Receptor
PDB id Resolution Class Description Source Keywords
3NGL 2.4 Å EC: 1.5.1.5 CRYSTAL STRUCTURE OF BIFUNCTIONAL 5,10-METHYLENETETRAHYDROFO DEHYDROGENASE / CYCLOHYDROLASE FROM THERMOPLASMA ACIDOPHILU THERMOPLASMA ACIDOPHILUM METHYLENETETRAHYDROFOLATE DEHYDROGENASE/CYCLOHYDROLASE CATAOXIDATION OF 510-METHYLENETETRAHYDROFOLATE TO 510- METHENYLTETRAHYDROFOLATE THE HYDROLYSIS OF 510- METHENYLTETRAHYDROFOLATE TO 10-FORMYLTETRAHYDROFOLATE OXIDOREDUCTASE HYDROLASE
Ref.: CRYSTAL STRUCTURE OF BIFUNCTIONAL 5,10-METHYLENETETRAHYDROFOLATE DEHYDROGENASE/CYCLOH FROM THERMOPLASMA ACIDOPHILUM BIOCHEM.BIOPHYS.RES.COMMUN. V. 406 459 2011
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
NAP A:305;
C:305;
Valid;
Valid;
none;
none;
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743.405 C21 H28 N7 O17 P3 c1cc(...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3NGL 2.4 Å EC: 1.5.1.5 CRYSTAL STRUCTURE OF BIFUNCTIONAL 5,10-METHYLENETETRAHYDROFO DEHYDROGENASE / CYCLOHYDROLASE FROM THERMOPLASMA ACIDOPHILU THERMOPLASMA ACIDOPHILUM METHYLENETETRAHYDROFOLATE DEHYDROGENASE/CYCLOHYDROLASE CATAOXIDATION OF 510-METHYLENETETRAHYDROFOLATE TO 510- METHENYLTETRAHYDROFOLATE THE HYDROLYSIS OF 510- METHENYLTETRAHYDROFOLATE TO 10-FORMYLTETRAHYDROFOLATE OXIDOREDUCTASE HYDROLASE
Ref.: CRYSTAL STRUCTURE OF BIFUNCTIONAL 5,10-METHYLENETETRAHYDROFOLATE DEHYDROGENASE/CYCLOH FROM THERMOPLASMA ACIDOPHILUM BIOCHEM.BIOPHYS.RES.COMMUN. V. 406 459 2011
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 3NGL - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 3NGL - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
50% Homology Family (9)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 1DIA Ki = 455 uM L24 C21 H25 N5 O6 c1cc(ccc1C....
2 1A4I - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
3 1DIG Ki = 431 uM L37 C17 H19 N7 O7 c1cc(ccc1C....
4 3NGL - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
5 4CJX - 9L9 C17 H19 N7 O7 c1cc(ccc1C....
6 4B4W - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
7 4B4U - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
8 4B4V - L34 C20 H21 N7 O7 c1cc(ccc1C....
9 5TC4 ic50 = 663 nM L34 C20 H21 N7 O7 c1cc(ccc1C....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: NAP; Similar ligands found: 127
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 NAD IBO 0.688 0.921053
10 NHD 0.68254 0.958904
11 NJP 0.661417 0.972973
12 NAJ PYZ 0.659091 0.898734
13 NFD 0.658915 0.934211
14 DND 0.619048 0.959459
15 NXX 0.619048 0.959459
16 ZID 0.605839 0.972603
17 NAQ 0.59854 0.922078
18 ATR 0.59292 0.917808
19 NAE 0.591241 0.946667
20 NDE 0.58042 0.986301
21 A22 0.571429 0.958904
