SMTL ID : 4aoj.1

Human TrkA in complex with the inhibitor AZ-23

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.75 Å

Oligo State

homo-12-mer

Ligands

12 x V4Z: 5-chloranyl-N2-[(1S)-1-(5-fluoranylpyridin-2-yl)ethyl]-N4-(3-propan-2-yloxy-1H-pyrazol-5-yl)pyrimidine-2,4-diamine(Non-covalent)

V4Z.1: 17 residues within 4Å: Chain A: L.49, V.57, A.75, V.106, F.122, E.123, Y.124, M.125, R.126, G.128, D.129, R.187, N.188, C.189, L.190, G.200, D.201 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:V.57, A:V.57 Hydrogen bonds: A:M.125, A:M.125, A:M.125 Water bridges: A:E.51, A:E.51, A:D.129, A:D.129 V4Z.4: 16 residues within 4Å: Chain B: L.49, V.57, A.75, F.122, E.123, Y.124, M.125, R.126, G.128, D.129, R.187, N.188, C.189, L.190, G.200, D.201 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:V.57, B:A.75 Hydrogen bonds: B:M.125, B:M.125, B:M.125 Water bridges: B:D.129, B:R.132 Halogen bonds: B:R.126 V4Z.7: 16 residues within 4Å: Chain C: L.49, V.57, A.75, F.122, E.123, Y.124, M.125, R.126, G.128, D.129, R.187, N.188, C.189, L.190, G.200, D.201 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:V.57, C:V.57, C:L.190, C:L.190 Hydrogen bonds: C:M.125, C:M.125, C:M.125 Water bridges: C:E.51 Halogen bonds: C:R.126 V4Z.10: 17 residues within 4Å: Chain D: L.49, V.57, A.75, V.106, F.122, E.123, Y.124, M.125, R.126, G.128, D.129, R.187, N.188, C.189, L.190, G.200, D.201 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:V.57, D:V.57 Hydrogen bonds: D:M.125, D:M.125, D:M.125 Water bridges: D:E.51, D:E.51, D:D.129, D:D.129 V4Z.13: 16 residues within 4Å: Chain E: L.49, V.57, A.75, F.122, E.123, Y.124, M.125, R.126, G.128, D.129, R.187, N.188, C.189, L.190, G.200, D.201 8 PLIP interactions: 8 interactions with chain E Hydrophobic interactions: E:V.57, E:A.75 Hydrogen bonds: E:M.125, E:M.125, E:M.125 Water bridges: E:D.129, E:R.132 Halogen bonds: E:R.126 V4Z.16: 16 residues within 4Å: Chain F: L.49, V.57, A.75, F.122, E.123, Y.124, M.125, R.126, G.128, D.129, R.187, N.188, C.189, L.190, G.200, D.201 9 PLIP interactions: 9 interactions with chain F Hydrophobic interactions: F:V.57, F:V.57, F:L.190, F:L.190 Hydrogen bonds: F:M.125, F:M.125, F:M.125 Water bridges: F:E.51 Halogen bonds: F:R.126 V4Z.19: 17 residues within 4Å: Chain G: L.49, V.57, A.75, V.106, F.122, E.123, Y.124, M.125, R.126, G.128, D.129, R.187, N.188, C.189, L.190, G.200, D.201 9 PLIP interactions: 9 interactions with chain G Hydrophobic interactions: G:V.57, G:V.57 Hydrogen bonds: G:M.125, G:M.125, G:M.125 Water bridges: G:E.51, G:E.51, G:D.129, G:D.129 V4Z.22: 16 residues within 4Å: Chain H: L.49, V.57, A.75, F.122, E.123, Y.124, M.125, R.126, G.128, D.129, R.187, N.188, C.189, L.190, G.200, D.201 8 PLIP interactions: 8 interactions with chain H Hydrophobic interactions: H:V.57, H:A.75 Hydrogen bonds: H:M.125, H:M.125, H:M.125 Water bridges: H:D.129, H:R.132 Halogen bonds: H:R.126 V4Z.25: 16 residues within 4Å: Chain I: L.49, V.57, A.75, F.122, E.123, Y.124, M.125, R.126, G.128, D.129, R.187, N.188, C.189, L.190, G.200, D.201 9 PLIP interactions: 9 interactions with chain I Hydrophobic interactions: I:V.57, I:V.57, I:L.190, I:L.190 Hydrogen bonds: I:M.125, I:M.125, I:M.125 Water bridges: I:E.51 Halogen bonds: I:R.126 V4Z.28: 17 residues within 4Å: Chain J: L.49, V.57, A.75, V.106, F.122, E.123, Y.124, M.125, R.126, G.128, D.129, R.187, N.188, C.189, L.190, G.200, D.201 9 PLIP interactions: 9 interactions with chain J Hydrophobic interactions: J:V.57, J:V.57 Hydrogen bonds: J:M.125, J:M.125, J:M.125 Water bridges: J:E.51, J:E.51, J:D.129, J:D.129 V4Z.31: 16 residues within 4Å: Chain K: L.49, V.57, A.75, F.122, E.123, Y.124, M.125, R.126, G.128, D.129, R.187, N.188, C.189, L.190, G.200, D.201 8 PLIP interactions: 8 interactions with chain K Hydrophobic interactions: K:V.57, K:A.75 Hydrogen bonds: K:M.125, K:M.125, K:M.125 Water bridges: K:D.129, K:R.132 Halogen bonds: K:R.126 V4Z.34: 16 residues within 4Å: Chain L: L.49, V.57, A.75, F.122, E.123, Y.124, M.125, R.126, G.128, D.129, R.187, N.188, C.189, L.190, G.200, D.201 9 PLIP interactions: 9 interactions with chain L Hydrophobic interactions: L:V.57, L:V.57, L:L.190, L:L.190 Hydrogen bonds: L:M.125, L:M.125, L:M.125 Water bridges: L:E.51 Halogen bonds: L:R.126

