Receptor
PDB id Resolution Class Description Source Keywords
3TUR 1.72 Å EC: 3.-.-.- CRYSTAL STRUCTURE OF M. TUBERCULOSIS LD-TRANSPEPTIDASE TYPE COMPLEXED WITH A PEPTIDOGLYCAN FRAGMENT MYCOBACTERIUM TUBERCULOSIS PROTEIN-PEPTIDOGLYCAN COMPLEX PEPTIDOGLYCAN BINDING PROTEIN
Ref.: TARGETING THE CELL WALL OF MYCOBACTERIUM TUBERCULOS STRUCTURE AND MECHANISM OF L,D-TRANSPEPTIDASE 2. STRUCTURE V. 20 2103 2012
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
0JC A:501;
A:502;
A:503;
A:504;
B:502;
B:503;
B:504;
B:505;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
764.162 C4 H16 I2 N4 Pt2 C1C[N...
6CL A:506;
Valid;
none;
submit data
191.205 C7 H15 N2 O4 C(C[C...
DGL A:505;
Valid;
none;
submit data
147.129 C5 H9 N O4 C(CC(...
PT B:501;
Invalid;
none;
submit data
195.078 Pt [Pt+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3TUR 1.72 Å EC: 3.-.-.- CRYSTAL STRUCTURE OF M. TUBERCULOSIS LD-TRANSPEPTIDASE TYPE COMPLEXED WITH A PEPTIDOGLYCAN FRAGMENT MYCOBACTERIUM TUBERCULOSIS PROTEIN-PEPTIDOGLYCAN COMPLEX PEPTIDOGLYCAN BINDING PROTEIN
Ref.: TARGETING THE CELL WALL OF MYCOBACTERIUM TUBERCULOS STRUCTURE AND MECHANISM OF L,D-TRANSPEPTIDASE 2. STRUCTURE V. 20 2103 2012
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 218 families.
1 4GSU - DWZ C17 H27 N3 O5 S C[C@H]1[C@....
2 3TUR - 6CL C7 H15 N2 O4 C(C[C@H](C....
70% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 176 families.
1 4GSU - DWZ C17 H27 N3 O5 S C[C@H]1[C@....
2 3TUR - 6CL C7 H15 N2 O4 C(C[C@H](C....
3 5DVP - POA C2 H5 O4 P C(C=O)P(=O....
50% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 143 families.
1 4GSU - DWZ C17 H27 N3 O5 S C[C@H]1[C@....
2 3TUR - 6CL C7 H15 N2 O4 C(C[C@H](C....
3 5DVP - POA C2 H5 O4 P C(C=O)P(=O....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 6CL; Similar ligands found: 25
No: Ligand ECFP6 Tc MDL keys Tc
1 6CL 1 1
2 API 0.655172 0.961538
3 NLE 0.529412 0.7
4 ORN 0.5 0.758621
5 LYS 0.5 0.766667
6 DLY 0.472222 0.733333
7 UN1 0.472222 0.888889
8 11C 0.472222 0.888889
9 DHH 0.459459 0.793103
10 NVA 0.454545 0.689655
11 ONH 0.447368 0.621622
12 2JJ 0.447368 0.615385
13 5OY 0.447368 0.615385
14 NPI 0.447368 0.857143
15 26P 0.435897 0.8
16 CIR 0.425 0.666667
17 HSE 0.424242 0.65625
18 DAB 0.424242 0.677419
19 DBB 0.419355 0.642857
20 ABA 0.419355 0.642857
21 ARG 0.414634 0.638889
22 DAR 0.414634 0.638889
23 2NP 0.414634 0.727273
24 6HN 0.414634 0.619048
25 HCS 0.411765 0.666667
Ligand no: 2; Ligand: DGL; Similar ligands found: 53
No: Ligand ECFP6 Tc MDL keys Tc
1 GLU 1 1
2 DGL 1 1
3 GGL 1 1
4 GLN 0.62963 0.821429
5 DGN 0.62963 0.821429
6 ONL 0.586207 0.821429
7 UN1 0.566667 0.96
8 11C 0.566667 0.96
9 HCS 0.555556 0.714286
10 HGA 0.53125 0.666667
11 NPI 0.53125 0.923077
12 HSE 0.518519 0.758621
13 DAB 0.518519 0.666667
14 MEQ 0.515152 0.71875
15 3O3 0.513514 0.727273
16 API 0.5 0.884615
17 NVA 0.5 0.740741
18 ASP 0.481481 0.846154
19 DAS 0.481481 0.846154
20 TNA 0.463415 0.685714
21 ABA 0.461538 0.692308
22 DSN 0.461538 0.655172
23 DBB 0.461538 0.692308
24 SER 0.461538 0.655172
25 RGP 0.459459 0.648649
26 ORN 0.451613 0.689655
27 HOZ 0.451613 0.666667
