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Receptor
PDB id Resolution Class Description Source Keywords
3JZ4 2.3 Å EC: 1.2.1.16 CRYSTAL STRUCTURE OF E. COLI NADP DEPENDENT ENZYME ESCHERICHIA COLI TETRAMER NADP BINDING NADP OXIDOREDUCTASE
Ref.: THE X-RAY CRYSTAL STRUCTURE OF ESCHERICHIA COLI SUC SEMIALDEHYDE DEHYDROGENASE; STRUCTURAL INSIGHTS INT NADP+/ENZYME INTERACTIONS. PLOS ONE V. 5 E9280 2010
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
NAP A:482;
B:482;
C:482;
D:482;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
submit data
743.405 C21 H28 N7 O17 P3 c1cc(...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3JZ4 2.3 Å EC: 1.2.1.16 CRYSTAL STRUCTURE OF E. COLI NADP DEPENDENT ENZYME ESCHERICHIA COLI TETRAMER NADP BINDING NADP OXIDOREDUCTASE
Ref.: THE X-RAY CRYSTAL STRUCTURE OF ESCHERICHIA COLI SUC SEMIALDEHYDE DEHYDROGENASE; STRUCTURAL INSIGHTS INT NADP+/ENZYME INTERACTIONS. PLOS ONE V. 5 E9280 2010
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 3JZ4 - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
70% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 3JZ4 - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
2 2W8Q - SIN C4 H6 O4 C(CC(=O)O)....
3 2W8R - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
50% Homology Family (63)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 5AC1 - TXE C21 H31 N7 O14 P2 c1nc(c2c(n....
2 5L2O ic50 = 0.76 uM 6ZW C14 H17 N O2 CCN(CC)c1c....
3 5L2N ic50 = 2.8 uM 6ZU C18 H16 O5 S CC1=C(C(=O....
4 1BXS - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
5 5ABM - TXE C21 H31 N7 O14 P2 c1nc(c2c(n....
6 5L2M Ki = 170 nM 6ZY C22 H25 N O4 Cc1c(oc2c1....
7 4X4L ic50 = 4.6 uM 3XG C21 H25 N3 O3 S2 CCOC(=O)CS....
8 5AC0 - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
9 4WP7 ic50 = 0.8 uM 3SR C22 H30 N6 O4 CC(C)CCn1c....
10 4WB9 - NAI C21 H29 N7 O14 P2 c1nc(c2c(n....
11 4WPN ic50 = 0.21 uM 3ST C19 H30 N6 O3 CC(C)CCn1c....
12 5AC2 - TXE C21 H31 N7 O14 P2 c1nc(c2c(n....
13 4I9B - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
14 4I3X - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
15 5N5S Kd = 31 uM NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
16 4PZ2 - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
17 1WNB - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
18 3IWK - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
19 4A0M - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
20 4GNZ - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
21 3RHR Kd = 5.7 uM NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
22 3RHJ Kd = 0.0073 uM NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
23 4GO2 - TAP C21 H28 N7 O16 P3 S c1cc(c[n+]....
24 2O2R - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
25 3RHL - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
26 3RHO Kd = 0.26 uM NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
27 3RHQ Kd = 9.2 uM NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
28 2O2Q - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
29 3JZ4 - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
30 1O01 - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
31 2ONM - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
32 2VLE - DZN C21 H20 O9 c1cc(ccc1C....
33 3INL - BXB C15 H11 Cl2 N O3 c1cc(c(c(c....
34 3SZ9 - I3E C11 H14 O CCc1ccc(cc....
35 4FR8 - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
36 1O04 - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
37 3INJ - BXB C15 H11 Cl2 N O3 c1cc(c(c(c....
38 2ONP - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
39 1O02 - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
40 5L13 Ki = 19 nM 6ZE C17 H18 O3 CCCC1=C(c2....