22 AMP NAD 0.571429 0.933333
23 NAJ 0.567164 0.986111
24 A2R 0.563025 0.932432
25 NDC 0.561644 0.922078
26 NA7 0.552846 0.907895
27 ODP 0.551471 0.935065
28 A2P 0.539823 0.930556
29 8ID 0.537313 0.910256
30 NAD BBN 0.525974 0.865854
31 NPW 0.525547 0.8875
32 CNA 0.521739 0.959459
33 NZQ 0.521739 0.910256
34 NAD CJ3 0.519231 0.835294
35 NDP 0.514493 0.922078
36 PO4 PO4 A A A A PO4 0.503937 0.930556
37 DG1 0.503401 0.922078
38 1DG 0.503401 0.922078
39 NAD TDB 0.5 0.696078
40 TXP 0.5 0.922078
41 NMN AMP PO4 0.492958 0.921053
42 XNP 0.492958 0.875
43 25L 0.492308 0.958904
44 25A 0.492063 0.972222
45 NAD NDT 0.490909 0.747368
46 NMN 0.486726 0.888889
47 NGD 0.485714 0.935065
48 2AM 0.477876 0.891892
49 ADP 0.458333 0.945205
50 PAP 0.451613 0.931507
51 ADP MG 0.45082 0.906667
52 BEF ADP 0.447154 0.883117
53 ADP BEF 0.447154 0.883117
54 A2D 0.445378 0.945205
55 AN2 0.442623 0.932432
56 ADP PO3 0.44 0.944444
57 SAP 0.44 0.896104
58 AGS 0.44 0.896104
59 M33 0.439024 0.906667
60 AR6 AR6 0.438849 0.945205
61 BA3 0.438017 0.945205
62 ATP MG 0.436508 0.906667
63 ADP BMA 0.43609 0.92
64 OAD 0.43609 0.92
65 ATP 0.435484 0.945205
66 OOB 0.435115 0.958904
67 B4P 0.434426 0.945205
68 AP5 0.434426 0.945205
69 GAP 0.433071 0.92
70 0WD 0.432432 0.922078
71 5FA 0.432 0.945205
72 2A5 0.432 0.87013
73 AQP 0.432 0.945205
74 00A 0.428571 0.909091
75 CA0 0.427419 0.92
76 ALF ADP 0.426357 0.871795
77 ADP ALF 0.426357 0.871795
78 ACP 0.424 0.92
79 NAJ PZO 0.423841 0.897436
80 9SN 0.423358 0.897436
81 VO4 ADP 0.423077 0.932432
82 ANP MG 0.423077 0.896104
83 ADP VO4 0.423077 0.932432
84 WAQ 0.422222 0.884615
85 ACQ 0.421875 0.92
86 V3L 0.421875 0.945205
87 ADQ 0.421053 0.92
88 AR6 0.420635 0.918919
89 APR 0.420635 0.918919
90 ATP A A A 0.42029 0.958333
91 CO7 0.419753 0.786517
92 1ZZ 0.419118 0.841463
93 3OD 0.419118 0.92
94 DLL 0.41791 0.958904
95 AD9 0.417323 0.92
96 NAX 0.416667 0.875
97 OVE 0.416667 0.857143
98 MYR AMP 0.416058 0.841463
99 AV2 0.415385 0.868421
100 A3P 0.414634 0.944444
101 NNR 0.414414 0.72973
102 ALF ADP 3PG 0.413793 0.8625
103 OMR 0.413793 0.831325
104 LA8 ALF 3PG 0.413793 0.8625
105 ANP 0.410853 0.92
106 A1R 0.410448 0.860759
107 ABM 0.409836 0.893333
108 AMP 0.408333 0.944444
109 A 0.408333 0.944444
110 SON 0.408 0.933333
111 PPS 0.407692 0.829268
112 5AL 0.407692 0.932432
113 TYR AMP 0.407143 0.933333
114 NAI 0.406897 0.909091
115 7D3 0.406504 0.857143
116 DAL AMP 0.406015 0.932432
117 ADX 0.404762 0.829268
118 ATF 0.40458 0.907895
119 3UK 0.404412 0.945946
120 AMP DBH 0.404255 0.894737
121 139 0.402685 0.875
122 AMP MG 0.401639 0.893333
123 50T 0.401575 0.906667
124 SRP 0.401515 0.907895
125 A A 0.40146 0.972222
