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Receptor
PDB id Resolution Class Description Source Keywords
4D9M 2.5 Å EC: 4.3.1.15 CRYSTAL STRUCTURE OF DIAMINOPROPIONATE AMMONIA LYASE FROM ES COLI IN COMPLEX WITH AMINOACRYLATE-PLP AZOMETHINE REACTION I NTERMEDIATE ESCHERICHIA COLI FOLD TYPE II PLP-DEPENDENT ENZYME TRYPTOPHAN SYNTHASE BETA LIKE PLP-DEPENDENT ENZYMES SUPERFAMILY LYASE
Ref.: CRYSTAL STRUCTURE OF ESCHERICHIA COLI DIAMINOPROPIO AMMONIA-LYASE REVEALS MECHANISM OF ENZYME ACTIVATIO CATALYSIS J.BIOL.CHEM. V. 287 20369 2012
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
0JO A:401;
B:401;
Valid;
Valid;
none;
none;
submit data
316.204 C11 H13 N2 O7 P Cc1c(...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4D9M 2.5 Å EC: 4.3.1.15 CRYSTAL STRUCTURE OF DIAMINOPROPIONATE AMMONIA LYASE FROM ES COLI IN COMPLEX WITH AMINOACRYLATE-PLP AZOMETHINE REACTION I NTERMEDIATE ESCHERICHIA COLI FOLD TYPE II PLP-DEPENDENT ENZYME TRYPTOPHAN SYNTHASE BETA LIKE PLP-DEPENDENT ENZYMES SUPERFAMILY LYASE
Ref.: CRYSTAL STRUCTURE OF ESCHERICHIA COLI DIAMINOPROPIO AMMONIA-LYASE REVEALS MECHANISM OF ENZYME ACTIVATIO CATALYSIS J.BIOL.CHEM. V. 287 20369 2012
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 4D9M - 0JO C11 H13 N2 O7 P Cc1c(c(c(c....
2 4D9N - DSN C3 H7 N O3 C([C@H](C(....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 4D9M - 0JO C11 H13 N2 O7 P Cc1c(c(c(c....
2 4D9N - DSN C3 H7 N O3 C([C@H](C(....
50% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 4D9M - 0JO C11 H13 N2 O7 P Cc1c(c(c(c....
2 4D9N - DSN C3 H7 N O3 C([C@H](C(....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 0JO; Similar ligands found: 64
No: Ligand ECFP6 Tc MDL keys Tc
1 0JO 1 1
2 4LM 0.71875 0.946429
3 FEV 0.69697 0.929825
4 F0G 0.656716 0.892857
5 KOU 0.647059 0.864407
6 EVM 0.637681 0.85
7 Z98 0.625 0.809524
8 EXT 0.61194 0.830508
9 PL6 0.611111 0.87931
10 FEJ 0.60274 0.847458
11 EPC 0.597015 0.857143
12 PZP 0.590164 0.807018
13 FOO 0.588235 0.877193
14 LLP 0.584416 0.796875
15 PLP 0.57377 0.803571
16 AN7 0.573529 0.839286
17 P3D 0.569444 0.738462
18 PUS 0.564103 0.73913
19 PL5 0.564103 0.836066
20 P70 0.564103 0.894737
21 MPM 0.56338 0.844828
22 EQJ 0.5625 0.784615
23 5DK 0.5625 0.784615
24 HCP 0.547945 0.803279
25 P89 0.530864 0.720588
26 6DF 0.526316 0.810345
27 PLP 999 0.5 0.79661
28 PLT 0.5 0.822581
29 PFM 0.5 0.864407
30 PLP PUT 0.493506 0.707692
31 O1G 0.465116 0.753846
32 PMP 0.462687 0.714286
33 P1T 0.460526 0.828125
34 MET PLP 0.457831 0.734375
35 PLR 0.453125 0.754386
36 PLP PHE 0.448276 0.79661
37 C6P 0.443038 0.753846
38 PDA 0.441558 0.738462
39 PDD 0.441558 0.738462
40 PP3 0.441558 0.738462