41 1NZX - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
42 4KWG ic50 = 2.4 uM 2AK C9 H6 Br N O2 Cc1cc2c(c(....
43 4KWF ic50 = 82 uM 3AK C15 H11 N O2 c1ccc(cc1)....
44 4FQF - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
45 1NZZ - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
46 5X5U - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
47 2W8Q - SIN C4 H6 O4 C(CC(=O)O)....
48 2W8R - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
49 1UXV - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
50 1UXR - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
51 1UXQ - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
52 2IMP - NAI C21 H29 N7 O14 P2 c1nc(c2c(n....
53 3ZQA - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
54 2WOX - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
55 5IUW - IAC C10 H9 N O2 c1ccc2c(c1....
56 5IUV - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
57 1O9J - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
58 4I8P - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
59 3IWJ - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
60 1T90 - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
61 6ALJ - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
62 6B5G Kd = 0.26 uM CQY C21 H26 N4 O4 S CCOc1ccsc1....
63 6B5H Kd = 1.1 uM CU4 C24 H17 F N4 O3 S CS(=O)(=O)....
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 : 3JZ4; Ligand: NAP; Similar sites found with APoc: 82
This union binding pocket(no: 1) in the query (biounit: 3jz4.bio1) has 26 residues
No: Leader PDB Ligand Sequence Similarity
1 6B79 ORA None
2 2IHK CSF 1.25313
3 5LKC FUC GLA A2G 1.62338
4 1OFL NGK GCD 1.6632
5 5JBE MAL 1.8711
6 2IZ1 ATR 1.89873
7 3PUN FUC GAL NDG FUC 2.21519
8 1LCF OXL 2.4948
9 2IU8 PLM 2.94118
10 2ZWI C5P 2.94906
11 5AHO TLA 2.97619
12 3LGS ADE 2.99625
13 5KJW 53C 3.0445
14 4R84 CSF 3.1185
15 5G48 1FL 3.20856
16 3F5A SIA GAL NAG 3.25203
17 1IK4 PGH 3.28947
18 5L2R MLA 3.3264
19 2Z4T C5P 3.3264
20 2DUR MAN MAN 3.55731
21 3UYW TAU 3.73832
22 4V3C C 3.86598
23 2NU8 COA 3.86598
24 2FKA BEF 3.87597
25 4DFU QUE 4.03727
26 5UAV TFB 4.03727
27 5UAV NDP 4.03727
28 1T36 U 4.158
29 4WCX MET 4.375
30 1JT2 FER 4.47761
31 3EJ0 11X 4.59184
32 4RW3 SHV 4.63576
33 3QSB 743 4.64481
34 2O1C PPV 4.66667
35 2B6N ALA PRO THR 4.67626
36 2Y65 ADP 4.93151
37 5DYO FLU 5.04587
38 6FA4 D1W 5.20231
39 1LSH PLD 5.40541
40 4XFR CIT 5.40541
41 5F7J ADE 5.40541
42 6H5E ANP 5.57769
43 1VHW ADN 6.32411
44 2VT3 ATP 6.97674
45 6GNO XDI 7.40741
46 1I7M CG 7.46269
47 3DZ6 M8E 7.46269
48 1L5Y BEF 7.74194
49 4ZTD ALA GLY ALA GLY ALA 7.90514
