Receptor
PDB id Resolution Class Description Source Keywords
1S07 2.42 Å EC: 2.6.1.62 CRYSTAL STRUCTURE OF THE R253A MUTANT OF 7,8-DIAMINOPELARGON SYNTHASE ESCHERICHIA COLI AMINOTRANSFERASE FOLD TYPE I SUBCLASS II HOMODIMER TRANS
Ref.: CONSERVED AND NONCONSERVED RESIDUES IN THE SUBSTRAT SITE OF 7,8-DIAMINOPELARGONIC ACID SYNTHASE FROM ES COLI ARE ESSENTIAL FOR CATALYSIS. BIOCHEMISTRY V. 43 1213 2004
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
IPA B:600;
Invalid;
none;
submit data
60.095 C3 H8 O CC(C)...
NA A:501;
B:502;
Part of Protein;
Part of Protein;
none;
none;
submit data
22.99 Na [Na+]
PLP A:430;
B:431;
Valid;
Valid;
none;
none;
submit data
247.142 C8 H10 N O6 P Cc1c(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1MLY 1.81 Å EC: 2.6.1.62 CRYSTAL STRUCTURE OF 7,8-DIAMINOPELARGONIC ACID SYNTHASE IN WITH THE CIS ISOMER OF AMICLENOMYCIN ESCHERICHIA COLI AMINOTRANSFERASE FOLD TYPE I SUBCLASS II AMICLENOMYCIN TRANSFERASE
Ref.: STRUCTURAL BASIS FOR THE INHIBITION OF THE BIOSYNTH BIOTIN BY THE ANTIBIOTIC AMICLENOMYCIN J.BIOL.CHEM. V. 277 43352 2002
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 1MLZ - TZA PLP n/a n/a
2 1MLY - ACZ PLP n/a n/a
3 1S07 - PLP C8 H10 N O6 P Cc1c(c(c(c....
70% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 1MLZ - TZA PLP n/a n/a
2 1MLY - ACZ PLP n/a n/a
3 1S07 - PLP C8 H10 N O6 P Cc1c(c(c(c....
50% Homology Family (29)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 4WYC Kd = 15 uM 3VS C10 H9 N3 O c1cc(ccc1C....
2 4CXR - 2BG C8 H8 N2 S c1ccc2c(c1....
3 3TFU - PL8 C16 H22 N3 O7 P Cc1c(c(c(c....
4 4MQR - 2B9 C14 H15 N4 O6 P CC1=C(/C(=....
5 4MQP - 2B1 C15 H15 N4 O5 P S Cc1c(c(c(c....
6 4XJO Kd = 132 nM 41O C20 H17 Cl N2 O2 c1cc(cc(c1....
7 5KGS Kd = 74 nM 6SR C21 H20 N2 O4 c1cc2c(cc1....
8 4W1W ic50 = 0.195 uM 3G8 C18 H17 N O3 S CCN(CC)c1c....
9 4WYG Kd = 6.8 uM 3W1 C11 H12 Cl N3 c1cc(ccc1C....
10 4MQQ - 2B6 C16 H15 N4 O6 P S Cc1c(c(c(c....
11 4XEW ic50 = 0.44 uM 40N C16 H10 F N O3 c1ccc(c(c1....
12 4W1V ic50 = 0.659 uM 3GS C16 H14 F N O5 S COC(=O)c1c....
13 4XJP Kd = 108 nM 41N C20 H20 N2 O4 CC(=O)c1cc....
14 4WYF Kd = 21.7 uM 3VX C11 H9 N O2 CC(=O)Nc1c....
15 4WYA Kd = 6.9 uM 3VQ C10 H8 N2 O S c1ccnc(c1)....
16 4W1X - 3G9 C19 H19 Cl N2 O2 CC(=O)c1cc....
17 5KGT - 6SQ C20 H20 Cl N O2 CC(=O)c1cc....
18 4WYE Kd = 41.8 uM 3VW C12 H15 N O c1ccc(cc1)....
19 4CXQ - KAP C9 H17 N O3 C[C@@H](C(....
