Receptor
PDB id Resolution Class Description Source Keywords
4JAO 2.05 Å EC: 2.3.1.- CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS PKS11 REVEAL INTERMEDIATES IN THE SYNTHESIS OF METHYL-BRANCHED ALKYLPYRO MYCOBACTERIUM TUBERCULOSIS LIPID BIOSYNTHESIS STRUCTURAL GENOMICS ENZYME FUNCTION INIKETOSYNTHASE ENZYME ALKYLPYRONE SYNTHESIS TRANSFERASE
Ref.: CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS POL SYNTHASE 11 (PKS11) REVEALS INTERMEDIATES IN THE SY OF METHYL-BRANCHED ALKYLPYRONES. J.BIOL.CHEM. V. 288 16484 2013
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
JAO C:401;
B:401;
Invalid;
Invalid;
none;
none;
submit data
270.494 C18 H38 O CCCCC...
PLM A:400;
D:400;
Valid;
Valid;
none;
none;
submit data
256.424 C16 H32 O2 CCCCC...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4JD3 2.25 Å EC: 2.3.1.- CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS PKS11 REVEAL INTERMEDIATES IN THE SYNTHESIS OF METHYL-BRANCHED ALKYLPYRO MYCOBACTERIUM TUBERCULOSIS LIPID BIOSYNTHESIS STRUCTURAL GENOMICS ENZYME FUNCTION INIKETOSYNTHASE ENZYME ALKYLPYRONE SYNTHESIS TRANSFERASE
Ref.: CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS POL SYNTHASE 11 (PKS11) REVEALS INTERMEDIATES IN THE SY OF METHYL-BRANCHED ALKYLPYRONES. J.BIOL.CHEM. V. 288 16484 2013
Members (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 28 families.
1 4JAP - COA C21 H36 N7 O16 P3 S CC(C)(CO[P....
2 4JD3 - COA C21 H36 N7 O16 P3 S CC(C)(CO[P....
3 4JAO - PLM C16 H32 O2 CCCCCCCCCC....
4 4JAT - PLM C16 H32 O2 CCCCCCCCCC....
5 4JAQ - COA C21 H36 N7 O16 P3 S CC(C)(CO[P....
70% Homology Family (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 25 families.
1 4JAP - COA C21 H36 N7 O16 P3 S CC(C)(CO[P....
2 4JD3 - COA C21 H36 N7 O16 P3 S CC(C)(CO[P....
3 4JAO - PLM C16 H32 O2 CCCCCCCCCC....
4 4JAT - PLM C16 H32 O2 CCCCCCCCCC....
5 4JAQ - COA C21 H36 N7 O16 P3 S CC(C)(CO[P....
50% Homology Family (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 24 families.
1 4JAP - COA C21 H36 N7 O16 P3 S CC(C)(CO[P....
2 4JD3 - COA C21 H36 N7 O16 P3 S CC(C)(CO[P....
3 4JAO - PLM C16 H32 O2 CCCCCCCCCC....
4 4JAT - PLM C16 H32 O2 CCCCCCCCCC....