41 TLP 0.43038 0.738462
42 2BK 0.43038 0.738462
43 2BO 0.43038 0.738462
44 PLS 0.43038 0.753846
45 PLP PVH 0.428571 0.720588
46 9TD 0.427083 0.728571
47 PXP 0.426471 0.704918
48 PPD 0.425 0.753846
49 PLG 0.421053 0.727273
50 P0P 0.42029 0.77193
51 PY5 0.419753 0.710145
52 PY6 0.416667 0.690141
53 GT1 0.414286 0.68254
54 PLP 142 0.410526 0.720588
55 7XF 0.409639 0.731343
56 PDG 0.409639 0.731343
57 PGU 0.409639 0.731343
58 ILP 0.409639 0.716418
59 PPG 0.409091 0.8
60 LPI 0.404762 0.680556
61 QLP 0.404762 0.690141
62 IN5 0.402597 0.707692
63 IK2 0.4 0.720588
64 HEY 0.4 0.761194
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4D9M; Ligand: 0JO; Similar sites found with APoc: 150
This union binding pocket(no: 1) in the query (biounit: 4d9m.bio1) has 23 residues
No: Leader PDB Ligand Sequence Similarity
1 1Z0N BCD None
2 4QM7 GTP 1.16959
3 2W8Q SIN 1.75879
4 2AWN ADP 1.83727
5 2W58 ADP 1.9802
6 6CGN DA 2.01005
7 2C3H GLC GLC 2.04082
8 4AG5 ADP 2.04082
9 1VAY AZA 2.09059
10 5KOD IAC 2.26131
11 5Z3I ADE 2.26415
12 1PVS 7HP 2.48227
13 1YQT ADP 2.51256
14 5YV5 ADP 2.51256
15 2O1V ADP 2.51256
16 1RRC ADP 2.65781
17 2Q8M AMP 2.71084
18 2RGO FAD 2.76382
19 3MBI HSX 2.78746
20 3MA0 XYP 2.8754
21 2F5X ASP 2.88462
22 3FXU TSU 2.95082
23 2OG2 MLI 3.06407
24 1YNS HPO 3.06513
25 4WZ6 ATP 3.10345
26 5VJN IR8 3.20856
27 4U00 ADP 3.27869
28 5TQZ GLC 3.33333
29 1SC3 MLI 3.37079
30 4WGF HX2 3.41463
31 2P3V SRT 3.51562
32 4BA5 PXG 3.51759
33 3LTW HLZ 3.57143
34 3B9Z CO2 3.60825
35 5V6F MAN BMA MAN 3.62319
36 3B9Q MLI 3.64238
37 4TVD BGC 3.76884
38 1G6H ADP 3.89105
39 1S9A BEZ 3.89105
40 5MW4 5JU 3.89222
41 1G4U AF3 3.91645
42 1X9I G6Q 3.97351
43 5D85 P1T 3.98773
44 5D85 FLC 3.98773
45 5A0U CHT 4.0201
46 2NSX IFM 4.0201
47 1U0J ADP 4.11985
48 1B0U ATP 4.19847
49 5LUB 3Y7 4.19847
50 1TL2 NDG 4.23729
51 4B5W PYR 4.29688
52 3CEV ARG 4.34783
53 2REG CHT 4.36242
54 4P83 U5P 4.3956
55 3O5N BR0 4.46429
56 3PCJ INO 4.5
57 5GVR LMR 4.70085
58 3A4M ADP 5
59 1CBK ROI 5
60 4TQK NAG 5.02513
61 5ZXD ATP 5.02513
62 2R4J FAD 5.02513
63 2R4J 13P 5.02513
64 2IOR ADP 5.10638
65 1MZV AMP 5.10638
66 4OUJ LBT 5.21173
67 4JLS 3ZE 5.26316
68 3PH4 AOS 5.32544
69 6HKE LMR 5.34591
70 6HKE MLT 5.34591
71 1O5O U5P 5.42986
72 4LO2 GAL BGC 5.44218
73 2HAW 2PN 5.50162
74 5NXX 3Q7 5.59701
75 2PZE ATP 5.67686
76 2JBH 5GP 5.77778
77 2BES RES 5.81395
78 5AOV GLV 5.95238
79 2PHX MAN MAN MAN MAN 5.95238
80 4B2D FBP 6.03015
81 4IP7 FBP 6.03015
82 3HEE R5P 6.04027
83 3THR C2F 6.14334
84 4XFR CIT 6.28141
85 3BRN SRO 6.36943
86 4KQP GLN 6.46552
87 3PC3 P1T 6.78392
88 4JBL MET 6.78466
89 4PPF FLC 6.85714
90 2ZQO NGA 6.92308
91 6C2Z P1T 6.93333
92 5IFK HPA 7.05128
