SMTL ID : 6pme.1

TRK-A IN COMPLEX WITH LIGAND

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

homo-12-mer

Ligands

12 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.20, I.21, C.95, E.97 Chain B: C.17 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Metal complexes: B:C.17, A:H.20, A:C.95, A:E.97 ZN.4: 5 residues within 4Å: Chain B: H.20, I.21, C.95, E.97 Chain C: C.17 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C Metal complexes: B:H.20, B:C.95, B:E.97, C:C.17 ZN.7: 5 residues within 4Å: Chain C: H.20, I.21, C.95, E.97 Chain G: C.17 4 PLIP interactions: 1 interactions with chain G, 3 interactions with chain C Metal complexes: G:C.17, C:H.20, C:C.95, C:E.97 ZN.9: 5 residues within 4Å: Chain D: H.20, I.21, C.95, E.97 Chain E: C.17 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain E Metal complexes: D:H.20, D:C.95, D:E.97, E:C.17 ZN.12: 5 residues within 4Å: Chain E: H.20, I.21, C.95, E.97 Chain F: C.17 4 PLIP interactions: 3 interactions with chain E, 1 interactions with chain F Metal complexes: E:H.20, E:C.95, E:E.97, F:C.17 ZN.15: 5 residues within 4Å: Chain F: H.20, I.21, C.95, E.97 Chain J: C.17 4 PLIP interactions: 3 interactions with chain F, 1 interactions with chain J Metal complexes: F:H.20, F:C.95, F:E.97, J:C.17 ZN.17: 5 residues within 4Å: Chain G: H.20, I.21, C.95, E.97 Chain H: C.17 4 PLIP interactions: 3 interactions with chain G, 1 interactions with chain H Metal complexes: G:H.20, G:C.95, G:E.97, H:C.17 ZN.20: 5 residues within 4Å: Chain H: H.20, I.21, C.95, E.97 Chain I: C.17 4 PLIP interactions: 3 interactions with chain H, 1 interactions with chain I Metal complexes: H:H.20, H:C.95, H:E.97, I:C.17 ZN.23: 5 residues within 4Å: Chain A: C.17 Chain I: H.20, I.21, C.95, E.97 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain I Metal complexes: A:C.17, I:H.20, I:C.95, I:E.97 ZN.25: 5 residues within 4Å: Chain J: H.20, I.21, C.95, E.97 Chain K: C.17 4 PLIP interactions: 3 interactions with chain J, 1 interactions with chain K Metal complexes: J:H.20, J:C.95, J:E.97, K:C.17 ZN.28: 5 residues within 4Å: Chain K: H.20, I.21, C.95, E.97 Chain L: C.17 4 PLIP interactions: 1 interactions with chain L, 3 interactions with chain K Metal complexes: L:C.17, K:H.20, K:C.95, K:E.97 ZN.31: 5 residues within 4Å: Chain D: C.17 Chain L: H.20, I.21, C.95, E.97 4 PLIP interactions: 3 interactions with chain L, 1 interactions with chain D Metal complexes: L:H.20, L:C.95, L:E.97, D:C.17

12 x OOY: N-[2,4-bis(morpholin-4-yl)phenyl]-3-phenoxybenzamide(Non-covalent)