5 4JAQ - COA C21 H36 N7 O16 P3 S CC(C)(CO[P....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: PLM; Similar ligands found: 52
No: Ligand ECFP6 Tc MDL keys Tc
1 MYR 1 1
2 F23 1 1
3 11A 1 1
4 STE 1 1
5 KNA 1 1
6 TDA 1 1
7 DCR 1 1
8 DAO 1 1
9 DKA 1 1
10 PLM 1 1
11 F15 1 1
12 OCA 0.956522 1
13 SHV 0.833333 0.952381
14 KTC 0.793103 0.875
15 AZ1 0.73913 0.64
16 6NA 0.72 0.904762
17 NER 0.71875 0.954545
18 OLA 0.71875 0.954545
19 ELA 0.71875 0.954545
20 VCA 0.666667 0.954545
21 PAM 0.666667 0.954545
22 PML 0.625 0.6
23 3LA 0.606061 0.8
24 LEA 0.6 0.809524
25 MYZ 0.588235 0.909091
26 12H 0.586207 0.615385
27 ODD 0.567568 0.913043
28 BRC 0.566667 0.666667
29 14V 0.555556 0.740741
30 M12 0.545455 0.869565
31 14U 0.542857 0.703704
32 EIC 0.538462 0.913043
33 EOD 0.538462 0.7
34 BUA 0.48 0.666667
35 RCL 0.468085 0.84
36 HXD 0.459459 0.807692
37 56S 0.459459 0.653846
38 ODT 0.452381 0.782609
39 3X1 0.444444 0.818182
40 LNL 0.44186 0.826087
41 CNS 0.435897 0.68
42 6UL 0.435897 0.68
43 5UF 0.432432 0.807692
44 243 0.428571 0.807692
45 GYM 0.418605 0.606061
46 PL3 0.413793 0.75
47 O8N 0.413793 0.75
48 1DO 0.413793 0.75
49 F09 0.413793 0.75
50 OC9 0.413793 0.75
51 DE1 0.413793 0.75
52 T25 0.403846 0.677419
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4JD3; Ligand: PLM; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 4jd3.bio2) has 25 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 4JD3; Ligand: COA; Similar sites found: 87
This union binding pocket(no: 2) in the query (biounit: 4jd3.bio2) has 42 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4OAS 2SW 0.003126 0.45634 None
2 2VOH CIT 0.00232 0.43259 None
3 1SN0 T44 0.02732 0.41249 None
4 2Z6C FMN 0.02165 0.4048 None
5 3ETG GWD 0.01142 0.42459 1.13314
6 2FN1 PYR 0.02667 0.40706 1.69972
7 1Z6T ADP 0.03053 0.40054 1.69972
8 1TMX HGX 0.0106 0.41334 1.70648
9 3CV2 COA 0.03334 0.42413 1.983
10 2G50 PYR 0.02086 0.42363 1.983
11 3RC3 ANP 0.02427 0.42267 2.26629
12 3ZGJ RMN 0.03931 0.41517 2.26629
13 1G6H ADP 0.01869 0.43636 2.33463
14 3SP6 IL2 0.02102 0.4054 2.45614
15 2NPA MMB 0.01852 0.40232 2.59259
16 3FEI CTM 0.006452 0.41717 2.62172
17 4R29 SAM 0.03043 0.41359 2.67857
18 4NON GDP 0.02126 0.42183 2.69231
19 2HI4 BHF 0.01571 0.4145 2.83286
20 4A4Z ANP 0.03618 0.40961 2.83286
21 3R75 PYR 0.04956 0.40008 2.83286
22 4QM7 GTP 0.04722 0.40345 2.92398
23 4H6B 10Y 0.03477 0.41421 3.07692
24 4H6B 10X 0.0408 0.40345 3.07692
25 3BD9 A3P 0.015 0.4259 3.21429
26 2X1L ADN 0.01139 0.42825 3.39943
27 3P2H NOO 0.02807 0.40231 3.48259
28 1M2Z BOG 0.0234 0.4401 3.50195
29 4LWU 20U 0.003428 0.45434 3.52941