20 4WYD Kd = 11.7 uM 3VR C12 H15 N3 CNCc1ccc(c....
21 3LV2 - SFG C15 H23 N7 O5 c1nc(c2c(n....
22 5TE2 - 7B9 C16 H22 N3 O7 P Cc1c(c(c(c....
23 4B9B - PLP C8 H10 N O6 P Cc1c(c(c(c....
24 4B98 - PXG C15 H17 N2 O7 P Cc1c(c(c(c....
25 1MLZ - TZA PLP n/a n/a
26 1MLY - ACZ PLP n/a n/a
27 1S07 - PLP C8 H10 N O6 P Cc1c(c(c(c....
28 3DU4 - KAP C9 H17 N O3 C[C@@H](C(....
29 3A8U - PLP C8 H10 N O6 P Cc1c(c(c(c....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: PLP; Similar ligands found: 55
No: Ligand ECFP6 Tc MDL keys Tc
1 PLP 1 1
2 PZP 0.729167 0.843137
3 EXT 0.62069 0.8
4 AN7 0.603448 0.918367
5 EPC 0.603448 0.862745
6 FOO 0.59322 0.849057
7 PLR 0.58 0.895833
8 4LM 0.57377 0.818182
9 0JO 0.57377 0.803571
10 P3D 0.571429 0.704918
11 MPM 0.564516 0.814815
12 KOU 0.555556 0.836364
13 HCP 0.546875 0.77193
14 6DF 0.545455 0.811321
15 PXL 0.541667 0.659574
16 Z98 0.537313 0.75
17 PXP 0.537037 0.862745
18 PMP 0.527273 0.767857
19 P0P 0.527273 0.916667
20 PL6 0.522388 0.818182
21 GT1 0.517857 0.830189
22 PFM 0.514706 0.803571
23 LLP 0.5 0.737705
24 PL5 0.479452 0.775862
25 PUS 0.479452 0.707692
26 MPL 0.473684 0.836364
27 PLG 0.46875 0.75
28 IN5 0.46875 0.758621
29 P89 0.466667 0.714286
30 PLP PUT 0.463768 0.684211
31 5DK 0.460526 0.725806
32 O1G 0.454545 0.75
33 PLP ABU 0.450704 0.706897
34 PLT 0.439024 0.762712
35 X04 0.431034 0.851852
36 PP3 0.426471 0.762712
37 P1T 0.426471 0.714286
38 PDD 0.426471 0.762712
39 PDA 0.426471 0.762712
40 IK2 0.42029 0.714286
41 33P 0.42029 0.745763
42 2BO 0.414286 0.793103
43 PLS 0.414286 0.779661
44 PMH 0.414286 0.619718
45 5PA 0.414286 0.714286
46 TLP 0.414286 0.793103
47 2BK 0.414286 0.793103
48 C6P 0.408451 0.75
49 PPD 0.408451 0.75
50 QLP 0.405405 0.681818
51 MP5 0.403509 0.666667
52 PY5 0.402778 0.703125
53 PLA 0.402778 0.703125
54 HEY 0.4 0.703125
55 PLP PHE 0.4 0.732143
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1MLY; Ligand: ACZ PLP; Similar sites found: 51
This union binding pocket(no: 1) in the query (biounit: 1mly.bio1) has 21 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1LW4 TLP 0.002883 0.41672 1.15274
2 1LW4 PLP 0.001691 0.41615 1.15274
3 5W71 9YM 0.009967 0.41977 1.3986
4 4K2M O1G 0.0009855 0.41787 1.6317
5 5W70 9YM 0.004645 0.40188 1.6317
6 4RD0 GDP 0.003436 0.40175 2.16867
7 3WXM GTP 0.005246 0.41426 2.7972
8 1DJ9 KAM 0.002199 0.42982 2.86458
9 1E5F PLP 0.008718 0.40293 3.21782
10 5K8B PDG 0.00166 0.40703 3.22581
11 2Z9V PXM 0.002155 0.45482 3.31633
12 2FYF PLP 0.01269 0.4111 3.7296
