SMTL ID : 8w2l.1

TRPM7 structure in complex with anticancer agent CCT128930 in closed state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

52 x POV: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate(Non-covalent)

POV.1: 20 residues within 4Å: Chain A: Y.1177, V.1244, M.1245, G.1248, K.1249, A.1252, N.1253, Y.1295 Chain B: V.1264, F.1268, L.1330, A.1332, V.1333, Y.1334, F.1336 Ligands: POV.2, POV.5, POV.6, M05.12, POV.19 Ligand excluded by PLIP POV.2: 18 residues within 4Å: Chain A: A.1262, L.1266, W.1284, S.1285, A.1287, K.1288, V.1291, Y.1295 Chain B: C.1310, A.1311, N.1312, W.1325, P.1328, F.1329 Ligands: POV.1, POV.5, POV.19, POV.50 Ligand excluded by PLIP POV.3: 8 residues within 4Å: Chain A: I.1187, I.1204, D.1208, H.1210, V.1211, A.1214 Ligands: POV.6, POV.7 Ligand excluded by PLIP POV.5: 15 residues within 4Å: Chain A: V.1251, A.1252, M.1254, F.1255, Y.1256, V.1258, M.1261, A.1262, I.1298 Chain B: F.1336 Chain D: W.1012, L.1234 Ligands: POV.1, POV.2, POV.50 Ligand excluded by PLIP POV.6: 15 residues within 4Å: Chain A: R.985, F.1174, S.1175, Y.1177, V.1180, I.1184, S.1188, I.1218, L.1221, N.1222, F.1225 Ligands: POV.1, POV.3, M05.12, POV.18 Ligand excluded by PLIP POV.7: 12 residues within 4Å: Chain A: F.1148, W.1173, I.1187, F.1190, V.1191, G.1194, L.1195, G.1198, A.1199, K.1200, V.1211 Ligands: POV.3 Ligand excluded by PLIP POV.8: 12 residues within 4Å: Chain A: L.1135, V.1138, W.1141, I.1142, I.1144, A.1145, F.1148, T.1149, F.1197, P.1385, I.1388 Ligands: POV.9 Ligand excluded by PLIP POV.9: 7 residues within 4Å: Chain A: L.1115, A.1116, V.1138, I.1142, L.1386 Ligands: POV.8, POV.10 Ligand excluded by PLIP POV.10: 14 residues within 4Å: Chain A: L.1115, A.1116, L.1118, F.1120, M.1122, L.1123, F.1126, Q.1139, I.1142, P.1385 Chain B: P.1282 Ligands: POV.9, POV.13, DU0.14 Ligand excluded by PLIP POV.11: 3 residues within 4Å: Chain D: M.1122 Ligands: POV.19, DU0.51 Ligand excluded by PLIP POV.13: 18 residues within 4Å: Chain A: W.1001, W.1012, I.1107, F.1110, W.1111, L.1115, L.1230, F.1233, L.1234, V.1236, N.1237, Q.1238 Chain B: V.1259, A.1262 Ligands: POV.10, POV.21, POV.24, POV.35 Ligand excluded by PLIP POV.15: 9 residues within 4Å: Chain A: P.1322, G.1323, W.1325 Chain D: H.1210, A.1214, L.1221 Ligands: POV.16, CLR.57, POV.59 Ligand excluded by PLIP POV.16: 13 residues within 4Å: Chain A: C.1310, C.1320, W.1325, F.1329 Chain D: W.1284, A.1287 Ligands: POV.15, POV.48, DU0.49, POV.54, POV.55, CLR.57, POV.64 Ligand excluded by PLIP POV.18: 10 residues within 4Å: Chain A: H.1210, A.1214, L.1221 Chain B: G.1321, P.1322, G.1323, W.1325 Ligands: CLR.4, POV.6, POV.19 Ligand excluded by PLIP POV.19: 14 residues within 4Å: Chain A: W.1284, A.1287 Chain B: D.1308, C.1310, C.1320, W.1325, F.1329 Ligands: POV.1, POV.2, CLR.4, POV.11, POV.18, POV.50, DU0.51 Ligand excluded by PLIP POV.20: 20 residues within 4Å: Chain B: Y.1177, V.1244, M.1245, G.1248, K.1249, A.1252, N.1253, Y.1295 Chain C: V.1264, S.1267, F.1268, L.1330, A.1332, V.1333, F.1336 Ligands: POV.21, POV.24, POV.25, M05.31, POV.35 Ligand excluded by PLIP POV.21: 17 residues within 4Å: Chain B: A.1262, W.1284, S.1285, A.1287, K.1288, V.1291, Y.1295 Chain C: C.1310, A.1311, N.1312, W.1325, P.1328, F.1329 Ligands: POV.13, POV.20, POV.24, POV.35 Ligand excluded by PLIP POV.22: 8 residues within 4Å: Chain B: I.1187, I.1204, D.1208, H.1210, V.1211, A.1214 Ligands: POV.25, POV.26 Ligand excluded by PLIP POV.24: 15 residues within 4Å: Chain A: W.1012, L.1234 Chain B: V.1251, A.1252, M.1254, F.1255, Y.1256, V.1258, M.1261, A.1262, I.1298 Chain C: F.1336 Ligands: POV.13, POV.20, POV.21 Ligand excluded by PLIP POV.25: 15 residues within 4Å: Chain B: R.985, F.1174, S.1175, Y.1177, V.1180, I.1184, S.1188, I.1218, L.1221, N.1222, F.1225 Ligands: POV.20, POV.22, M05.31, POV.34 Ligand excluded by PLIP POV.26: 12 residues within 4Å: Chain B: F.1148, W.1173, I.1187, F.1190, V.1191, G.1194, L.1195, G.1198, A.1199, K.1200, V.1211 Ligands: POV.22 Ligand excluded by PLIP POV.27: 11 residues within 4Å: Chain B: L.1135, W.1141, I.1142, I.1144, A.1145, F.1148, T.1149, F.1197, P.1385, I.1388 Ligands: POV.28 Ligand excluded by PLIP POV.28: 7 residues within 4Å: Chain B: A.1116, V.1138, I.1142, P.1383, L.1386 Ligands: POV.27, POV.29 Ligand excluded by PLIP POV.29: 14 residues within 4Å: Chain B: L.1115, A.1116, L.1118, F.1120, M.1122, L.1123, F.1126, Q.1139, I.1142, P.1385 Chain C: P.1282 Ligands: POV.28, POV.32, DU0.33 Ligand excluded by PLIP POV.30: 3 residues within 4Å: Chain B: W.1284 Ligands: DU0.14, POV.35 Ligand excluded by PLIP POV.32: 18 residues within 4Å: Chain B: W.1001, W.1012, I.1107, F.1110, W.1111, L.1115, L.1230, F.1233, L.1234, V.1236, N.1237, Q.1238 Chain C: V.1259, A.1262 Ligands: POV.29, POV.37, POV.40, POV.53 Ligand excluded by PLIP POV.34: 10 residues within 4Å: Chain B: H.1210, A.1214, L.1221 Chain C: G.1321, P.1322, G.1323, W.1325 Ligands: CLR.23, POV.25, POV.35 Ligand excluded by PLIP POV.35: 13 residues within 4Å: Chain B: W.1284, A.1287 Chain C: C.1310, C.1320, W.1325, F.1329 Ligands: POV.13, DU0.14, POV.20, POV.21, CLR.23, POV.30, POV.34 Ligand excluded by PLIP POV.36: 21 residues within 4Å: Chain C: Y.1177, I.1224, V.1244, M.1245, G.1248, K.1249, A.1252, N.1253, Y.1295 Chain D: V.1264, F.1268, L.1330, A.1332, V.1333, Y.1334, F.1336 Ligands: POV.37, POV.40, POV.41, M05.47, POV.53 Ligand excluded by PLIP POV.37: 16 residues within 4Å: Chain C: A.1262, W.1284, S.1285, K.1288, V.1291, Y.1295 Chain D: C.1310, A.1311, N.1312, W.1325, P.1328, F.1329 Ligands: POV.32, POV.36, POV.40, POV.53 Ligand excluded by PLIP POV.38: 8 residues within 4Å: Chain C: I.1187, I.1204, D.1208, H.1210, V.1211, A.1214 Ligands: POV.41, POV.42 Ligand excluded by PLIP POV.40: 14 residues within 4Å: Chain B: W.1012, L.1234 Chain C: V.1251, A.1252, M.1254, F.1255, Y.1256, V.1258, M.1261, A.1262 Chain D: F.1336 Ligands: POV.32, POV.36, POV.37 Ligand excluded by PLIP POV.41: 15 residues within 4Å: Chain C: R.985, F.1174, S.1175, Y.1177, V.1180, I.1184, S.1188, I.1218, L.1221, N.1222, F.1225 Ligands: POV.36, POV.38, M05.47, POV.52 Ligand excluded by PLIP POV.42: 12 residues within 4Å: Chain C: F.1148, W.1173, I.1187, F.1190, V.1191, G.1194, L.1195, G.1198, A.1199, K.1200, V.1211 Ligands: POV.38 Ligand excluded by PLIP POV.43: 11 residues within 4Å: Chain C: L.1135, W.1141, I.1142, I.1144, A.1145, F.1148, T.1149, F.1197, P.1385, I.1388 Ligands: POV.44 Ligand excluded by PLIP POV.44: 7 residues within 4Å: Chain C: A.1116, V.1138, I.1142, P.1383, L.1386 Ligands: POV.43, POV.45 Ligand excluded by PLIP POV.45: 14 residues within 4Å: Chain C: L.1115, A.1116, L.1118, F.1120, M.1122, L.1123, F.1126, Q.1139, I.1142, P.1385 Chain D: P.1282 Ligands: POV.44, POV.48, DU0.49 Ligand excluded by PLIP POV.46: 4 residues within 4Å: Chain B: M.1122 Chain C: W.1284 Ligands: DU0.33, POV.53 Ligand excluded by PLIP POV.48: 19 residues within 4Å: Chain C: W.1001, W.1012, L.1020, I.1107, F.1110, W.1111, L.1115, L.1230, F.1233, L.1234, V.1236, N.1237, Q.1238 Chain D: V.1259, A.1262 Ligands: POV.16, POV.45, POV.55, POV.58 Ligand excluded by PLIP POV.50: 19 residues within 4Å: Chain A: V.1259, A.1262, L.1266 Chain D: W.1001, W.1012, I.1107, F.1110, W.1111, L.1115, L.1230, F.1233, L.1234, V.1236, N.1237, Q.1238 Ligands: POV.2, POV.5, POV.19, POV.63 Ligand excluded by PLIP POV.52: 11 residues within 4Å: Chain C: H.1210, A.1214, L.1221 Chain D: C.1320, G.1321, P.1322, G.1323, W.1325 Ligands: CLR.39, POV.41, POV.53 Ligand excluded by PLIP POV.53: 14 residues within 4Å: Chain C: W.1284, A.1287 Chain D: D.1308, C.1310, C.1320, W.1325, F.1329 Ligands: POV.32, DU0.33, POV.36, POV.37, CLR.39, POV.46, POV.52 Ligand excluded by PLIP POV.54: 19 residues within 4Å: Chain A: S.1267, F.1268, L.1330, A.1332, V.1333, F.1336 Chain D: Y.1177, V.1244, M.1245, G.1248, K.1249, A.1252, N.1253, Y.1295 Ligands: POV.16, POV.55, POV.58, POV.59, M05.65 Ligand excluded by PLIP POV.55: 15 residues within 4Å: Chain A: C.1310, N.1312, W.1325, P.1328, F.1329 Chain D: A.1262, W.1284, S.1285, K.1288, V.1291, Y.1295 Ligands: POV.16, POV.48, POV.54, POV.58 Ligand excluded by PLIP POV.56: 8 residues within 4Å: Chain D: I.1187, I.1204, D.1208, H.1210, V.1211, A.1214 Ligands: POV.59, POV.60 Ligand excluded by PLIP POV.58: 15 residues within 4Å: Chain A: F.1336 Chain C: W.1012, L.1234 Chain D: V.1251, A.1252, M.1254, F.1255, Y.1256, V.1258, M.1261, A.1262, I.1298 Ligands: POV.48, POV.54, POV.55 Ligand excluded by PLIP POV.59: 15 residues within 4Å: Chain D: R.985, F.1174, S.1175, Y.1177, V.1180, I.1184, S.1188, I.1218, L.1221, N.1222, F.1225 Ligands: POV.15, POV.54, POV.56, M05.65 Ligand excluded by PLIP POV.60: 12 residues within 4Å: Chain D: F.1148, W.1173, I.1187, F.1190, V.1191, G.1194, L.1195, G.1198, A.1199, K.1200, V.1211 Ligands: POV.56 Ligand excluded by PLIP POV.61: 11 residues within 4Å: Chain D: L.1135, W.1141, I.1142, I.1144, A.1145, F.1148, T.1149, F.1197, P.1385, I.1388 Ligands: POV.62 Ligand excluded by PLIP POV.62: 7 residues within 4Å: Chain D: A.1116, V.1138, I.1142, P.1383, L.1386 Ligands: POV.61, POV.63 Ligand excluded by PLIP POV.63: 12 residues within 4Å: Chain D: L.1115, A.1116, L.1118, F.1120, M.1122, L.1123, F.1126, Q.1139, I.1142, P.1385 Ligands: POV.50, POV.62 Ligand excluded by PLIP POV.64: 4 residues within 4Å: Chain C: M.1122 Chain D: W.1284 Ligands: POV.16, DU0.49 Ligand excluded by PLIP

