D: H.217, H.219, H.486, H.508, D.563 Ligands: AMP.8 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.217, D:H.219, D:H.486, D:D.563, H2O.26

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

SO4.2: 8 residues within 4Å: Chain A: S.221, Y.293, R.302, K.307, S.341, Y.343, Q.372, P.374 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:S.221, A:S.221, A:S.341, A:Q.372 Water bridges: A:R.302, A:R.302 Salt bridges: A:R.302, A:K.307 SO4.4: 7 residues within 4Å: Chain B: S.221, Y.293, R.302, K.307, S.341, Y.343, Q.372 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:S.221, B:S.221, B:S.341, B:S.341, B:Q.372 Water bridges: B:R.302 Salt bridges: B:R.302, B:K.307 SO4.6: 7 residues within 4Å: Chain C: S.221, Y.293, R.302, K.307, S.341, Y.343, Q.372 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:S.221, C:S.221, C:S.341, C:S.341, C:Q.372 Water bridges: C:S.221, C:R.302, C:Y.343, C:Y.343 Salt bridges: C:R.302, C:K.307 SO4.9: 5 residues within 4Å: Chain B: R.545 Chain D: R.513, K.514, L.541, R.545 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain B Salt bridges: D:R.513, D:K.514, D:R.545, B:R.545

1 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.8: 19 residues within 4Å: Chain D: H.219, S.221, F.286, N.290, Y.293, R.302, K.307, S.341, Y.343, Q.372, P.374, L.376, V.426, D.427, D.428, H.486, D.563, D.564 Ligands: ZN.7 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:H.219, D:S.221, D:S.221, D:S.221, D:N.290, D:S.341, D:Q.372, D:D.564 Water bridges: D:R.302, D:R.302, D:S.341 Salt bridges: D:R.302

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kitao, Y. et al., The discovery of 3,3-dimethyl-1,2,3,4-tetrahydroquinoxaline-1-carboxamides as AMPD2 inhibitors with a novel mechanism of action. Bioorg.Med.Chem.Lett. (2023)

Release Date

2023-01-18

Peptides

AMP deaminase 2: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

AMP deaminase 2

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