SMTL ID : 3a2c.1

Crystal structure of a pyrazolopyrimidine inhibitor complex bound to MAPKAP Kinase-2 (MK2)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

homo-12-mer

Ligands

24 x PDY: N~7~-(4-ethoxyphenyl)-6-methyl-N~5~-[(3S)-piperidin-3-yl]pyrazolo[1,5-a]pyrimidine-5,7-diamine(Non-covalent)

PDY.1: 14 residues within 4Å: Chain A: V.38, Q.40, A.51, V.78, M.98, E.99, C.100, L.101, D.102, E.150, N.151, L.153, T.166, D.167 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:V.38, A:V.38, A:L.153, A:T.166 Hydrogen bonds: A:L.101, A:L.101, A:E.150 PDY.2: 4 residues within 4Å: Chain A: G.219, Y.220, P.221, Y.224 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.220, A:Y.224 pi-Stacking: A:Y.224 PDY.3: 12 residues within 4Å: Chain B: V.38, Q.40, A.51, V.78, E.99, C.100, L.101, E.150, N.151, L.153, T.166, D.167 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:V.38, B:V.38, B:L.153 Hydrogen bonds: B:L.101, B:L.101, B:E.150 PDY.4: 4 residues within 4Å: Chain B: Y.220, P.221, Y.224, S.225 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:Y.220, B:Y.220 Hydrogen bonds: B:S.225 pi-Stacking: B:Y.224 PDY.5: 14 residues within 4Å: Chain C: V.38, Q.40, A.51, V.78, M.98, E.99, C.100, L.101, D.102, E.150, N.151, L.153, T.166, D.167 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:V.38, C:V.78, C:L.153 Hydrogen bonds: C:Q.40, C:L.101, C:L.101, C:E.150 PDY.6: 4 residues within 4Å: Chain C: Y.220, P.221, Y.224, S.225 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:Y.220, C:Y.220, C:P.221, C:Y.224 Hydrogen bonds: C:S.225, C:S.225 pi-Stacking: C:Y.224 PDY.7: 14 residues within 4Å: Chain D: V.38, Q.40, A.51, V.78, M.98, E.99, C.100, L.101, D.102, E.150, N.151, L.153, T.166, D.167 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:V.38, D:V.38, D:L.153 Hydrogen bonds: D:L.101, D:L.101, D:E.150, D:T.166 PDY.8: 5 residues within 4Å: Chain D: F.107, Y.220, P.221, Y.224, S.225 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:F.107, D:Y.220, D:Y.224, D:Y.224 Hydrogen bonds: D:S.225 PDY.9: 12 residues within 4Å: Chain E: V.38, Q.40, A.51, V.78, E.99, C.100, L.101, E.150, N.151, L.153, T.166, D.167 6 PLIP interactions: 6 interactions with chain E Hydrophobic interactions: E:V.38, E:V.38, E:L.153 Hydrogen bonds: E:L.101, E:L.101, E:E.150 PDY.10: 4 residues within 4Å: Chain E: Y.220, P.221, Y.224, S.225 6 PLIP interactions: 6 interactions with chain E Hydrophobic interactions: E:Y.220, E:Y.220, E:P.221, E:Y.224 Hydrogen bonds: E:S.225 pi-Stacking: E:Y.224 PDY.11: 14 residues within 4Å: Chain F: V.38, Q.40, A.51, V.78, M.98, E.99, C.100, L.101, D.102, E.150, N.151, L.153, T.166, D.167 6 PLIP interactions: 6 interactions with chain F Hydrophobic interactions: F:V.38, F:L.153 Hydrogen bonds: F:Q.40, F:L.101, F:L.101, F:E.150 PDY.12: 6 residues within 4Å: Chain F: G.219, Y.220, P.221, Y.224, S.225, L.229 6 PLIP interactions: 6 interactions with chain F Hydrophobic interactions: F:Y.220, F:Y.220, F:L.229 Hydrogen bonds: F:S.225, F:S.225 pi-Stacking: F:Y.224 PDY.14: 14 residues within 4Å: Chain G: V.38, Q.40, A.51, V.78, M.98, E.99, C.100, L.101, D.102, E.150, N.151, L.153, T.166, D.167 8 PLIP interactions: 8 interactions with chain G Hydrophobic interactions: G:V.38, G:Q.40, G:L.153, G:T.166 Hydrogen bonds: G:L.101, G:L.101, G:E.150, G:T.166 PDY.15: 5 residues within 4Å: Chain G: I.215, Y.220, P.221, Y.224, S.225 7 PLIP interactions: 