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SMTL ID : 8a68.1

Small molecule stabilizer (compound 5) for C-RAF(pS259) and 14-3-3

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

2 x GLN- ARG- SER- THR- SEP- THR- PRO- ASN- VAL: RAF proto-oncogene serine/threonine-protein kinase(Non-covalent)

GLN-ARG-SER-THR-SEP-THR-PRO-ASN-VAL.1:

22 residues within 4Å:

Chain A: N.47, V.51, K.54, N.55, R.61, R.65, K.127, R.134, Y.135, G.176, L.179, N.180, V.183, Y.186, E.187, L.223, I.224, L.227, N.231, L.234, W.235
Ligands: L7U.5

27 PLIP interactions:

27 interactions with chain A

Hydrophobic interactions: A:N.47, A:V.51
Hydrogen bonds: A:N.55, A:Y.135, A:N.180, A:N.180, A:N.180, A:E.187, A:E.187, A:N.231, A:N.231, A:N.231, A:W.235
Water bridges: A:K.54, A:K.54, A:K.54, A:K.54, A:N.55, A:R.61, A:R.61, A:R.61, A:R.65, A:E.187, A:E.187
Salt bridges: A:K.54, A:R.61, A:R.134

GLN-ARG-SER-THR-SEP-THR-PRO-ASN-VAL.6:

22 residues within 4Å:

Chain B: N.47, V.51, K.54, N.55, R.61, R.65, K.127, R.134, Y.135, G.176, L.179, N.180, V.183, Y.186, E.187, L.223, I.224, L.227, N.231, L.234, W.235
Ligands: L7U.10

27 PLIP interactions:

27 interactions with chain B

Hydrophobic interactions: B:N.47, B:V.51
Hydrogen bonds: B:N.55, B:Y.135, B:N.180, B:N.180, B:N.180, B:E.187, B:E.187, B:E.187, B:N.231, B:N.231, B:N.231, B:W.235
Water bridges: B:K.54, B:K.54, B:K.54, B:K.54, B:N.55, B:R.61, B:R.61, B:R.61, B:R.65, B:E.187
Salt bridges: B:K.54, B:R.61, B:R.134

6 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)

MG.2:	0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)
MG.3:	1 residues within 4Å: Chain A: E.7 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.7, H₂O.3
MG.4:	3 residues within 4Å: Chain A: R.90, E.91, E.94 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:E.94, H₂O.1, H₂O.2, H₂O.6, H₂O.10
MG.7:	0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)
MG.8:	1 residues within 4Å: Chain B: E.7 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.7, H₂O.16
MG.9:	3 residues within 4Å: Chain B: R.90, E.91, E.94 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:E.94, H₂O.14, H₂O.15, H₂O.19, H₂O.23

2 x L7U: ~{N}-[2-[2-(dimethylamino)ethyldisulfanyl]ethyl]-1-[(2~{R})-2-(6-methoxynaphthalen-2-yl)propanoyl]piperidine-4-carboxamide(Non-covalent)

L7U.5:

15 residues within 4Å:

Chain A: C.43, E.44, N.47, F.124, K.127, P.172, I.173, G.176, D.220, L.223, I.224
Ligands: GLN-ARG-SER-THR-SEP-THR-PRO-ASN-VAL.1, GLN-ARG-SER-THR-SEP-THR-PRO-ASN-VAL.1, GLN-ARG-SER-THR-SEP-THR-PRO-ASN-VAL.1, GLN-ARG-SER-THR-SEP-THR-PRO-ASN-VAL.1

5 PLIP interactions:

5 interactions with chain A

Hydrophobic interactions: A:P.172, A:L.223, A:I.224, A:I.224
Hydrogen bonds: A:N.47

L7U.10:

15 residues within 4Å:

Chain B: C.43, E.44, N.47, F.124, K.127, P.172, I.173, G.176, D.220, L.223, I.224
Ligands: GLN-ARG-SER-THR-SEP-THR-PRO-ASN-VAL.6, GLN-ARG-SER-THR-SEP-THR-PRO-ASN-VAL.6, GLN-ARG-SER-THR-SEP-THR-PRO-ASN-VAL.6, GLN-ARG-SER-THR-SEP-THR-PRO-ASN-VAL.6

5 PLIP interactions:

5 interactions with chain B

Hydrophobic interactions: B:P.172, B:L.223, B:I.224, B:I.224
Hydrogen bonds: B:N.47

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Kenanova, D.N. et al., A Systematic Approach to the Discovery of Protein-Protein Interaction Stabilizers. Acs Cent.Sci. (2023)

Release Date

2023-04-26

Peptides

14-3-3 protein sigma: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Export Alignment

Secondary Structure
NoneDSSPPSIPREDSSpro

Colour Scheme

Fade MismatchesEnhance Mismatches

ChainUnique ChainRainbow2° StructureBfactorBfactor RangeSOAEntropyClustalHydrophobicSizeChargedPolarProlineSer/ThrCysteineAliphaticAromaticNo Colour

Background

3D Viewer
NGLPV2D

14-3-3 protein sigma

Toggle Identical (AB)

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