-->
Receptor
PDB id Resolution Class Description Source Keywords
2Y5D 1.4 Å EC: 1.2.1.3 CRYSTAL STRUCTURE OF C296A MUTANT OF THE BOX PATHWAY ENCODED ALDH FROM BURKHOLDERIA XENOVORANS LB400 BURKHOLDERIA XENOVORANS LB400 OXIDOREDUCTASE
Ref.: ELUCIDATING THE REACTION MECHANISM OF THE BENZOATE OXIDATION PATHWAY ENCODED ALDEHYDE DEHYDROGENASE FR BURKHOLDERIA XENOVORANS LB400. PROTEIN SCI. V. 20 1048 2011
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GOL A:1523;
B:1531;
Invalid;
Invalid;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
NAP A:1525;
B:1533;
Valid;
Valid;
none;
none;
submit data
743.405 C21 H28 N7 O17 P3 c1cc(...
P6G A:1524;
B:1532;
Invalid;
Invalid;
none;
none;
submit data
282.331 C12 H26 O7 C(COC...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2Y5D 1.4 Å EC: 1.2.1.3 CRYSTAL STRUCTURE OF C296A MUTANT OF THE BOX PATHWAY ENCODED ALDH FROM BURKHOLDERIA XENOVORANS LB400 BURKHOLDERIA XENOVORANS LB400 OXIDOREDUCTASE
Ref.: ELUCIDATING THE REACTION MECHANISM OF THE BENZOATE OXIDATION PATHWAY ENCODED ALDEHYDE DEHYDROGENASE FR BURKHOLDERIA XENOVORANS LB400. PROTEIN SCI. V. 20 1048 2011
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 2VRO - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
2 2Y5D - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 2VRO - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
2 2Y5D - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
50% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 2VRO - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
2 2Y5D - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: NAP; Similar ligands found: 123
No: Ligand ECFP6 Tc MDL keys Tc
1 NAP 1 1
2 NA0 0.881356 0.986301
3 TAP 0.872881 0.934211
4 NDO 0.840336 0.972603
5 NAD 0.811966 0.986111
6 N01 0.733871 0.958904
7 A3D 0.712 0.972603
8 NBP 0.707692 0.935065
9 NHD 0.68254 0.958904
10 NJP 0.661417 0.972973
11 NFD 0.658915 0.934211
12 NXX 0.619048 0.959459
13 DND 0.619048 0.959459
14 AMP NAD 0.606061 0.958904
15 ZID 0.605839 0.972603
16 NAQ 0.59854 0.922078
17 ATR 0.59292 0.917808
18 NAE 0.591241 0.946667
19 NDE 0.58042 0.986301
20 A22 0.571429 0.958904
21 NAJ 0.567164 0.986111
22 A2R 0.563025 0.932432
23 NDC 0.561644 0.922078
24 NA7 0.552846 0.907895
25 ODP 0.551471 0.935065
26 A2P 0.539823 0.930556
27 8ID 0.537313 0.910256
28 NPW 0.525547 0.8875
29 NZQ 0.521739 0.910256
30 CNA 0.521739 0.959459
31 NDP 0.514493 0.922078
32 PO4 PO4 A A A A PO4 0.503937 0.930556
33 1DG 0.503401 0.922078
34 DG1 0.503401 0.922078
35 TXP 0.5 0.922078
36 NMN AMP PO4 0.492958 0.921053
37 XNP 0.492958 0.875
38 25L 0.492308 0.958904
39 25A 0.492063 0.972222
40 NMN 0.486726 0.888889
