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Receptor
PDB id Resolution Class Description Source Keywords
2QE0 2.19 Å EC: 1.2.1.9 THIOACYLENZYME INTERMEDIATE OF GAPN FROM S. MUTANS, NEW DATA INTEGRATION AND REFINEMENT. STREPTOCOCCUS MUTANS ALDH GAPN TERNARY COMPLEX OXIDOREDUCTASE
Ref.: THE FIRST CRYSTAL STRUCTURE OF A THIOACYLENZYME INT IN THE ALDH FAMILY: NEW COENZYME CONFORMATION AND R TO CATALYSIS BIOCHEMISTRY V. 45 2978 2006
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
G3H A:800;
B:800;
C:800;
D:800;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
submit data
170.058 C3 H7 O6 P C([C@...
NAP A:1476;
B:2476;
C:3476;
D:4476;
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
2QE0 2.19 Å EC: 1.2.1.9 THIOACYLENZYME INTERMEDIATE OF GAPN FROM S. MUTANS, NEW DATA INTEGRATION AND REFINEMENT. STREPTOCOCCUS MUTANS ALDH GAPN TERNARY COMPLEX OXIDOREDUCTASE
Ref.: THE FIRST CRYSTAL STRUCTURE OF A THIOACYLENZYME INT IN THE ALDH FAMILY: NEW COENZYME CONFORMATION AND R TO CATALYSIS BIOCHEMISTRY V. 45 2978 2006
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 2QE0 - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
2 2ID2 - 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 2 families.
1 2QE0 - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
2 2ID2 - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
50% Homology Family (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 4I3W - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
2 2QE0 - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
3 2ID2 - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
4 1UXN - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
5 1KY8 Kd = 1 uM NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
6 1UXU - G3H C3 H7 O6 P C([C@H](C=....
7 1UXT - NAD C21 H27 N7 O14 P2 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 : 2QE0; Ligand: NAP; Similar sites found with APoc: 167
This union binding pocket(no: 1) in the query (biounit: 2qe0.bio1) has 40 residues
No: Leader PDB Ligand Sequence Similarity
1 1UO4 PIH None
2 5ZXD ATP 1.26316
3 5KJW 53C 1.40515
4 4QO5 NAG 1.47368
5 4WCX MET 1.47368
6 1VJ7 GPX 1.52672
7 2ZWI C5P 1.60858
8 5EZ1 ICB 1.80505
9 4DFU QUE 1.86335
10 1CBK ROI 1.875
11 1G51 AMP 1.89474
12 4TVD BGC 1.89474
13 4FFG 0U8 1.89474
14 1K0E TRP 1.98676
15 5O96 SAM 2.04082
16 3LJU IP9 2.07254
17 2Z4T C5P 2.10526
18 5W7B MYR 2.1327
19 3DLS ADP 2.38806
20 2WTN FER 2.39044
21 2Z49 AMG 2.5463
22 2Y91 98J 2.64151
23 1MT1 AG2 2.65487
24 1N13 AG2 2.65487
25 2QQD AG2 2.67857
26 3GD8 GOL 2.69058
27 2F2G HMH 2.71493
28 2Q4X HMH 2.71493
29 4G17 0VN 2.72727
30 4D3S BOG 2.73038