7 interactions with chain G Hydrophobic interactions: G:I.215, G:Y.220, G:Y.220, G:Y.224 Hydrogen bonds: G:S.225, G:S.225 pi-Stacking: G:Y.224 PDY.16: 13 residues within 4Å: Chain H: V.38, Q.40, A.51, V.78, M.98, E.99, C.100, L.101, E.150, N.151, L.153, T.166, D.167 6 PLIP interactions: 6 interactions with chain H Hydrophobic interactions: H:V.38, H:L.153, H:T.166 Hydrogen bonds: H:L.101, H:L.101, H:E.150 PDY.17: 8 residues within 4Å: Chain G: Y.189 Chain H: F.107, I.215, G.219, Y.220, P.221, Y.224, S.225 6 PLIP interactions: 6 interactions with chain H Hydrophobic interactions: H:I.215, H:P.221, H:Y.224 Hydrogen bonds: H:S.225, H:S.225 pi-Stacking: H:Y.224 PDY.18: 13 residues within 4Å: Chain I: V.38, Q.40, A.51, V.78, E.99, C.100, L.101, D.102, E.150, N.151, L.153, T.166, D.167 7 PLIP interactions: 7 interactions with chain I Hydrophobic interactions: I:V.38, I:L.153, I:T.166 Hydrogen bonds: I:L.101, I:L.101, I:E.150, I:T.166 PDY.19: 5 residues within 4Å: Chain I: F.107, Y.220, P.221, Y.224, S.225 3 PLIP interactions: 3 interactions with chain I Hydrophobic interactions: I:Y.224 Hydrogen bonds: I:S.225 pi-Stacking: I:Y.224 PDY.20: 13 residues within 4Å: Chain J: V.38, Q.40, A.51, V.78, M.98, E.99, C.100, L.101, E.150, N.151, L.153, T.166, D.167 7 PLIP interactions: 7 interactions with chain J Hydrophobic interactions: J:V.38, J:V.78, J:L.153 Hydrogen bonds: J:L.101, J:L.101, J:E.150, J:T.166 PDY.21: 6 residues within 4Å: Chain J: F.107, I.215, Y.220, P.221, Y.224, S.225 6 PLIP interactions: 6 interactions with chain J Hydrophobic interactions: J:F.107, J:I.215, J:Y.220, J:Y.220 Hydrogen bonds: J:S.225 pi-Stacking: J:Y.224 PDY.22: 13 residues within 4Å: Chain K: V.38, Q.40, A.51, V.78, M.98, E.99, C.100, L.101, E.150, N.151, L.153, T.166, D.167 9 PLIP interactions: 9 interactions with chain K Hydrophobic interactions: K:V.38, K:V.38, K:Q.40, K:T.166 Hydrogen bonds: K:Q.40, K:L.101, K:L.101, K:E.150, K:T.166 PDY.23: 6 residues within 4Å: Chain K: F.107, I.215, G.219, Y.220, P.221, Y.224 6 PLIP interactions: 6 interactions with chain K Hydrophobic interactions: K:F.107, K:I.215, K:Y.220, K:P.221, K:Y.224 pi-Stacking: K:Y.224 PDY.24: 13 residues within 4Å: Chain L: V.38, Q.40, A.51, V.78, E.99, C.100, L.101, D.102, E.150, N.151, L.153, T.166, D.167 6 PLIP interactions: 6 interactions with chain L Hydrophobic interactions: L:V.38, L:L.153 Hydrogen bonds: L:Q.40, L:L.101, L:L.101, L:E.150 PDY.25: 4 residues within 4Å: Chain L: Y.220, P.221, Y.224, S.225 5 PLIP interactions: 5 interactions with chain L Hydrophobic interactions: L:Y.220, L:Y.220, L:Y.224 Hydrogen bonds: L:S.225 pi-Stacking: L:Y.224

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

SO4.13: 6 residues within 4Å: Chain F: S.225, N.226, H.227, S.232, G.234, R.238 7 PLIP interactions: 7 interactions with chain F Hydrogen bonds: F:S.225, F:N.226, F:N.226, F:S.232, F:G.234 Salt bridges: F:H.227, F:R.238

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fujino, A. et al., Structural analysis of an MK2-inhibitor complex: insight into the regulation of the secondary structure of the Gly-rich loop by TEI-I01800. Acta Crystallogr.,Sect.D (2010)

Release Date

2010-05-12

Peptides

MAP kinase-activated protein kinase 2: ABCDEFGHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

MAP kinase-activated protein kinase 2

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