126 FA5 0.4 0.933333
127 3AM 0.4 0.90411
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3NGL; Ligand: NAP; Similar sites found: 189
This union binding pocket(no: 1) in the query (biounit: 3ngl.bio1) has 23 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5H81 NAP 0.0001135 0.46485 1.44928
2 2NAD NAD 0.001258 0.44839 1.81159
3 2ZB3 NDP 0.001002 0.44455 1.81159
4 1PGP 6PG 0.002582 0.43572 1.81159
5 5GZ6 NDP 0.001138 0.4303 1.81159
6 5GZ6 7C3 0.001395 0.41547 1.81159
7 3GFB NAD 0.0005577 0.41248 1.81159
8 2E5V FAD 0.01942 0.40314 1.81159
9 4PLG NAI 0.00001558 0.53579 2.17391
10 5M67 ADE 0.00004168 0.5302 2.17391
11 5M67 NAD 0.00004595 0.52825 2.17391
12 5M67 3D1 0.00005038 0.52641 2.17391
13 3WLE NAD 0.00006749 0.50604 2.17391
14 4W6Z 8ID 0.0003773 0.47284 2.17391
15 2DFV NAD 0.0004017 0.46011 2.17391
16 4PLG OXM 0.007748 0.44315 2.17391
17 1HYH NAD 0.0002499 0.41059 2.17391
18 5JY6 NAD 0.0196 0.40775 2.17391
19 1NYT NAP 0.001008 0.41315 2.21402
20 4JK3 NAD 0.0001182 0.4812 2.3166
21 9LDT NAD 0.0001944 0.47851 2.53623
22 5KKA 6V0 0.001394 0.44256 2.53623
23 1KOL NAD 0.002063 0.44005 2.53623
24 2CVQ NDP 0.0002217 0.42099 2.53623
25 9LDB NAD 0.0002247 0.41337 2.53623
26 4NTD FAD 0.01098 0.40976 2.53623
27 1GAD NAD 0.006444 0.4068 2.53623
28 2VYN NAD 0.008382 0.40463 2.53623
29 3OJO NAD 0.005728 0.4044 2.53623
30 2GZ3 NAP 0.001126 0.46429 2.89855
31 5VKT NAP 0.0004325 0.46187 2.89855
32 4KP7 NAP 0.009446 0.42087 2.89855
33 3WQQ IB3 0.007795 0.4194 2.89855
34 4KP7 1UQ 0.0113 0.41389 2.89855
35 3B1F NAD 0.002669 0.41048 2.89855
36 2RAB NAD 0.0289 0.40889 2.89855
37 3CIF NAD 0.007883 0.40579 2.89855
38 3CIF G3H 0.01071 0.4049 2.89855
39 1DSS NAD 0.007163 0.40337 2.89855
40 2DBZ NAP 0.009215 0.40285 2.89855
41 4J4H NAI 0.0005371 0.47715 3.0888
42 4J4H 1J1 0.0005371 0.47715 3.0888
43 1GUZ NAD 0.00001109 0.52908 3.26087
44 1SOW NAD 0.00001565 0.52789 3.26087
45 1UXG NAD 0.00005364 0.51322 3.26087
46 1U3U NAD 0.0001429 0.49905 3.26087
47 1U3U BNF 0.0001429 0.49905 3.26087
48 1X7D NAD 0.0008784 0.44703 3.26087
49 1X7D ORN 0.001591 0.44624 3.26087
50 2YVF NAD 0.0134 0.42244 3.26087
51 2YVF FAD 0.01299 0.42244 3.26087
52 1VJT NAD 0.002464 0.41219 3.26087
53 4DSG FAD 0.03217 0.40489 3.26087
54 1YS4 NAP 0.005652 0.40299 3.26087
55 4RPL FAD 0.04164 0.40007 3.26087
56 2EV9 SKM 0.002413 0.43213 3.42205
57 2EV9 NAP 0.002413 0.43213 3.42205
58 2A92 NAI 0.00001259 0.53203 3.62319
59 1LDM NAD 0.0000716 0.43231 3.62319
60 1WB4 SXX 0.01782 0.41492 3.62319
61 4A0S NAP 0.00697 0.4107 3.62319
62 5BUK FAD 0.01905 0.40436 3.62319
63 4WAS NAP 0.01395 0.40307 3.62319
64 5FI3 NAP 0.001562 0.43766 3.92157
65 1EZ4 NAD 0.0001174 0.48133 3.98551
