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Receptor
PDB id Resolution Class Description Source Keywords
4FL0 2.3 Å EC: 2.6.1.- CRYSTAL STRUCTURE OF ALD1 FROM ARABIDOPSIS THALIANA ARABIDOPSIS THALIANA STRUCTURAL GENOMICS PROTEIN STRUCTURE INITIATIVE ISRAEL STPROTEOMICS CENTER ISPC SANDWICH FOLD AND ARCHITECTURE PARESISTANCE PLP NBINDING TRANSFERASE
Ref.: STRUCTURE OF ALD1, A PLANT-SPECIFIC HOMOLOGUE OF TH UNIVERSAL DIAMINOPIMELATE AMINOTRANSFERASE ENZYME O BIOSYNTHESIS. ACTA CRYSTALLOGR.,SECT.F V. 69 84 2013
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
PLP A:501;
B:501;
Valid;
Valid;
none;
none;
submit data
247.142 C8 H10 N O6 P Cc1c(...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4FL0 2.3 Å EC: 2.6.1.- CRYSTAL STRUCTURE OF ALD1 FROM ARABIDOPSIS THALIANA ARABIDOPSIS THALIANA STRUCTURAL GENOMICS PROTEIN STRUCTURE INITIATIVE ISRAEL STPROTEOMICS CENTER ISPC SANDWICH FOLD AND ARCHITECTURE PARESISTANCE PLP NBINDING TRANSFERASE
Ref.: STRUCTURE OF ALD1, A PLANT-SPECIFIC HOMOLOGUE OF TH UNIVERSAL DIAMINOPIMELATE AMINOTRANSFERASE ENZYME O BIOSYNTHESIS. ACTA CRYSTALLOGR.,SECT.F V. 69 84 2013
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 4FL0 - PLP C8 H10 N O6 P Cc1c(c(c(c....
70% Homology Family (9)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 4FL0 - PLP C8 H10 N O6 P Cc1c(c(c(c....
2 2Z1Z - MLT C4 H6 O5 C([C@H](C(....
3 3EIB - PLP C8 H10 N O6 P Cc1c(c(c(c....
4 3EI8 - PL5 C15 H22 N3 O9 P Cc1c(c(c(c....
5 3EI6 - PL4 C15 H24 N3 O9 P Cc1c(c(c(c....
6 2Z20 - PLP C8 H10 N O6 P Cc1c(c(c(c....
7 3EI9 - PL6 C13 H17 N2 O9 P Cc1c(c(c(c....
8 3EI5 - PGU C13 H19 N2 O9 P Cc1c(c(c(c....
9 3EIA - PL6 C13 H17 N2 O9 P Cc1c(c(c(c....
50% Homology Family (9)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 4FL0 - PLP C8 H10 N O6 P Cc1c(c(c(c....
2 2Z1Z - MLT C4 H6 O5 C([C@H](C(....
3 3EIB - PLP C8 H10 N O6 P Cc1c(c(c(c....
4 3EI8 - PL5 C15 H22 N3 O9 P Cc1c(c(c(c....
5 3EI6 - PL4 C15 H24 N3 O9 P Cc1c(c(c(c....
6 2Z20 - PLP C8 H10 N O6 P Cc1c(c(c(c....
7 3EI9 - PL6 C13 H17 N2 O9 P Cc1c(c(c(c....
8 3EI5 - PGU C13 H19 N2 O9 P Cc1c(c(c(c....