30 3LXI CAM 0.01557 0.43838 3.68272
31 3B6C SDN 0.004278 0.46833 3.84615
32 1OI6 TMP 0.02075 0.42834 3.90244
33 4HBM 0Y7 0.01666 0.41327 4.16667
34 3C8Z 5CA 0.0194 0.40416 4.24929
35 3DZD ADP 0.03565 0.40018 4.24929
36 5E89 TD2 0.02913 0.40453 4.31655
37 1LVG ADP 0.04113 0.41407 4.54545
38 1F4F TP3 0.0436 0.40885 4.92424
39 3HYW DCQ 0.01787 0.43553 5.09915
40 3KMZ EQO 0.007208 0.40709 5.26316
41 4OKD GLC GLC GLC 0.04136 0.41706 5.38244
42 5TWO 7MV 0.01664 0.40726 5.51471
43 3HQP OXL 0.03251 0.40799 5.66572
44 4WN5 MVC 0.01415 0.40489 6.08696
45 5E5U MLI 0.02986 0.41361 6.43939
46 5FUS DAO 0.0218 0.41755 6.62021
47 3N5C GDP 0.04336 0.40543 6.79012
48 2Z9I GLY ALA THR VAL 0.04337 0.40422 6.79012
49 1FNN ADP 0.01335 0.41473 7.08215
50 5AHS SIN 0.0491 0.40742 7.08215
51 5VGR GDP 0.03059 0.4005 7.08215
52 4ZGM 32M 0.04453 0.41722 7.37705
53 4KBA 1QM 0.03752 0.41241 7.55287
54 2B6N ALA PRO THR 0.01916 0.41241 7.55396
55 3KO0 TFP 0.03348 0.41387 7.92079
56 1XPM HMG 0.00816 0.40242 8.08081
57 3GYT DL4 0.007599 0.41407 8.19672
58 2PZI AXX 0.01317 0.42881 8.2153
59 4RLT FSE 0.01612 0.42431 8.22785
60 3H78 BE2 0.00009192 0.47808 8.49858
61 4HSE ADP 0.02387 0.41552 8.78187
62 3OGN 3OG 0.01509 0.41534 8.87097
63 3I9U DTU 0.04536 0.40854 9.5057
64 4MPO AMP 0.02329 0.42051 9.80392
65 1JJ7 ADP 0.02703 0.42997 10
66 5HTX ADP 0.04561 0.40425 10.1983
67 2PRG BRL 0.01352 0.41764 10.2273
68 3JUQ AJD 0.0141 0.40496 10.2703
69 3JUQ AKD 0.01526 0.40081 10.2703
70 4I67 G G G RPC 0.009915 0.43924 10.3448
71 4PPF FLC 0.04379 0.4169 10.5714
72 5NBW 8SK 0.04331 0.4021 10.7477
73 3WFD AXO 0.02526 0.4217 10.7981
74 3W9R A8S 0.03588 0.40636 11.1111
75 3SK2 GRI 0.03361 0.41881 11.3636
76 1FWV SGA MAG FUC 0.03334 0.42329 11.9403
77 1VKJ A3P 0.02132 0.40226 12.9825
78 4YSX E23 0.03334 0.41916 30.1282
79 1HZP DAO 0.0003701 0.41986 34.0299
80 5BQS 4VN 0.007682 0.42945 34.3653
81 1EBL COA 0.003014 0.44153 38.4858
82 5BNS 4VM 0.001933 0.43373 38.4858
83 3EUT DCR 0.00006592 0.49543 39.9433
84 5WX3 COA 0.0000000004303 0.72137 45.3258
85 2D3M COA 0.0000000016 0.7214 46.1756
86 1EE0 CAA 0.000000001357 0.68518 47.3088
87 3AWJ COA 0.00000000019 0.50366 47.3088
Pocket No.: 3; Query (leader) PDB : 4JD3; Ligand: PLM; Similar sites found: 65
This union binding pocket(no: 3) in the query (biounit: 4jd3.bio2) has 44 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4OAS 2SW 0.00342 0.45634 None
2 2VOH CIT 0.002487 0.43259 None
3 2FN1 PYR 0.02841 0.40706 1.69972
4 1Z6T ADP 0.03307 0.40054 1.69972
5 1TMX HGX 0.01162 0.41334 1.70648
6 3CV2 COA 0.03554 0.42413 1.983
