SMTL ID : 4np3.1

Crystal structure of the murine cd44 hyaluronan binding domain complex with a small molecule

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.61 Å

Oligo State

monomer

Ligands

1 x 2L2: 2-[(4-METHYL-1H-IMIDAZOL-5-YL)METHYL]-1,2,3,4-TETRAHYDROISOQUINOLIN-8-AMINE

2L2.1: 11 residues within 4Å: Chain A: N.6, V.7, T.8, E.18, G.21, R.59, V.130, N.131, R.132 Ligands: MES.3, SO4.4 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:N.6, A:R.132 Hydrogen bonds: A:V.7 Salt bridges: A:E.18 pi-Cation interactions: A:R.132

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

DMS.2: 7 residues within 4Å: Chain A: C.9, C.111, T.112, S.113, N.131, R.132, D.133 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.132, A:D.133 Salt bridges: A:D.133

1 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.3: 2 residues within 4Å: Chain A: R.132 Ligands: 2L2.1 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.132

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

SO4.4: 1 residues within 4Å: Ligands: 2L2.1 1 PLIP interactions: 1 interactions with chain A Water bridges: A:G.21 SO4.5: 6 residues within 4Å: Chain A: R.10, F.15, F.37, S.39, N.102, V.114 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.39, A:N.102 Water bridges: A:R.10 Salt bridges: A:R.10 SO4.6: 5 residues within 4Å: Chain A: Y.86, I.87, L.88, V.89, T.90 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.86, A:Y.86, A:V.89, A:T.90, A:T.90, A:T.90

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, L.K. et al., Fragment-Based Identification of an Inducible Binding Site on Cell Surface Receptor CD44 for the Design of Protein-Carbohydrate Interaction Inhibitors. J.Med.Chem. (2014)

Release Date

2014-04-16

Peptides

CD44 antigen: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

CD44 antigen

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