OOY.2: 15 residues within 4Å: Chain A: L.32, A.58, F.105, E.106, Y.107, M.108, R.109, G.111, D.112, R.170, L.173, G.183, F.185, G.186, S.188 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.32, A:A.58, A:F.105, A:Y.107, A:L.173 Hydrogen bonds: A:M.108 OOY.5: 15 residues within 4Å: Chain B: A.58, V.89, F.105, E.106, Y.107, M.108, R.109, G.111, D.112, R.115, L.173, G.183, F.185, G.186, I.191 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:A.58, B:V.89, B:F.105, B:F.105, B:Y.107, B:L.173 Hydrogen bonds: B:M.108 OOY.8: 17 residues within 4Å: Chain C: L.32, G.33, A.58, V.89, F.105, E.106, Y.107, M.108, R.109, G.111, D.112, R.115, L.173, G.183, F.185, G.186, M.187 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:L.32, C:L.32, C:A.58, C:V.89, C:F.105, C:Y.107, C:L.173, C:L.173 Hydrogen bonds: C:M.108 OOY.10: 15 residues within 4Å: Chain D: L.32, A.58, F.105, E.106, Y.107, M.108, R.109, G.111, D.112, R.170, L.173, G.183, F.185, G.186, S.188 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:L.32, D:A.58, D:F.105, D:Y.107, D:L.173 Hydrogen bonds: D:M.108 OOY.13: 15 residues within 4Å: Chain E: A.58, V.89, F.105, E.106, Y.107, M.108, R.109, G.111, D.112, R.115, L.173, G.183, F.185, G.186, I.191 7 PLIP interactions: 7 interactions with chain E Hydrophobic interactions: E:A.58, E:V.89, E:F.105, E:F.105, E:Y.107, E:L.173 Hydrogen bonds: E:M.108 OOY.16: 17 residues within 4Å: Chain F: L.32, G.33, A.58, V.89, F.105, E.106, Y.107, M.108, R.109, G.111, D.112, R.115, L.173, G.183, F.185, G.186, M.187 9 PLIP interactions: 9 interactions with chain F Hydrophobic interactions: F:L.32, F:L.32, F:A.58, F:V.89, F:F.105, F:Y.107, F:L.173, F:L.173 Hydrogen bonds: F:M.108 OOY.18: 15 residues within 4Å: Chain G: L.32, A.58, F.105, E.106, Y.107, M.108, R.109, G.111, D.112, R.170, L.173, G.183, F.185, G.186, S.188 6 PLIP interactions: 6 interactions with chain G Hydrophobic interactions: G:L.32, G:A.58, G:F.105, G:Y.107, G:L.173 Hydrogen bonds: G:M.108 OOY.21: 15 residues within 4Å: Chain H: A.58, V.89, F.105, E.106, Y.107, M.108, R.109, G.111, D.112, R.115, L.173, G.183, F.185, G.186, I.191 7 PLIP interactions: 7 interactions with chain H Hydrophobic interactions: H:A.58, H:V.89, H:F.105, H:F.105, H:Y.107, H:L.173 Hydrogen bonds: H:M.108 OOY.24: 17 residues within 4Å: Chain I: L.32, G.33, A.58, V.89, F.105, E.106, Y.107, M.108, R.109, G.111, D.112, R.115, L.173, G.183, F.185, G.186, M.187 9 PLIP interactions: 9 interactions with chain I Hydrophobic interactions: I:L.32, I:L.32, I:A.58, I:V.89, I:F.105, I:Y.107, I:L.173, I:L.173 Hydrogen bonds: I:M.108 OOY.26: 15 residues within 4Å: Chain J: L.32, A.58, F.105, E.106, Y.107, M.108, R.109, G.111, D.112, R.170, L.173, G.183, F.185, G.186, S.188 6 PLIP interactions: 6 interactions with chain J Hydrophobic interactions: J:L.32, J:A.58, J:F.105, J:Y.107, J:L.173 Hydrogen bonds: J:M.108 OOY.29: 15 residues within 4Å: Chain K: A.58, V.89, F.105, E.106, Y.107, M.108, R.109, G.111, D.112, R.115, L.173, G.183, F.185, G.186, I.191 7 PLIP interactions: 7 interactions with chain K Hydrophobic interactions: K:A.58, K:V.89, K:F.105, K:F.105, K:Y.107, K:L.173 Hydrogen bonds: K:M.108 OOY.32: 17 residues within 4Å: Chain L: L.32, G.33, A.58, V.89, F.105, E.106, Y.107, M.108, R.109, G.111, D.112, R.115, L.173, G.183, F.185, G.186, M.187 9 PLIP interactions: 9 interactions with chain L Hydrophobic interactions: L:L.32, L:L.32, L:A.58, L:V.89, L:F.105, L:Y.107, L:L.173, L:L.173 Hydrogen bonds: L:M.108

8 x SRT: S,R MESO-TARTARIC ACID(Non-covalent)

SRT.3: 6 residues within 4Å: Chain A: H.87, S.148, Q.149, A.152, H.294, Q.298 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.87, A:S.148 Salt bridges: A:H.87, A:H.294 SRT.6: 8 residues within 4Å: Chain B: H.87, A.145, S.148, Q.149, A.152, H.294, Q.298, A.301 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.148, B:S.148 Salt bridges: B:H.87, B:H.294 SRT.11: 6 residues within 4Å: Chain D: H.87, S.148, Q.149, A.152, H.294, Q.298 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:H.87, D:S.148 Salt bridges: D:H.87, D:H.294 SRT.14: 8 residues within 4Å: Chain E: H.87, A.145, S.148, Q.149, A.152, H.294, Q.298, A.301 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:S.148, E:S.148 Salt bridges: E:H.87, E:H.294 SRT.19: 6 residues within 4Å: Chain G: H.87, S.148, Q.149, A.152, H.294, Q.298 4 PLIP interactions: 4 interactions with chain G Hydrogen bonds: G:H.87, G:S.148 Salt bridges: G:H.87, G:H.294 SRT.22: 8 residues within 4Å: Chain H: H.87, A.145, S.148, Q.149, A.152, H.294, Q.298, A.301 4 PLIP interactions: 4 interactions with chain H Hydrogen bonds: H:S.148, H:S.148 Salt bridges: H:H.87, H:H.294 SRT.27: 6 residues within 4Å: Chain J: H.87, S.148, Q.149, A.152, H.294, Q.298 4 PLIP interactions: 4 interactions with chain J Hydrogen bonds: J:H.87, J:S.148 Salt bridges: J:H.87, J:H.294 SRT.30: 8 residues within 4Å: Chain K: H.87, A.145, S.148, Q.149, A.152, H.294, Q.298, A.301 4 PLIP interactions: 4 interactions with chain K Hydrogen bonds: K:S.148, K:S.148 Salt bridges: K:H.87, K:H.294

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Subramanian, G. et al., Synthetic inhibitor leads of human tropomyosin receptor kinase A ( h TrkA). Rsc Med Chem (2020)

Release Date

2020-02-26

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

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