9 3EIA - PL6 C13 H17 N2 O9 P Cc1c(c(c(c....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: PLP; Similar ligands found: 62
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 F0G 0.564516 0.865385
12 MPM 0.564516 0.814815
13 FEV 0.555556 0.803571
14 KOU 0.555556 0.836364
15 HCP 0.546875 0.77193
16 EVM 0.546875 0.821429
17 6DF 0.545455 0.811321
18 PXL 0.541667 0.659574
19 Z98 0.537313 0.75
20 PXP 0.537037 0.862745
21 PMP 0.527273 0.767857
22 P0P 0.527273 0.916667
23 PL6 0.522388 0.818182
24 GT1 0.517857 0.830189
25 PFM 0.514706 0.803571
26 FEJ 0.514706 0.851852
27 LLP 0.5 0.737705
28 P70 0.5 0.833333
29 PUS 0.479452 0.707692
30 PL5 0.479452 0.775862
31 MPL 0.473684 0.836364
32 PLG 0.46875 0.75
33 IN5 0.46875 0.758621
34 P89 0.466667 0.714286
35 PLP PUT 0.463768 0.672131
36 EQJ 0.460526 0.725806
37 5DK 0.460526 0.725806
38 O1G 0.454545 0.75
39 PLT 0.439024 0.762712
40 X04 0.431034 0.851852
41 PDD 0.426471 0.762712
42 PP3 0.426471 0.762712
43 PDA 0.426471 0.762712
44 P1T 0.426471 0.714286
45 33P 0.42029 0.745763
46 IK2 0.42029 0.714286
47 TLP 0.414286 0.793103
48 2BK 0.414286 0.793103
49 PLS 0.414286 0.779661
50 2BO 0.414286 0.793103
51 5PA 0.414286 0.714286
52 PMH 0.414286 0.619718
53 9TD 0.413793 0.671642
54 PLP 999 0.410959 0.796296
55 PPD 0.408451 0.75
56 C6P 0.408451 0.75
57 QLP 0.405405 0.681818
58 MP5 0.403509 0.666667
59 PLA 0.402778 0.703125
60 PY5 0.402778 0.703125
61 HEY 0.4 0.703125
62 PLP PHE 0.4 0.732143
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4FL0; Ligand: PLP; Similar sites found with APoc: 136
This union binding pocket(no: 1) in the query (biounit: 4fl0.bio1) has 16 residues
No: Leader PDB Ligand Sequence Similarity
1 2R2N PMP 1.41176
2 2R2N KYN 1.41176
3 1GTE FMN 1.53509
4 1GTE IUR 1.53509
5 6CD1 PLS 1.75824
6 6CD1 PLG 1.75824
7 4X7G 3Y8 1.99203
8 2OGA PGU 2.00501
9 2WA4 069 2.00573
10 1O69 X04 2.03046
11 5GVL PLG 2.0362
12 5GVL GI8 2.0362
13 1DJ9 KAM 2.08333
14 4LNL PLG 2.1021
15 4LNL 2BO 2.1021
16 4LNL 2BK 2.1021
17 6CZY PMP 2.20994
18 1MDZ DCS 2.29008
19 1MDZ PLP 2.29008
20 3WGC PLG 2.34604
21 2PO3 T4K 2.35849
22 1J0X NAD 2.40964
23 4JE5 PMP 2.41228
24 4JE5 PLP 2.41228
25 1PMO PLR 2.41228
26 5O0J 8BR 2.42826
27 2B1Q TRE 2.45902
28 3FSM 2NC 2.46305
29 3KA2 2NC 2.46305
30 4K2M O1G 2.48307
31 2G50 PYR 2.85088
32 3V1Y NAD 3.2641
33 4IYO 0JO 3.27456
34 4IY7 0JO 3.27456
35 4IY7 KOU 3.27456
36 2XBN PMP 3.27869
37 1T9D FAD 3.28947
38 5XFV FMN 3.29341
39 3DR4 G4M 3.32481
40 4AZJ SEP PLP 3.33333
41 5VEG FMN 3.37079
42 3ZRR PXG 3.38542
