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Receptor
PDB id Resolution Class Description Source Keywords
3EI9 1.55 Å EC: 2.6.1.83 CRYSTAL STRUCTURE OF K270N VARIANT OF LL-DIAMINOPIMELATE AMINOTRANSFERASE FROM ARABIDOPSIS THALIANA COMPLEXED WITH LE XTERNAL ALDIMINE FORM ARABIDOPSIS THALIANA AMINOTRANSFERASE LYSINE BIOSYNTHESIS PYRIDOXAL 5-prime PHOSPHATEXTERNAL ALDIMINE LL-DIAMINOPIMELATE CHLOROPLAST PYRIDOXPHOSPHATE TRANSFERASE TRANSIT PEPTIDE
Ref.: MECHANISM OF SUBSTRATE RECOGNITION AND PLP-INDUCED CONFORMATIONAL CHANGES IN LL-DIAMINOPIMELATE AMINOTRANSFERASE FROM ARABIDOPSIS THALIANA. J.MOL.BIOL. V. 384 1314 2008
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GOL A:434;
A:435;
A:436;
B:434;
B:435;
B:436;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
PL6 A:433;
B:433;
Valid;
Valid;
none;
none;
submit data
376.256 C13 H17 N2 O9 P Cc1c(...
SO4 A:437;
A:438;
B:437;
Invalid;
Invalid;
Invalid;
none;
none;
none;
submit data
96.063 O4 S [O-]S...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3EI9 1.55 Å EC: 2.6.1.83 CRYSTAL STRUCTURE OF K270N VARIANT OF LL-DIAMINOPIMELATE AMINOTRANSFERASE FROM ARABIDOPSIS THALIANA COMPLEXED WITH LE XTERNAL ALDIMINE FORM ARABIDOPSIS THALIANA AMINOTRANSFERASE LYSINE BIOSYNTHESIS PYRIDOXAL 5-prime PHOSPHATEXTERNAL ALDIMINE LL-DIAMINOPIMELATE CHLOROPLAST PYRIDOXPHOSPHATE TRANSFERASE TRANSIT PEPTIDE
Ref.: MECHANISM OF SUBSTRATE RECOGNITION AND PLP-INDUCED CONFORMATIONAL CHANGES IN LL-DIAMINOPIMELATE AMINOTRANSFERASE FROM ARABIDOPSIS THALIANA. J.MOL.BIOL. V. 384 1314 2008
Members (8)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 2Z1Z - MLT C4 H6 O5 C([C@H](C(....
2 3EIB - PLP C8 H10 N O6 P Cc1c(c(c(c....
3 3EI8 - PL5 C15 H22 N3 O9 P Cc1c(c(c(c....
4 3EI6 - PL4 C15 H24 N3 O9 P Cc1c(c(c(c....
5 2Z20 - PLP C8 H10 N O6 P Cc1c(c(c(c....
6 3EI9 - PL6 C13 H17 N2 O9 P Cc1c(c(c(c....
7 3EI5 - PGU C13 H19 N2 O9 P Cc1c(c(c(c....