24 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain A: H.37, I.38, C.112, E.114 Chain F: C.34 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain F Metal complexes: A:H.37, A:C.112, A:E.114, A:E.114, F:C.34 ZN.3: 4 residues within 4Å: Chain A: E.48, E.51, K.56 Chain F: H.178 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.48, A:E.48, A:E.51 ZN.5: 5 residues within 4Å: Chain A: C.34 Chain B: H.37, I.38, C.112, E.114 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Metal complexes: B:H.37, B:C.112, B:E.114, A:C.34 ZN.6: 4 residues within 4Å: Chain A: H.178 Chain B: E.48, E.51, K.56 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Metal complexes: B:E.48, B:E.48, B:E.51, A:H.178, A:H.178 ZN.8: 5 residues within 4Å: Chain B: C.34 Chain C: H.37, I.38, C.112, E.114 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain B Metal complexes: C:H.37, C:C.112, C:E.114, B:C.34 ZN.9: 4 residues within 4Å: Chain B: H.178 Chain C: E.48, E.51, K.56 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:E.48, C:E.48, C:E.51 ZN.11: 5 residues within 4Å: Chain C: C.34 Chain D: H.37, I.38, C.112, E.114 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain C Metal complexes: D:H.37, D:C.112, D:E.114, D:E.114, C:C.34 ZN.12: 4 residues within 4Å: Chain C: H.178 Chain D: E.48, E.51, K.56 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:E.48, D:E.48, D:E.51 ZN.14: 5 residues within 4Å: Chain D: C.34 Chain E: H.37, I.38, C.112, E.114 4 PLIP interactions: 3 interactions with chain E, 1 interactions with chain D Metal complexes: E:H.37, E:C.112, E:E.114, D:C.34 ZN.15: 4 residues within 4Å: Chain D: H.178 Chain E: E.48, E.51, K.56 5 PLIP interactions: 3 interactions with chain E, 2 interactions with chain D Metal complexes: E:E.48, E:E.48, E:E.51, D:H.178, D:H.178 ZN.17: 5 residues within 4Å: Chain E: C.34 Chain F: H.37, I.38, C.112, E.114 4 PLIP interactions: 3 interactions with chain F, 1 interactions with chain E Metal complexes: F:H.37, F:C.112, F:E.114, E:C.34 ZN.18: 4 residues within 4Å: Chain E: H.178 Chain F: E.48, E.51, K.56 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:E.48, F:E.48, F:E.51 ZN.20: 5 residues within 4Å: Chain G: H.37, I.38, C.112, E.114 Chain L: C.34 5 PLIP interactions: 4 interactions with chain G, 1 interactions with chain L Metal complexes: G:H.37, G:C.112, G:E.114, G:E.114, L:C.34 ZN.21: 4 residues within 4Å: Chain G: E.48, E.51, K.56 