43 4AML GYU 3.50877
44 3C3N FMN 3.52564
45 3B8X G4M 3.58974
46 2WK9 PLP 3.59897
47 2WK9 PLG 3.59897
48 4U5I BXP 3.72208
49 6F6D AKG 3.72807
50 4ZSY RW2 3.72807
51 6C28 WCA 3.76344
52 3HQP OXL 3.94737
53 2PTR 2SA 3.94737
54 4E3Q PMP 3.94737
55 2FNU PMP UD1 4
56 3MWS 017 4.0404
57 5WS9 OXL 4.16667
58 2FYF PLP 4.27136
59 1VJO PLP 4.3257
60 2YIP YIO 4.34783
61 2TPL HPP 4.38596
62 6ECG PM9 4.3956
63 1C0I BE2 4.40771
64 1C0I FAD 4.40771
65 5TXR PLP 4.60526
66 3WIR BGC 4.60526
67 6EWR PMP 4.68384
68 4ZAH T5K 4.79798
69 3NWQ 2NC 5.05051
70 1ELU PDA 5.64103
71 3FRK TQP 5.70175
72 1JS3 PLP 142 5.70175
73 5U23 TQP 5.75916
74 5W70 9YM 5.8427
75 2Z9V PXM 5.86735
76 1E5F PLP 6.43564
77 3B1J NAD 6.48968
78 4WXG 2BO 6.54206
79 1C7O PPG 6.76692
80 2X5F PLP 6.97674
81 2O4N TPV 7.07071
82 5X2Z 3LM 7.28643
83 5X30 7XF 7.28643
84 5X30 4LM 7.28643
85 1DFO PLG 7.43405
86 3NUB UD0 7.52089
87 3MJY FMN 8.09249
88 3MJY IJZ 8.09249
89 1ZM1 BGC BGC BGC 8.29876
90 1TOI HCI 8.33333
91 4HVK PMP 8.37696
92 1FC4 AKB PLP 8.4788
93 1TV5 FMN 8.57788
94 5IWQ PLP 8.75576
95 6DND PLP 8.75912
96 1LW4 TLP 8.93372
97 1LW4 PLP 8.93372
98 3PD6 PMP 8.97756
99 3PDB PMP 8.97756
100 5M3Z NLE 9.29648
101 5M3Z PLP 9.29648
102 5M3Z PY6 9.29648
103 1OXO IK2 9.47631
104 6C9B EGV 9.84043
105 2R5C C6P 10.0233
106 2R5E QLP 10.0233
107 3BWN PMP 10.2302
108 3BWN PMP PHE 10.2302
109 1CL2 PPG 10.3797
110 4RKC PMP 10.5528
111 6C3C EJ1 10.8959
112 3CQ5 PMP 11.3821
113 3HRD FAD 11.8182
114 3OIX FMN 11.8841
115 1SIV PSI 12.1212
116 1AJS PLA 12.1359
117 1IDA 0PO 13.1313
118 1LC8 33P 13.1868
119 5K8B PDG 15.8809
120 1B9I PXG 16.7526
121 2AY3 MPP 19.0355
122 1UU1 PMP HSA 20
123 5W19 9TD 21.9298
124 4M2K PLP 22.4138
125 1M7Y PPG 22.9885
126 1GEX PLP HSA 23.8764
127 5VEQ PMP 25.3041
128 6C92 EQJ 26.8617
129 6C8T EQJ 26.8617
130 5T4J PLP ABU 29.589
131 2HOX P1T 33.7237
132 2ZYJ PGU 35.5164
133 2ZC0 PMP 38.3292
134 1GCK ASP PLP 41.2987
135 1XI9 PLP 41.3793
136 2X5D PLP 41.5049
Pocket No.: 2; Query (leader) PDB : 4FL0; Ligand: PLP; Similar sites found with APoc: 15
This union binding pocket(no: 2) in the query (biounit: 4fl0.bio1) has 17 residues
No: Leader PDB Ligand Sequence Similarity
1 3ZNN 4WL 1.44092
2 3ZNN FAD 1.44092
3 5NMX NAP 2.35294
4 2XVE FAD 2.41228
5 1K12 FUC 3.79747
6 4Q5M ROC 3.94089
7 2FXD DR7 5.05051
8 6C8X BVR 5.05051
9 1TUF AZ1 5.52995
10 2P3B 3TL 6.06061
11 1YAA MAE 10.4369
12 2P3C 3TL 12.1212
13 4YHQ G10 14.1414
14 4M8X KGQ 16.1616
15 3GGU 017 19.1919
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