41 NGD 0.485714 0.935065
42 9JJ 0.481707 0.8875
43 2AM 0.477876 0.891892
44 ADP 0.458333 0.945205
45 PAP 0.451613 0.931507
46 A2D 0.445378 0.945205
47 AN2 0.442623 0.932432
48 7L1 0.441558 0.777778
49 ADP PO3 0.44 0.944444
50 SAP 0.44 0.896104
51 AGS 0.44 0.896104
52 M33 0.439024 0.906667
53 AR6 AR6 0.438849 0.945205
54 BA3 0.438017 0.945205
55 OAD 0.43609 0.92
56 ADP BMA 0.43609 0.92
57 DQV 0.435714 0.958904
58 HEJ 0.435484 0.945205
59 ATP 0.435484 0.945205
60 OOB 0.435115 0.958904
61 B4P 0.434426 0.945205
62 AP5 0.434426 0.945205
63 GAP 0.433071 0.92
64 0WD 0.432432 0.922078
65 2A5 0.432 0.87013
66 5FA 0.432 0.945205
67 AQP 0.432 0.945205
68 AT4 0.430894 0.907895
69 00A 0.428571 0.909091
70 DAL AMP 0.427481 0.932432
71 CA0 0.427419 0.92
72 ADP ALF 0.426357 0.871795
73 ALF ADP 0.426357 0.871795
74 9X8 0.425373 0.871795
75 ACP 0.424 0.92
76 NAJ PZO 0.423841 0.897436
77 9SN 0.423358 0.897436
78 ADP VO4 0.423077 0.932432
79 VO4 ADP 0.423077 0.932432
80 WAQ 0.422222 0.884615
81 V3L 0.421875 0.945205
82 ACQ 0.421875 0.92
83 ADQ 0.421053 0.92
84 AR6 0.420635 0.918919
85 APR 0.420635 0.918919
86 ATP A A A 0.42029 0.958333
87 CO7 0.419753 0.786517
88 3OD 0.419118 0.92
89 1ZZ 0.419118 0.841463
90 DLL 0.41791 0.958904
91 AD9 0.417323 0.92
92 NAX 0.416667 0.875
93 OVE 0.416667 0.857143
94 MYR AMP 0.416058 0.841463
95 AV2 0.415385 0.868421
96 A3P 0.414634 0.944444
97 NNR 0.414414 0.72973
98 OMR 0.413793 0.831325
99 6YZ 0.412214 0.92
100 ANP 0.410853 0.92
101 A1R 0.410448 0.860759
102 ABM 0.409836 0.893333
103 A 0.408333 0.944444
104 AMP 0.408333 0.944444
105 SON 0.408 0.933333
106 PPS 0.407692 0.829268
107 5AL 0.407692 0.932432
108 NAI 0.406897 0.909091
109 7D3 0.406504 0.857143
110 ADX 0.404762 0.829268
111 ATF 0.40458 0.907895
112 3UK 0.404412 0.945946
113 TYR AMP 0.404255 0.921053
114 AMP DBH 0.404255 0.894737
115 139 0.402685 0.875
116 50T 0.401575 0.906667
117 SRP 0.401515 0.907895
118 A A 0.40146 0.972222
119 B5V 0.40146 0.933333
120 A3R 0.4 0.860759
121 3AM 0.4 0.90411
122 B5M 0.4 0.921053
123 FA5 0.4 0.933333
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2Y5D; Ligand: NAP; Similar sites found with APoc: 118
This union binding pocket(no: 1) in the query (biounit: 2y5d.bio1) has 27 residues
No: Leader PDB Ligand Sequence Similarity
1 6B79 ORA None
2 5KK4 44E None
3 3COB ADP 1.35501
4 5KJW 53C 1.40515
5 4V3C C 1.54639
6 4JGP PYR 1.84332
7 2D3N GLC GLC GLC 1.85567
8 4X1B MLI 1.87266
9 4R84 CSF 1.98807
10 4L80 OXL 2.01149
11 6EOM ALA LYS 2.05993
12 5G48 1FL 2.13904
13 2ZWI C5P 2.14477
14 3KYF 5GP 5GP 2.1645
15 4DFU QUE 2.17391
16 3PUN FUC GAL NDG FUC 2.21519
17 4OJP MAL 2.24719
18 2PNC CLU 2.43446
19 5JFL NAD 2.48092