4 x CLR: CHOLESTEROL(Non-covalent)

CLR.4: 10 residues within 4Å: Chain A: Y.1177, I.1224, F.1225, V.1228 Chain B: W.1325, L.1326, F.1329, L.1330 Ligands: POV.18, POV.19 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:L.1326, B:F.1329, B:L.1330, A:I.1224, A:F.1225, A:F.1225 Hydrogen bonds: A:Y.1177 CLR.23: 10 residues within 4Å: Chain B: Y.1177, I.1224, F.1225, V.1228 Chain C: W.1325, L.1326, F.1329, L.1330 Ligands: POV.34, POV.35 7 PLIP interactions: 3 interactions with chain C, 4 interactions with chain B Hydrophobic interactions: C:L.1326, C:F.1329, C:L.1330, B:I.1224, B:F.1225, B:F.1225 Hydrogen bonds: B:Y.1177 CLR.39: 10 residues within 4Å: Chain C: Y.1177, I.1224, F.1225, V.1228 Chain D: W.1325, L.1326, F.1329, L.1330 Ligands: POV.52, POV.53 7 PLIP interactions: 3 interactions with chain D, 4 interactions with chain C Hydrophobic interactions: D:L.1326, D:F.1329, D:L.1330, C:I.1224, C:F.1225, C:F.1225 Hydrogen bonds: C:Y.1177 CLR.57: 9 residues within 4Å: Chain A: W.1325, L.1326, L.1330 Chain D: Y.1177, I.1224, F.1225, V.1228 Ligands: POV.15, POV.16 8 PLIP interactions: 4 interactions with chain A, 4 interactions with chain D Hydrophobic interactions: A:W.1325, A:W.1325, A:L.1326, A:L.1330, D:I.1224, D:F.1225, D:F.1225 Hydrogen bonds: D:Y.1177