50 3EFS BTN 8.15451
51 4CNK MEU 8.18414
52 1NE7 16G 8.3045
53 5NM7 GLY 8.64662
54 1RJW ETF 9.73451
55 4F4S EFO 11.8421
56 5TVF CGQ 12.3077
57 1XVB BHL 13.0977
58 1C5C TK4 14.0187
59 4UEC MGT 14.6739
60 3QXV MTX 15.0794
61 3KCC CMP 18.0769
62 2QQC AG2 18.8679
63 2XG5 EC2 21.9653
64 2XG5 EC5 21.9653
65 1EZ0 NAP 22.9412
66 3IWD M2T 26.4706
67 5JFL NAD 31.1069
68 5DBV COA 35.2809
69 2Y5D NAP 39.501
70 4LH0 GLV 40.5405
71 4NS3 NAD 40.5405
72 3HAZ NAD 42.2037
73 5UCD NAP 42.2319
74 5KF6 NAD 43.0353
75 4OE4 NAD 44.9064
76 4YWV SSN 46.8817
77 2BJK NAD 47.1933
78 1KY8 NAP 48.2328
79 4ZUL UN1 49.2724
80 3VZ3 NAP 49.453
81 3VZ3 SSN 49.453
82 4I3V NAD 49.896
Pocket No.: 2; Query (leader) PDB : 3JZ4; Ligand: NAP; Similar sites found with APoc: 27
This union binding pocket(no: 2) in the query (biounit: 3jz4.bio1) has 25 residues
No: Leader PDB Ligand Sequence Similarity
1 5GQX GLC GLC GLC GLC 2.079
2 1Q8A HCS 2.079
3 3BOF HCS 2.079
4 6F5W KG1 2.16802
5 4YJK URA 2.38095
6 4X1B MLI 2.7027
7 3JUC PCA 3.26797
8 3ESS 18N 3.47826
9 1MFI FHC 3.50877
10 2VAR AMP 3.51438
11 5IFK HPA 3.52564
12 3QPB URA 3.5461
13 2J73 GLC GLC GLC GLC 3.8835
14 1VMK GUN 3.97112
15 5W75 SUC 4.08163
16 1F9V ADP 4.32277
17 4MPO AMP 5.22876
18 1NVM NAD 5.44872
19 1RYO OXL 5.8104
20 5NC1 NAG 5.90717
21 4JGP PYR 5.99078
22 4USI AKG 6.49351
23 1ONI BEZ 7.97101
24 5BTX CMP 8.21918
25 3TD3 GLY 13.8211
26 1C3X 8IG 13.9098
27 4G86 BNT 24.2958
Pocket No.: 3; Query (leader) PDB : 3JZ4; Ligand: NAP; Similar sites found with APoc: 29
This union binding pocket(no: 3) in the query (biounit: 3jz4.bio1) has 28 residues
No: Leader PDB Ligand Sequence Similarity
1 1US5 GLU 1.91083
2 1BW9 PPY 1.96629
3 1C1D PHE 1.97183
4 1C1X HFA 1.97183
5 1V6A TRE 2.10843
6 3G5N PB2 2.31092
7 1NW4 IMH 2.53623
8 3ALT MLB 2.54777
9 2BQP GLC 3.4188
10 3QPB R1P 3.5461
11 2UWN SCR 3.74332
12 5ZXD ATP 3.9501
13 4IMO PWZ 3.97727
14 3RK0 AMP 4.21941
15 1OFS SUC 4.27807
16 1KZL CRM 4.32692
17 1VAY AZA 5.22648
18 2WE0 UMP 5.24476
19 1EWK GLU 5.30612
20 1GPM AMP 5.61331
21 3BRE C2E 6.14525
22 2GQS C2R 6.32911
23 3NZ1 3NY 7.66284
24 4GKY MAN 8.42912
25 2FMD MAN MAN 12.5
26 4WGF HX2 13.1707
27 4OOP DUP 13.8554
28 1G4U AF3 14.3603
29 3P48 DUP 18.3673
Pocket No.: 4; Query (leader) PDB : 3JZ4; Ligand: NAP; Similar sites found with APoc: 6
This union binding pocket(no: 4) in the query (biounit: 3jz4.bio1) has 26 residues
No: Leader PDB Ligand Sequence Similarity
1 1PDZ PGA 2.07373
2 4FE2 AIR 3.52941
3 1I9Z 2IP 3.7464
4 3Q85 GNP 4.14201
5 4M6T SAM 8.19672
6 5KIQ SIA GAL NAG FUC 12.1827
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