93 3ZEI AWH 7.09677
94 3LN9 FLC 7.19424
95 2ARC ARA 7.31707
96 3ZVS MLI 7.5
97 1GXU 2HP 7.69231
98 3KC1 2T6 7.71513
99 1D6S PLP MET 7.76398
100 1D6S MET PLP 7.76398
101 3VC3 C6P 7.84884
102 5C2N NAG 8.33333
103 2PS1 ORO 8.40708
104 1JJ7 ADP 8.46154
105 5XHA FRU 8.79397
106 2DT9 THR 8.98204
107 6CUZ FEV 9.02062
108 6AM8 PLT 9.34343
109 6AM8 TRP 9.34343
110 6AR9 3L4 9.55882
111 2QMC GTB 9.57447
112 3MMH SME 9.58084
113 6AMI TRP 9.59596
114 2ZL4 ALA ALA ALA ALA 9.69388
115 1G8S MET 10
116 3HQP FDP 10.0503
117 1XTT U5P 10.1852
118 3KIH GDL 10.3093
119 2WHX ADP 10.5528
120 2JK0 ASP 10.7692
121 2VHL GLP 10.8586
122 1KJ8 GAR 10.9974
123 5I7A 68Q 11.0429
124 1VB3 KPA 11.0553
125 3TUR DGL 11.1498
126 4D9C PMP 11.6959
127 4F9C 0SX 11.8056
128 2V57 PRL 12.1053
129 1XXR MAN 12.4224
130 5ODQ 9SB 12.8141
131 3KIF GDL 13.2075
132 3K7S R52 13.4078
133 1FQK ALF 13.6054
134 5FQ0 FLC 14.0351
135 3KMT SAH 14.2857
136 1CX9 NHP 14.3577
137 1MFA GLA MMA ABE 15
138 2CBZ ATP 15.1899
139 5FII PHE 15.6863
140 1V7C HEY 15.9544
141 2D2F ADP 16.8
142 3X44 PUS 17.4699
143 5B3A 0JO 17.9949
144 4YMU ATP 20
145 5LWY OLB 20.5607
146 4QYS PLP SEP 21.1055
147 4QYS PLR 21.1055
148 3L6R MLI 25.1445
149 3L6C MLI 30.6785
150 1J0D 5PA 35.1906
Pocket No.: 2; Query (leader) PDB : 4D9M; Ligand: 0JO; Similar sites found with APoc: 59
This union binding pocket(no: 2) in the query (biounit: 4d9m.bio1) has 24 residues
No: Leader PDB Ligand Sequence Similarity
1 3ZO7 K6H None
2 2HHP FLC 1.25628
3 3CL7 HYN 1.2987
4 4CIB 7UZ 1.75879
5 5K0A FAD 1.81818
6 1OCU PIB 1.85185
7 1YFS ALA 2.01005
8 3WXL ADP 2.26131
9 2JAJ D20 2.42215
10 3EGI ADP 2.42718
11 3VEH 0GA 2.51256
12 3QTP 2PG 2.51256
13 1S20 TLA 2.64706
14 1W8S FBP 3.04183
15 4K6B GLU 3.10559
16 5ECP GSH 3.13901
17 4L8F MTX 3.20513
18 2X0K PPV 3.25444
19 4CP9 GAL CN8 3.30579
20 2VVG ADP 3.42857
21 6GH3 M1P 3.51759
22 1OXV ANP 3.68272
23 3CQL NAG 3.7037
24 3KAL HGS 3.76884
25 4YSW URC 3.76884
26 4L77 CNL 3.76884
27 1L7N ALF 4.2654
28 3A75 GLU 4.42708
29 1GRN AF3 4.4335
30 2HIM ASN 4.7486
31 2HIM ASP 4.7486
32 4FGC PQ0 4.84848
33 1TE2 PGA 4.86726
34 2CI5 HCS 4.92958
35 3QRY DMJ 5.02513
36 4FHT DHB 5.09554
37 3PGL RZX 5.55556
38 3ZW2 NAG GAL FUC 5.74713
39 2HZL PYR 5.75342
40 1GPE FAD 6.28141
41 4BGB ADP 6.76923
42 1Q8A HCS 6.78392
43 2GOO NDG 7.01754
44 2AJH MET 7.14286
45 4D81 ADP 7.77385
46 4B2Z P5S 7.78894
47 1XX6 ADP 7.8534
48 6AZQ C5J 8.01527
49 5ZI9 FLC 8.84615
50 1Y7I SAL 9.32836
51 5YSI NCA 9.86842
52 2NU5 NAG 10.6557
53 1EQ2 ADQ 11.9355
54 1A5V Y3 12.0253
55 1N4K I3P 12.0735
56 1H70 CIR 12.1569
57 1OYF MHN 12.3967
58 1P0Z FLC 18.3206
59 1XXA ARG 26.9231
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