7 2G50 PYR 0.02229 0.42363 1.983
8 3ZGJ RMN 0.04209 0.41517 2.26629
9 1G6H ADP 0.01998 0.43636 2.33463
10 2NPA MMB 0.0192 0.40336 2.59259
11 3FEI CTM 0.006223 0.41974 2.62172
12 4R29 SAM 0.03274 0.41359 2.67857
13 4NON GDP 0.02292 0.42183 2.69231
14 2HI4 BHF 0.01709 0.4145 2.83286
15 4A4Z ANP 0.03888 0.40961 2.83286
16 4H6B 10Y 0.03732 0.41421 3.07692
17 2FDW D3G 0.01234 0.4403 3.11615
18 3BD9 A3P 0.01624 0.4259 3.21429
19 1NF8 BOG 0.0493 0.41444 3.38164
20 2X1L ADN 0.01237 0.42825 3.39943
21 1M2Z BOG 0.02483 0.4401 3.50195
22 4LWU 20U 0.003748 0.45434 3.52941
23 3LXI CAM 0.01673 0.43838 3.68272
24 3B6C SDN 0.004635 0.46833 3.84615
25 4HBM 0Y7 0.01812 0.41327 4.16667
26 3C8Z 5CA 0.02137 0.40395 4.24929
27 5E89 TD2 0.03151 0.40453 4.31655
28 3F81 STT 0.04886 0.41486 4.37158
29 3HYW DCQ 0.01914 0.43553 5.09915
30 5MES 7LT 0.03858 0.40638 5.21739
31 4OKD GLC GLC GLC 0.04411 0.41706 5.38244
32 5TWO 7MV 0.01815 0.40726 5.51471
33 4WN5 MVC 0.01551 0.40489 6.08696
34 5E5U MLI 0.03158 0.41361 6.43939
35 5FUS DAO 0.02354 0.41755 6.62021
36 3N5C GDP 0.04654 0.40543 6.79012
37 2Z9I GLY ALA THR VAL 0.04616 0.40422 6.79012
38 1FNN ADP 0.01456 0.41473 7.08215
39 4ZGM 32M 0.0473 0.41722 7.37705
40 4KBA 1QM 0.04024 0.41241 7.55287
41 2B6N ALA PRO THR 0.0204 0.41241 7.55396
42 3KO0 TFP 0.03562 0.41387 7.92079
43 2PZI AXX 0.01427 0.42881 8.2153
44 4RLT FSE 0.01744 0.42431 8.22785
45 3H78 BE2 0.0001053 0.47808 8.49858
46 4HSE ADP 0.02576 0.41552 8.78187
47 3OGN 3OG 0.01642 0.41534 8.87097
48 1JJ7 ADP 0.02884 0.42997 10
49 5HTX ADP 0.04895 0.40425 10.1983
50 4I67 G G G RPC 0.01074 0.43924 10.3448
51 4PPF FLC 0.04651 0.4169 10.5714
52 3SK2 GRI 0.03596 0.41881 11.3636
53 5BVB DOG 0.04688 0.41436 11.3636
54 1VKJ A3P 0.02322 0.40226 12.9825
55 1AX2 NDG GAL 0.04798 0.41196 13.3891
56 4YSX E23 0.03573 0.41916 30.1282
57 1HZP DAO 0.0004293 0.41188 34.0299
58 5BQS 4VN 0.008392 0.42945 34.3653
59 5BNS 4VM 0.001708 0.43802 38.4858
60 3EUT DCR 0.00003581 0.50905 39.9433
61 5WX3 COA 0.0000000005273 0.72137 45.3258
62 2D3M COA 0.000000001924 0.7214 46.1756
63 1EE0 CAA 0.000000001662 0.68518 47.3088
64 3AWJ COA 0.0000000002298 0.49032 47.3088
65 1D6H COA 0.000000003062 0.5866 49.5751
Pocket No.: 4; Query (leader) PDB : 4JD3; Ligand: COA; Similar sites found: 33
This union binding pocket(no: 4) in the query (biounit: 4jd3.bio1) has 43 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4N14 WR7 0.01643 0.42025 1.91083
2 3OBT SLB 0.01608 0.40125 1.983
3 3HMO STU 0.034 0.40205 2.33918
4 5JZJ AN2 0.02525 0.40847 2.6936
5 4RQL SNE 0.01188 0.44031 2.83286
6 2WU6 DKI 0.0161 0.40328 2.83286