28 AE5 0.447368 0.727273
29 DCY 0.444444 0.642857
30 CYS 0.444444 0.642857
31 C2N 0.444444 0.666667
32 NLE 0.4375 0.689655
33 S2G 0.433333 0.653846
34 2HG 0.433333 0.653846
35 ASN 0.428571 0.677419
36 26P 0.428571 0.857143
37 3GC 0.425 0.705882
38 MET 0.424242 0.625
39 MSE 0.424242 0.606061
40 DLY 0.424242 0.666667
41 MED 0.424242 0.625
42 BIX 0.418605 0.631579
43 MF3 0.416667 0.625
44 CBH 0.414634 0.774194
45 LYS 0.411765 0.645161
46 DHH 0.411765 0.851852
47 SHR 0.409091 0.774194
48 2NP 0.405405 0.71875
49 LEU 0.4 0.642857
50 5OY 0.4 0.648649
51 AS2 0.4 0.84
52 2JJ 0.4 0.648649
53 ONH 0.4 0.611111
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3TUR; Ligand: DGL; Similar sites found: 35
This union binding pocket(no: 1) in the query (biounit: 3tur.bio1) has 12 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3V2Q PLM 0.0259 0.41291 None
2 1I2B NAD 0.01359 0.44913 1.74216
3 4B5W PYR 0.02619 0.42104 1.95312
4 1YID ATP 0.005426 0.43132 2.09059
5 2IYA UDP 0.008774 0.42331 3.13589
6 2WTX UDP 0.02516 0.4209 3.13589
7 3LOO B4P 0.04326 0.40661 3.13589
8 2HVW DCP 0.04747 0.40857 3.26087
9 1T8U A3P 0.03004 0.40019 3.30882
10 4KQP GLN 0.01267 0.40028 3.44828
11 5JY4 ISC 0.01339 0.4135 3.48432
12 5JXZ ISJ 0.0171 0.40763 3.48432
13 5JXZ ISC 0.01857 0.40763 3.48432
14 1VR0 3SL 0.01381 0.40007 3.64372
15 4TR9 ASP TRP ASN 0.01994 0.40058 3.83275
16 1ZRH A3P 0.007358 0.43343 4.0146
17 4Z24 FAD 0.01691 0.43238 4.18118
18 4COL DTP 0.01611 0.40877 4.18118
19 3M8U GDS 0.0161 0.42091 4.52962
20 1VKJ A3P 0.009698 0.42496 4.5614
21 5KKA 6V0 0.03459 0.41016 4.87805
22 3Q9T FAY 0.02248 0.42429 5.92335
23 3VP6 HLD 0.02309 0.4092 6.62021
24 1N07 FMN 0.01676 0.43217 6.74847
25 1N07 ADP 0.01257 0.42456 6.74847
26 2Q4H AMP 0.004363 0.45172 6.96864
27 4USF 6UI 0.02718 0.40549 7.66551
28 4QA8 PJZ 0.03032 0.40289 7.86026
29 3MPI FAD 0.03264 0.41406 8.01394
30 1FIQ MTE 0.04228 0.40358 10.1045
31 4AT0 FAD 0.01148 0.44929 10.453
32 4C3Y FAD 0.04797 0.40848 10.8014
33 3T3C 017 0.02942 0.41027 13.1313
34 1LQA NDP 0.03248 0.41423 14.2857
35 2Q2A ARG 0.01539 0.40349 14.7059
Pocket No.: 2; Query (leader) PDB : 3TUR; Ligand: 6CL; Similar sites found: 11
This union binding pocket(no: 2) in the query (biounit: 3tur.bio1) has 13 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4B5W PYR 0.04707 0.40633 1.95312
2 1YID ATP 0.007939 0.42076 2.09059
3 2OGA PGU 0.02138 0.40904 2.43902
4 5JY4 ISC 0.02191 0.40196 3.48432
5 1ZRH A3P 0.01205 0.42112 4.0146
6 1VKJ A3P 0.01571 0.41443 4.5614
7 3Q9T FAY 0.03282 0.41666 5.92335
8 2Q4H AMP 0.01727 0.42145 6.96864
9 2UUU FAD 0.04284 0.42012 9.7561
10 2UUU PL3 0.04284 0.42012 9.7561
11 2NNQ T4B 0.03752 0.41347 16.7939
Pocket No.: 3; Query (leader) PDB : 3TUR; Ligand: DGL; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 3tur.bio3) has 25 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 3TUR; Ligand: 6CL; Similar sites found: 1
This union binding pocket(no: 4) in the query (biounit: 3tur.bio3) has 28 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3IHB GLU 0.02922 0.40548 6.27178
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