4 x M05: 4-(4-chlorobenzyl)-1-(7H-pyrrolo[2,3-d]pyrimidin-4-yl)piperidin-4-aminium

M05.12: 14 residues within 4Å: Chain A: S.1175, D.1176, Y.1177, F.1178, D.1232, A.1235, V.1236, M.1245, W.1365, Q.1368, R.1369, F.1372 Ligands: POV.1, POV.6 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.1178, A:A.1235, A:V.1236, A:F.1372 Hydrogen bonds: A:Y.1177, A:D.1232 M05.31: 13 residues within 4Å: Chain B: S.1175, D.1176, Y.1177, F.1178, D.1232, A.1235, M.1245, W.1365, Q.1368, R.1369, F.1372 Ligands: POV.20, POV.25 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:F.1178, B:A.1235, B:Q.1368, B:F.1372 Hydrogen bonds: B:Y.1177, B:D.1232 M05.47: 13 residues within 4Å: Chain C: S.1175, D.1176, Y.1177, F.1178, D.1232, A.1235, M.1245, W.1365, Q.1368, R.1369, F.1372 Ligands: POV.36, POV.41 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:F.1178, C:A.1235, C:Q.1368, C:F.1372 Hydrogen bonds: C:Y.1177, C:D.1232 M05.65: 13 residues within 4Å: Chain D: S.1175, D.1176, Y.1177, F.1178, D.1232, A.1235, M.1245, W.1365, Q.1368, R.1369, F.1372 Ligands: POV.54, POV.59 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:F.1178, D:A.1235, D:Q.1368, D:F.1372 Hydrogen bonds: D:Y.1177, D:D.1232

4 x DU0: 2-[2-[(1~{S},2~{S},4~{S},5'~{R},6~{R},7~{S},8~{R},9~{S},12~{S},13~{R},16~{S})-5',7,9,13-tetramethylspiro[5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icos-18-ene-6,2'-oxane]-16-yl]oxyethyl]propane-1,3-diol(Non-covalent)

DU0.14: 9 residues within 4Å: Chain A: M.1122, T.1125 Chain B: P.1282, S.1283, W.1284, I.1290 Ligands: POV.10, POV.30, POV.35 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:W.1284, B:I.1290 DU0.33: 10 residues within 4Å: Chain B: M.1122, T.1125, F.1126 Chain C: P.1282, S.1283, W.1284, I.1290 Ligands: POV.29, POV.46, POV.53 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:T.1125, B:F.1126, C:W.1284, C:I.1290 DU0.49: 10 residues within 4Å: Chain C: M.1122, T.1125, F.1126 Chain D: P.1282, S.1283, W.1284, I.1290 Ligands: POV.16, POV.45, POV.64 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:F.1126, D:W.1284, D:I.1290 DU0.51: 8 residues within 4Å: Chain A: P.1282, S.1283, W.1284, I.1290 Chain D: M.1122, T.1125 Ligands: POV.11, POV.19 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain A Hydrophobic interactions: D:T.1125, A:W.1284, A:I.1290

1 x CA: CALCIUM ION(Non-covalent)

CA.17: 4 residues within 4Å: Chain A: G.1300 Chain B: G.1300 Chain C: G.1300 Chain D: G.1300 4 PLIP interactions: 1 interactions with chain B, 1 interactions with chain D, 1 interactions with chain A, 1 interactions with chain C Metal complexes: B:G.1300, D:G.1300, A:G.1300, C:G.1300

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nadezhdin, K.D. et al., Structural basis of selective TRPM7 inhibition by the anticancer agent CCT128930. Cell Rep (2024)

Release Date

2024-04-17

Peptides

Green fluorescent protein,Transient receptor potential cation channel subfamily M member 7: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Membrane

We predict this structure to be a membrane protein.
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Green fluorescent protein,Transient receptor potential cation channel subfamily M member 7