8 3EIA - PL6 C13 H17 N2 O9 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: PL6; Similar ligands found: 64
No: Ligand ECFP6 Tc MDL keys Tc
1 PL6 1 1
2 KOU 0.761194 0.87931
3 PL5 0.706667 0.913793
4 F0G 0.695652 0.909091
5 5DK 0.679487 0.854839
6 EQJ 0.679487 0.854839
7 P70 0.662338 0.910714
8 PUS 0.662338 0.776119
9 FEJ 0.64 0.862069
10 EPC 0.637681 0.872727
11 0JO 0.611111 0.87931
12 PLT 0.604651 0.836066
13 Z98 0.597403 0.883333
14 FEV 0.594595 0.847458
15 4LM 0.589041 0.862069
16 EVM 0.565789 0.864407
17 6DF 0.564103 0.824561
18 LLP 0.560976 0.868852
19 MET PLP 0.548781 0.774194
20 EXT 0.540541 0.910714
21 PLP 0.522388 0.818182
22 MPM 0.519481 0.859649
23 PLP PHE 0.517241 0.810345
24 PZP 0.514706 0.821429
25 AN7 0.506667 0.821429
26 HCP 0.506329 0.847458
27 P3D 0.506329 0.806452
28 FOO 0.5 0.859649
29 PLP 999 0.5 0.810345
30 P89 0.494253 0.784615
31 3QP 0.493671 0.888889
32 PDG 0.481928 0.825397
33 PGU 0.481928 0.825397
34 PFM 0.481928 0.847458
35 PLP PVH 0.478261 0.731343
36 KET 0.46988 0.929825
37 76U 0.453488 0.8125
38 O1G 0.450549 0.793651
39 EA5 0.448276 0.787879
40 N5F 0.448276 0.8125
41 PLS 0.433735 0.793651
42 PPD 0.428571 0.822581
43 PP3 0.426829 0.75
44 PDD 0.426829 0.75
45 PDA 0.426829 0.75
46 PLP MYB 0.425532 0.710145
47 QLP 0.425287 0.776119
48 PLG 0.425 0.793651
49 P0P 0.424658 0.785714
50 PY5 0.423529 0.772727
51 PLP PUT 0.423529 0.774194
52 2BK 0.416667 0.75
53 TLP 0.416667 0.75
54 2BO 0.416667 0.75
55 PLR 0.414286 0.767857
56 7XF 0.413793 0.796875
57 C6P 0.411765 0.793651
58 PXP 0.410959 0.716667
59 LPI 0.409091 0.73913
60 KAM 0.408602 0.784615
61 AQ3 0.40625 0.746269
62 PY6 0.404494 0.75
63 PLP 142 0.4 0.757576
64 ORX 0.4 0.784615
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3EI9; Ligand: PL6; Similar sites found with APoc: 139
This union binding pocket(no: 1) in the query (biounit: 3ei9.bio1) has 25 residues
No: Leader PDB Ligand Sequence Similarity
1 4W6Z ETF 1.44092
2 4RF7 ARG 1.62037
3 6FOG OXL 1.78571
4 3DR4 G4M 1.79028
5 3NNT DQA 1.81159
6 5W70 9YM 1.85185
7 5GVL PLG 1.85185
8 5GVL GI8 1.85185
9 4WBD CIT 2.08333
10 5W71 PLP 2.27273
11 5W71 9YM 2.27273
12 4E3Q PMP 2.31481
13 6EWR PMP 2.34192
14 5K8B PDG 2.48139
15 6CZY PMP 2.48619
16 1VJO PLP 2.54453
17 4HVK PMP 2.6178
18 1FDJ 2FP 2.75482
19 2Y0I AKG 2.84091
20 2FNU PMP UD1 2.93333
21 5YKT PMP 3.03688
22 4CD6 IFM BMA 3.125
23 5HJQ I3P 3.19149
24 6ECG PM9 3.24074
25 2TPL HPP 3.24074
26 5ENZ UDP 3.37662
27 2WK9 PLG 3.59897
28 2WK9 PLP 3.59897
29 2B1Q TRE 3.68852
30 1PMO PLR 3.7037
31 1JS3 PLP 142 3.7037
32 1XKD ICT 3.7037
33 1DFO PLG 3.83693
34 4DXJ 0M9 3.8674
35 4ZAH T5K 3.93519
36 1CL2 PPG 4.05063