20 1PDZ PGA 2.53456
21 2G30 ALA ALA PHE 2.71318
22 4A9C B5F 2.8481
23 5A9A UTP 2.88066
24 5IFK HPA 2.88462
25 2FKA BEF 3.10078
26 2NU8 COA 3.125
27 5F6U 5VK 3.18471
28 5YJS SAL 3.33333
29 4WCX MET 3.33333
30 5O3Q CMP 3.33333
31 5UAV NDP 3.41615
32 5UAV TFB 3.41615
33 5YLF BGC 3.59281
34 2X1E X1E 3.64146
35 4XFM THE 3.66379
36 1LCF OXL 3.74532
37 4ZDJ UTP 3.74532
38 4PTN GXV 3.79009
39 4ZTD ALA GLY ALA GLY ALA 3.95257
40 3CBC DBS 4.0404
41 3SAO DBH 4.375
42 1FDJ 13P 4.40771
43 6GNO XDI 4.44444
44 1I7M CG 4.47761
45 3NZ1 3NY 4.5977
46 4HZ0 1AV 4.69484
47 2IU8 PLM 4.81283
48 3SQG COM 5.01792
49 2XG5 EC2 5.04587
50 2XG5 EC5 5.04587
51 4RYV ZEA 5.16129
52 6FA4 D1W 5.20231
53 5AOG IAC 5.21173
54 2QHV OC9 5.2381
55 5DBV COA 5.24345
56 5OCG 9R5 5.29101
57 1RJW ETF 5.30973
58 1OFL NGK GCD 5.40541
59 1T36 U 5.80524
60 2Z4T C5P 6.03113
61 3GDN MXN 6.14203
62 1LSH PLD 6.26959
63 3QSB 743 6.55738
64 4JCA CIT 6.58683
65 3HUN ZZ7 6.62252
66 2WD7 VGD 6.71642
67 5L2R MLA 6.74157
68 2VT3 ATP 7.44186
69 2XOC ADP 7.49064
70 4NTX AMR 8.33333
71 1UYY BGC BGC 8.39695
72 5CLO NS8 8.47458
73 5DYO FLU 8.7156
74 5Y4R C2E 9.65517
75 2CYC TYR 9.86667
76 2YLN CYS 10.6007
77 2O1C PPV 10.6667
78 3IWD M2T 11.2903
79 2QL9 CIT 11.3402
80 2D3Y DU 11.8721
81 1V3S ATP 12.069
82 4RW3 SHV 12.5828
83 1VMK GUN 12.6354
84 1EZ0 NAP 18.4314
85 4LH0 GLV 20.412
86 3RHJ NAP 21.6634
87 4NS3 NAD 22.8464
88 2BJK NAD 24.2248
89 5KF6 NAD 27.3408
90 4ZUL UN1 27.9026
91 5UCD NAP 28.6517
92 4OE4 NAD 28.6517
93 5N5S NAP 29.7087
94 6MVU K4V 29.7753
95 4YWV SSN 32.2581
96 3IWJ NAD 33.2008
97 4PXL NAD 33.2689
98 1KY8 NAP 33.7325
99 4PZ2 NAD 34.2697
100 5X5U NAD 34.4554
101 1T90 NAD 35.1852
102 3HAZ NAD 35.206
103 3IWK NAD 36.1829
104 3EFV NAD 36.3636
105 5IUW IAC 36.6197
106 5IUW NAD 36.6197
107 4A0M NAD 36.8952
108 4I8P NAD 37.3077
109 2IMP NAI 37.7871
110 3JZ4 NAP 39.501
111 3VZ3 NAP 39.6061
112 3VZ3 SSN 39.6061
113 4I9B NAD 39.7004
114 6B5G CQY 40.1623
115 6B5G NAD 40.1623
116 2WME NAP 43.0712
117 2WOX NDP 43.0712
118 2QE0 NAP 43.3684
Pocket No.: 2; Query (leader) PDB : 2Y5D; Ligand: NAP; Similar sites found with APoc: 21
This union binding pocket(no: 2) in the query (biounit: 2y5d.bio1) has 29 residues
No: Leader PDB Ligand Sequence Similarity
1 1J78 OLA 1.96507
2 5AOA PPI 2.0979
3 4L9Z OXL 2.24719
4 3WCS MAN NAG 2.43446
5 5XHA FRU 2.62172
6 3JU6 ARG 2.97297
7 5F7U GLC GLC 3.18352
8 3RK0 AMP 3.79747
9 4UBS DIF 4.11985
10 1J6X MET 4.375
11 1J2Z SOG 4.44444
12 5NC1 NAG 4.64135
13 1ZGS XMM 5.36913
14 3BRE C2E 5.58659
15 3R51 MMA 5.625
16 4C2W ANP 5.73477
17 1KZL CRM 5.76923
18 5J8Q ALA 8.21256
19 5C8W PCG 8.39161
20 1VBO MAN MAN MAN 13.4228
21 4WOH 4NP 15.6627
APoc FAQ
Feedback