31 2FYF PLP 2.76382
32 1KAE NAD 2.76498
33 4XFM THE 2.80172
34 1KZL CRM 2.88462
35 4J26 EST 2.91667
36 4J24 EST 2.91667
37 4Z7X 3CX 2.94118
38 2GEK GDP 2.95567
39 3QSB 743 3.00546
40 3KMZ EQO 3.00752
41 1VL1 CIT 3.01724
42 3BRE C2E 3.07263
43 4BG4 ADP 3.08989
44 1EJH M7G 3.15789
45 1HPG BOC ALA ALA PRO GLU 3.20856
46 2IMG MLT 3.31126
47 5N1X 8HH 3.38983
48 2PEL LBT 3.38983
49 5CC2 CKA 3.39623
50 5W8X UDP 3.40314
51 4XFR CIT 3.51288
52 4G86 BNT 3.52113
53 3EJ0 11X 3.57143
54 5L2R MLA 3.57895
55 1T36 U 3.57895
56 5YJS SAL 3.58974
57 3ITA AIC 3.69318
58 1F9V ADP 3.7464
59 2IU8 PLM 4.01069
60 1KYQ NAD 4.0146
61 1H5S TMP 4.09556
62 1H5T TYD 4.09556
63 4CS9 AMP 4.2328
64 3BJE R1P 4.29799
65 3RZ3 U94 4.37158
66 1CY2 TMP 4.42105
67 1ZEA DVA DPR GLY DSN DGN DHI DTY DAS DSN 4.62963
68 1PZL MYR 4.64135
69 3TW1 AHN 4.64135
70 3TY3 GGG 4.64481
71 2RDE C2E 4.78088
72 3FS1 MYR 4.78261
73 2XCU C5P 4.81283
74 1VG9 GDP 4.86486
75 1VG1 GDP 4.86486
76 1JHG TRP 4.9505
77 5DX3 EST 4.98084
78 5DXG EST 4.98084
79 1ZX5 LFR 5
80 4ZDJ UTP 5.05263
81 1JGS SAL 5.07246
82 4MG9 27K 5.09804
83 1VHW ADN 5.13834
84 4V3C C 5.15464
85 1Q8O MAN MMA 5.15873
86 3OVR 5SP 5.26316
87 2NU8 COA 5.41237
88 4R84 CSF 5.47368
89 5KHD C2E 5.49451
90 1PDZ PGA 5.52995
91 5G48 1FL 5.88235
92 1OFU GDP 5.9375
93 3KO0 TFP 5.94059
94 2VT3 ATP 6.04651
95 4GKY MAN 6.13027
96 1JAY F42 6.13208
97 1TZD ADP 6.18182
98 4B98 PXG 6.25
99 3SHR CMP 6.35452
100 2GBB CIT 6.41026
101 1SBR VIB 6.5
102 5XVH TLA 6.53595
103 6CB2 OLC 6.82594
104 1J2Z SOG 7.03704
105 5YF9 NIO 7.07965
106 3H0L ADP 7.11297
107 2HFU MEV 7.22892
108 2G30 ALA ALA PHE 7.36434
109 5IXK 6EW 7.45614
110 2XG5 EC5 7.51445
111 2XG5 EC2 7.51445
112 5NM7 GLY 7.5188
113 2XYA 7L4 7.69231
114 1MID LAP 7.69231
115 3K56 IS3 7.89474
116 3NZ1 3NY 8.04598
117 1M2Z BOG 8.17121
118 6GR0 F8W 8.62069
119 6FA4 D1W 8.67052
120 5OM2 DXT 8.94309
121 1TV5 N8E 9.02935
122 1UYY BGC BGC 9.16031
123 3Q60 ATP 9.16442
124 3KP6 SAL 9.27152
125 3O01 DXC 9.41558
126 1LSH PLD 10.1053
127 5TVF CGQ 10.5882
128 5T46 MGP 10.6061
129 3EFS BTN 11.588
130 4CNK MEU 12.2762
131 5EXK MET 12.3867
132 3DZ6 M8E 13.4328
133 1I7M CG 13.4328
134 3UYW TAU 13.5514
135 5FUI APY 13.6364
136 2VCN ISZ 13.7931
137 3WUR O4B 14.0351
138 4RYV ZEA 14.1935
139 5CX6 CDP 14.3158
140 4OGQ 7PH 14.7059
141 3IWD M2T 16.129
142 3GU3 SAH 19.3662
143 5BXV MGP 20.4545
144 1UO5 PIH 26.4706
145 5DBV COA 28.5393
146 5JFL NAD 30.1527
147 1EZ0 NAP 33.8947
148 5KF6 NAD 38.5263
149 4LH0 GLV 38.7368
150 3HAZ NAD 40.8421
151 4OE4 NAD 42.9474
152 2Y5D NAP 43.3684
153 6FK3 PPI 43.7895
154 5UCD NAP 43.9825
155 4NS3 NAD 44.2105
156 4YWV SSN 44.5161
157 5N5S NAP 44.8421
158 3EFV NAD 45.8874