37 3B8X G4M 4.10256
38 4BHL ARG 4.21348
39 1OJK BGC BGC 4.22886
40 1FC4 AKB PLP 4.2394
41 1II5 GLU 4.29185
42 1O69 X04 4.31472
43 4JE5 PMP 4.39815
44 4JE5 PLP 4.39815
45 5W19 9TD 4.39815
46 2PO3 T4K 4.39815
47 6CD1 PLG 4.39815
48 6CD1 PLS 4.39815
49 3NUB UD0 4.45682
50 4UYG 73B 4.4586
51 2YDW WSH 4.57516
52 3ZRR PXG 4.6875
53 3FRK TQP 4.86111
54 1DJ9 KAM 4.94792
55 2YIP YIO 5.07246
56 3BF1 PAU 5.22088
57 1F6D UDP 5.31915
58 4IY7 0JO 5.54156
59 4IYO 0JO 5.54156
60 4IY7 KOU 5.54156
61 5TXR PLP 5.55556
62 5DT6 GLU 5.61798
63 1E5F PLP 5.94059
64 4LNL PLG 6.00601
65 4LNL 2BO 6.00601
66 4LNL 2BK 6.00601
67 3IVM ZPR 6.01852
68 5X30 7XF 6.03015
69 5X30 4LM 6.03015
70 5X2Z 3LM 6.03015
71 4K55 H6P 6.45161
72 5W6Y TRP 6.64557
73 1LW4 PLP 7.20461
74 1LW4 TLP 7.20461
75 2X5F PLP 7.2093
76 2XBN PMP 7.49415
77 4FLP JQ1 7.56302
78 3WGC PLG 7.62463
79 6C3C EJ1 7.74818
80 4AZJ SEP PLP 7.77778
81 4UYF 73B 7.79221
82 1ELU PDA 7.94872
83 2CST MAE 8.0292
84 5IWQ PLP 8.10185
85 2C3H GLC GLC 8.16327
86 2GUE NAG 8.19672
87 4CP8 MLI 8.33333
88 1WYV PLP AOA 8.44749
89 2OGA PGU 8.5213
90 2FYF PLP 8.54271
91 5U23 TQP 8.56481
92 2HOX P1T 8.66511
93 2R5E QLP 8.85781
94 2R5C C6P 8.85781
95 2UVO NAG 9.35672
96 4RKC PMP 10.3015
97 1TOI HCI 10.4167
98 2Z9V PXM 10.4592
99 3PD6 PMP 10.9726
100 3PDB PMP 10.9726
101 3PD6 KYN 10.9726
102 1YAA MAE 11.165
103 1LC8 33P 11.2637
104 5AEW BNL 12.766
105 2AY3 MPP 12.9442
106 6C9B EGV 14.3617
107 6C92 EQJ 14.3617
108 6C8T EQJ 14.3617
109 6C92 EGV 14.3617
110 1GEX PLP HSA 14.5833
111 1OXO IK2 15.0463
112 5M3Z PLP 16.3317
113 5M3Z PY6 16.3317
114 4R5Z PMP 16.8937
115 4R5Z SIN 16.8937
116 2R2N PMP 17.6471
117 2R2N KYN 17.6471
118 3BWN PMP 19.6759
119 3BWN PMP PHE 19.6759
120 1UU1 PMP HSA 19.7015
121 5VOM 9GY 20.1342
122 5T4J PLP ABU 20.5479
123 5LWY OLB 20.5607
124 3FVU IAC 22.7488
125 4M2K PLP 22.9064
126 1C7O PPG 22.9167
127 5VEQ PMP 23.601
128 6DND PLP 23.601
129 1M7Y PPG 24.0741
130 3CQ5 PMP 28.7263
131 1AJS PLA 29.1667
132 2ZYJ PGU 31.4815
133 1V2F HCI 34.3832
134 1U08 PLP 36.0104
135 1GCK ASP PLP 36.3426
136 2ZC0 PMP 38.8889
137 2X5D PLP 39.5631
138 1GDE GLU PLP 40.1028
139 1XI9 PLP 41.6256
Pocket No.: 2; Query (leader) PDB : 3EI9; Ligand: PL6; Similar sites found with APoc: 12
This union binding pocket(no: 2) in the query (biounit: 3ei9.bio1) has 25 residues
No: Leader PDB Ligand Sequence Similarity
1 5WS9 OXL 1.38889
2 2W5T GP9 1.65094
3 2HIM ASN 1.67598
4 2G3F IZC 3.56295
5 4LZB URA 4.20168
6 4E1O PLP PVH 4.62963
7 3R6U CHT 6.69014
8 3ITJ CIT 7.39645
9 4LYQ MAN BMA BMA 8.10185
10 3R51 MMA 8.125
11 4AML GYU 9.35672
12 2UVO NDG 9.35672
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