13 1DFO PLG 0.005707 0.40586 4.1958
14 2P3V SRT 0.02248 0.40471 4.29688
15 5X2Z 3LM 0.002667 0.42886 4.52261
16 5X30 4LM 0.002593 0.42256 4.52261
17 5X30 7XF 0.003042 0.41572 4.52261
18 3WGC PLG 0.001558 0.43654 4.69208
19 1VJO PLP 0.0008006 0.44952 5.08906
20 1M32 PLP 0.006532 0.43114 5.7377
21 1PMO PLR 0.01384 0.40109 6.99301
22 1GWN GTP 0.007775 0.40004 7.69231
23 3ZRR PXG 0.002597 0.41326 9.11458
24 4LNL PLG 0.002443 0.43207 9.30931
25 4LNL 2BO 0.003265 0.42211 9.30931
26 2EW1 GNP 0.00783 0.40337 9.95025
27 4PPF FLC 0.03488 0.40212 12.5714
28 1FC4 AKB PLP 0.005673 0.40408 13.986
29 4K7O EKZ 0.01951 0.40396 18.4524
30 5DDW 5B6 0.000000006601 0.627 22.8438
31 4ZSY RW2 0.000000003452 0.63857 27.5058
32 4ZM4 PLP 0.00000004725 0.64842 31.4685
33 4ZM4 P3B 0.00000002583 0.61862 31.4685
34 4AOA IK2 0.000000002386 0.69736 32.1678
35 4ADC PLP 0.000000006305 0.60128 34.7291
36 3BS8 PMP 0.0000000933 0.64429 37.9953
37 2CJH AKG 0.00000004572 0.63984 37.9953
38 2YKX AKG 0.003079 0.43521 38.2284
39 3FQ8 PMP 0.000000008563 0.66687 38.4075
40 1ZC9 PMP 0.0000006645 0.57284 40.3263
41 5G09 6DF 0.0000000004737 0.68993 40.7925
42 1SFF IK2 0.000000001034 0.67517 41.784
43 4E3Q PMP 0.0000000005404 0.76207 42.4242
44 5G4J EXT 0.0000006871 0.57222 43.722
45 4UOX PLP 0.000000003307 0.71247 45.9207
46 4UOX PUT 0.000000001821 0.70262 45.9207
47 4UOX PLP PUT 0.000000007616 0.66521 45.9207
48 5WYF ILP 0.00000002001 0.6233 45.9207
49 4UHO PLP 0.00000002246 0.70772 46.3869
50 4BA5 PXG 0.0000001714 0.61409 47.3193
51 2OAT PFM 0.000000004225 0.67643 48.2517
Pocket No.: 2; Query (leader) PDB : 1MLY; Ligand: ACZ PLP; Similar sites found: 19
This union binding pocket(no: 2) in the query (biounit: 1mly.bio1) has 23 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5W71 PLP 0.0006623 0.42437 1.3986
2 4M2K PLP 0.01023 0.41931 1.47783
3 1CZA G6P 0.01943 0.40129 1.6317
4 1U08 PLP 0.004848 0.4308 1.81347
5 3QPB URA 0.0251 0.40299 2.12766
6 4OKD GLC GLC GLC 0.02519 0.40836 2.7972
7 2FN1 PYR 0.02062 0.40526 2.7972
8 3KYF 5GP 5GP 0.01426 0.40789 3.0303
9 2HHP FLC 0.02553 0.42662 3.20755
10 1B9I PXG 0.002446 0.40487 3.35052
11 4IY7 KOU 0.005464 0.40511 4.78589
12 4IY7 0JO 0.005918 0.40363 4.78589
13 4IYO 0JO 0.0071 0.40025 4.78589
14 3VMF GTP 0.007045 0.40217 5.09383
15 3PD6 PMP 0.006634 0.42415 5.23691
16 3PDB PMP 0.007875 0.41629 5.23691
17 3VP6 HLD 0.001646 0.40755 7.69231
18 2RI1 GLP 0.004759 0.44731 10.2128
19 4D06 X8W 0.0446 0.4057 10.2473
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