159 6MVU K4V 46.1053
160 4ZUL UN1 47.3684
161 2BJK NAD 48
162 3VZ3 NAP 48.14
163 3VZ3 SSN 48.14
164 5X5U NAD 48.4211
165 4PXL NAD 49.2632
166 5L13 6ZE 49.4737
167 1O9J NAD 49.6842
Pocket No.: 2; Query (leader) PDB : 2QE0; Ligand: NAP; Similar sites found with APoc: 53
This union binding pocket(no: 2) in the query (biounit: 2qe0.bio1) has 41 residues
No: Leader PDB Ligand Sequence Similarity
1 6B79 ORA None
2 2ZUX RAM 1.26316
3 1BGV GLU 1.78174
4 3AQT RCO 2.04082
5 3RK0 AMP 2.1097
6 3UBM COA 2.19298
7 6BR8 PGV 2.38095
8 2IXB NAD 2.47748
9 2Z48 NGA 2.5463
10 5AYV NAP 2.589
11 3NJQ NJQ 2.59067
12 2RI1 GLP 2.97872
13 4OKS 2T9 3.23276
14 5N26 CPT 3.2967
15 4XG0 CIT 3.51288
16 1V59 NAD 3.57895
17 2UWN SCR 3.74332
18 4NZ6 DLY 3.83387
19 3V0H I3P 3.83481
20 3BP1 GUN 4.13793
21 5EP2 AZU 4.29688
22 2OFW ADX 4.32692
23 4H0I MMA 4.38247
24 5NNS AKR 4.44444
25 1I36 NAP 4.54545
26 5DEP UD1 4.65116
27 1M2T ADE 4.72441
28 1DTL BEP 4.96894
29 5WGQ EST 4.98084
30 5WGD EST 4.98084
31 5YLF BGC 5.08982
32 4MGD 27N 5.09804
33 4TV1 36M 5.17928
34 3GWN FAD 5.26316
35 4IHL 1F5 5.53191
36 5X62 SAH 6.15764
37 3EYY MLI 6.2069
38 2QX0 PH2 6.28931
39 2RNF UM3 6.66667
40 4ONT SIA GAL BGC 6.94006
41 2GNK ATP 7.14286
42 3CL7 HYN 7.46753
43 1L0I PSR 7.69231
44 5C1M OLC 8
45 1T0S BML 10.4651
46 1VCE SAH 11.6981
47 1WNG SAH 11.6981
48 1ZQ9 SAM 12.2807
49 1UPR 4IP 13.0081
50 4PTN GXV 13.7026
51 5CB8 ADX 15.736
52 1MFI FHC 15.7895
53 4RJD TFP 16.6667
Pocket No.: 3; Query (leader) PDB : 2QE0; Ligand: NAP; Similar sites found with APoc: 25
This union binding pocket(no: 3) in the query (biounit: 2qe0.bio1) has 39 residues
No: Leader PDB Ligand Sequence Similarity
1 4WG0 CHD None
2 1B4B ARG None
3 1TZJ A3B 1.18343
4 2VL1 GLY GLY 1.68776
5 1EWK GLU 2.10526
6 2YK7 CSF 2.14724
7 5EY0 ILE 2.52632
8 1SES AMP 2.85036
9 1UI0 URA 2.92683
10 1CT9 AMP 3.15789
11 1B4N GUA 3.36842
12 1W5F G2P 3.39943
13 4XMF HSM 4.34783
14 3WSG CIT 4.36508
15 1TVP CBI 4.43686
16 3AB4 THR 4.49438
17 2D3Y DU 5.93607
18 1NU4 MLA 6.18557
19 3EB9 FLC 7.5188
20 6CZY PMP 7.73481
21 5OCG 9R5 7.93651
22 1XZ3 ICF 8.62069
23 1VBO MAN MAN MAN 9.39597
24 4UEC MGT 10.8696
25 3GUZ PAF 14.7727
Pocket No.: 4; Query (leader) PDB : 2QE0; Ligand: NAP; Similar sites found with APoc: 11
This union binding pocket(no: 4) in the query (biounit: 2qe0.bio1) has 39 residues
No: Leader PDB Ligand Sequence Similarity
1 4MBY BGC SIA GAL 3.59712
2 4Q0A 4OA 3.97351
3 1QPR PHT 4.22535
4 5ZI9 FLC 4.61538
5 3H4V DVP 4.86111
6 3VSV XYS 5.05263
7 4WOE ADP 5.68421
8 5AHO TLA 6.84524
9 5C8W PCG 9.79021
10 4V1F BQ1 22.093
11 5EOO CIT 22.2642
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