7 2FDW D3G 0.04502 0.40893 3.11615
8 5X8I SQZ 0.01875 0.41825 3.46821
9 4AVB CMP 0.04427 0.40244 3.9039
10 5FCF GLY GLY GLY 0.04623 0.40726 3.96601
11 4Q86 AMP 0.02769 0.40967 4.24929
12 2WGV CIT 0.04504 0.41027 4.43548
13 2B9J ADP 0.03517 0.40132 4.53258
14 5MES 7LT 0.04038 0.40453 5.21739
15 4D52 GXL 0.03638 0.41568 5.39683
16 4D52 GIV 0.0371 0.4149 5.39683
17 4D4U FUC GAL 0.02977 0.40884 5.39683
18 1W2D ADP 0.0342 0.41175 5.66038
19 1J78 VDY 0.02161 0.42627 6.79887
20 1ULE GLA GAL NAG 0.01952 0.42375 7.33333
21 4R78 AMP 0.04754 0.40763 7.44337
22 1UGY GLA BGC 0.01195 0.44276 7.5188
23 1UGY GLA GLC 0.02506 0.40249 7.5188
24 1JAC AMG 0.03308 0.40229 7.5188
25 2F6U CIT 0.04797 0.41116 7.69231
26 4HK8 XYP XYP XYP XYP XYP XYP 0.01534 0.40423 12.1693
27 2GUC MAN 0.01657 0.40605 14.7541
28 5A7C 5D4 0.03475 0.41189 15.0442
29 5V3D FCN 0.04486 0.41308 15.1724
30 2A19 ANP 0.04898 0.40342 15.4286
31 1DZK PRZ 0.01729 0.42003 23.5669
32 4XBT FLC 0.03609 0.40383 28.3871
33 1D6H COA 0.00000000122 0.59597 49.5751
Pocket No.: 5; Query (leader) PDB : 4JD3; Ligand: PLM; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 5) in the query (biounit: 4jd3.bio1) has 24 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 6; Query (leader) PDB : 4JD3; Ligand: PLM; Similar sites found: 30
This union binding pocket(no: 6) in the query (biounit: 4jd3.bio1) has 44 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4N14 WR7 0.01695 0.42025 1.91083
2 3OBT SLB 0.01658 0.40125 1.983
3 3HMO STU 0.03533 0.40205 2.33918
4 2WU6 DKI 0.01684 0.40328 2.83286
5 5X8I SQZ 0.0195 0.41825 3.46821
6 1OI6 TMP 0.01203 0.44353 3.90244
7 4AVB CMP 0.04588 0.40244 3.9039
8 5FCF GLY GLY GLY 0.04762 0.40726 3.96601
9 4Q86 AMP 0.02877 0.40967 4.24929
10 2WGV CIT 0.04649 0.41027 4.43548
11 2B9J ADP 0.03653 0.40132 4.53258
12 4D52 GXL 0.03754 0.41568 5.39683
13 4D52 GIV 0.03828 0.4149 5.39683
14 4D4U FUC GAL 0.0307 0.40884 5.39683
15 1W2D ADP 0.03545 0.41175 5.66038
16 1J78 VDY 0.02241 0.42627 6.79887
17 5VGR GDP 0.01916 0.41209 7.08215
18 1ULE GLA GAL NAG 0.02015 0.42375 7.33333
19 4R78 AMP 0.04918 0.40763 7.44337
20 1UGY GLA BGC 0.01233 0.44276 7.5188
21 1UGY GLA GLC 0.0258 0.40249 7.5188
22 1JAC AMG 0.03404 0.40229 7.5188
23 2F6U CIT 0.04958 0.41116 7.69231
24 4MPO AMP 0.04468 0.40452 9.80392
25 4HK8 XYP XYP XYP XYP XYP XYP 0.01604 0.40423 12.1693
26 2GUC MAN 0.01708 0.40605 14.7541
27 5A7C 5D4 0.03579 0.41189 15.0442
28 5V3D FCN 0.0463 0.41308 15.1724
29 1DZK PRZ 0.01799 0.42003 23.5669
30 4XBT FLC 0.03746 0.40383 28.3871
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