Chain L: H.178 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:E.48, G:E.48, G:E.51 ZN.23: 5 residues within 4Å: Chain G: C.34 Chain H: H.37, I.38, C.112, E.114 4 PLIP interactions: 1 interactions with chain G, 3 interactions with chain H Metal complexes: G:C.34, H:H.37, H:C.112, H:E.114 ZN.24: 4 residues within 4Å: Chain G: H.178 Chain H: E.48, E.51, K.56 5 PLIP interactions: 2 interactions with chain G, 3 interactions with chain H Metal complexes: G:H.178, G:H.178, H:E.48, H:E.48, H:E.51 ZN.26: 5 residues within 4Å: Chain H: C.34 Chain I: H.37, I.38, C.112, E.114 4 PLIP interactions: 3 interactions with chain I, 1 interactions with chain H Metal complexes: I:H.37, I:C.112, I:E.114, H:C.34 ZN.27: 4 residues within 4Å: Chain H: H.178 Chain I: E.48, E.51, K.56 3 PLIP interactions: 3 interactions with chain I Metal complexes: I:E.48, I:E.48, I:E.51 ZN.29: 5 residues within 4Å: Chain I: C.34 Chain J: H.37, I.38, C.112, E.114 5 PLIP interactions: 4 interactions with chain J, 1 interactions with chain I Metal complexes: J:H.37, J:C.112, J:E.114, J:E.114, I:C.34 ZN.30: 4 residues within 4Å: Chain I: H.178 Chain J: E.48, E.51, K.56 3 PLIP interactions: 3 interactions with chain J Metal complexes: J:E.48, J:E.48, J:E.51 ZN.32: 5 residues within 4Å: Chain J: C.34 Chain K: H.37, I.38, C.112, E.114 4 PLIP interactions: 3 interactions with chain K, 1 interactions with chain J Metal complexes: K:H.37, K:C.112, K:E.114, J:C.34 ZN.33: 4 residues within 4Å: Chain J: H.178 Chain K: E.48, E.51, K.56 5 PLIP interactions: 3 interactions with chain K, 2 interactions with chain J Metal complexes: K:E.48, K:E.48, K:E.51, J:H.178, J:H.178 ZN.35: 5 residues within 4Å: Chain K: C.34 Chain L: H.37, I.38, C.112, E.114 4 PLIP interactions: 1 interactions with chain K, 3 interactions with chain L Metal complexes: K:C.34, L:H.37, L:C.112, L:E.114 ZN.36: 4 residues within 4Å: Chain K: H.178 Chain L: E.48, E.51, K.56 3 PLIP interactions: 3 interactions with chain L Metal complexes: L:E.48, L:E.48, L:E.51

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, T. et al., Discovery of Disubstituted Imidazo[4,5-B]Pyridines and Purines as Potent Trka Inhibitors. Acs Med.Chem.Lett. (2012)

Release Date

2012-08-15

Peptides

HIGH AFFINITY NERVE GROWTH FACTOR RECEPTOR: ABCDEFGHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
A

E
B

F
C

G
A

H
B

I
C

J
A

K
B

L
C

HIGH AFFINITY NERVE GROWTH FACTOR RECEPTOR