66 2CDC NAP 0.001077 0.47644 3.98551
67 2CDC XYS 0.001077 0.47644 3.98551
68 2CDC XYP 0.001103 0.47595 3.98551
69 1CDO NAD 0.0002303 0.4688 3.98551
70 1YB5 NAP 0.0011 0.4497 3.98551
71 1B8U OAA 0.0009603 0.44965 3.98551
72 1B8U NAD 0.0004169 0.44849 3.98551
73 2HJR APR 0.0002545 0.44423 3.98551
74 1F8F NAD 0.0003378 0.43085 3.98551
75 1J49 NAD 0.002225 0.42958 3.98551
76 5KVS 6XR 0.002953 0.42955 3.98551
77 1UP7 NAD 0.001949 0.4275 3.98551
78 1I0Z NAI 0.0001225 0.42707 3.98551
79 5KVS NAP 0.002182 0.42379 3.98551
80 1SC6 NAD 0.004868 0.41877 3.98551
81 2V3A FAD 0.007306 0.41771 3.98551
82 3VPH NAD 0.0002827 0.40189 3.98551
83 3VPH OXM 0.0001922 0.40017 3.98551
84 3HVJ 705 0.008815 0.41089 4.0724
85 4K28 NAD 0.0005831 0.42254 4.08922
86 1DXY NAD 0.001234 0.43758 4.34783
87 3JV7 NAD 0.0001442 0.42357 4.34783
88 1C1X NAD 0.0016 0.40028 4.34783
89 4YMH SAH 0.002643 0.41504 4.58333
90 1O6Z NAD 0.00004988 0.49336 4.71014
91 1OMO NAD 0.0002902 0.46094 4.71014
92 5MDH NAD 0.000396 0.46038 4.71014
93 1NVM NAD 0.001602 0.44123 4.71014
94 3JYN NDP 0.00324 0.42778 4.71014
95 1BXG NAD 0.00302 0.42093 4.71014
96 4MDH NAD 0.0005849 0.41189 4.71014
97 5J7X FAD 0.01731 0.40086 4.71014
98 1GQ2 NAP 0.00002104 0.45741 5.07246
99 1R37 NAD 0.001043 0.45072 5.07246
100 1LJ8 NAD 0.002979 0.4077 5.07246
101 1M2W NAD 0.002716 0.40424 5.07246
102 2X2T GAL NGA 0.021 0.4136 5.22876
103 2JHF NAD 0.0005016 0.5207 5.43478
104 1O0S NAI 0.0001799 0.45144 5.43478
105 5UAV NDP 0.004393 0.42545 5.43478
106 5UAV TFB 0.004393 0.42545 5.43478
107 3A06 FOM 0.004802 0.42373 5.43478
108 3A06 NDP 0.004264 0.42373 5.43478
109 5JWC FAD 0.0069 0.41561 5.43478
110 3T31 FAD 0.0155 0.41543 5.43478
111 3T31 DCQ 0.01658 0.41543 5.43478
112 1OBB NAD 0.001374 0.41137 5.43478
113 3CBG SAH 0.006442 0.40885 5.60345
114 4XB2 NDP 0.001834 0.42529 5.7971
115 4XB2 HSE 0.003457 0.42529 5.7971
116 5U8U FAD 0.01412 0.42323 5.7971
117 2AQJ TRP 0.03036 0.40364 5.7971
118 2AQJ FAD 0.0313 0.40364 5.7971
119 3CMC NAD 0.03915 0.40251 5.7971
120 1DRV A3D 0.001958 0.42232 5.86081
121 1MAI I3P 0.0225 0.41653 6.10687
122 1HYE NAP 0.003727 0.41229 6.15942
123 1LLU NAD 0.0001554 0.41029 6.52174
124 1XHC FAD 0.01279 0.40475 6.52174
125 1V8B NAD 0.00006063 0.5081 6.88406
126 3OND ADN 0.0001438 0.50441 6.88406
127 1P0F NAP 0.0006791 0.45624 6.88406
128 2QRK AMP 0.001271 0.45174 6.88406
129 2ZB4 5OP 0.001295 0.45137 6.88406
130 2ZB4 NAP 0.00122 0.45137 6.88406
131 1NVT NAP 0.0009827 0.43848 6.88406
132 4D04 NAP 0.02355 0.41139 6.88406
133 4D04 FAD 0.02355 0.41139 6.88406
134 1MO9 KPC 0.03998 0.4082 6.88406
135 1LTH NAD 0.00008556 0.45656 7.24638
136 2GAG NAD 0.01513 0.40251 7.24638
137 2DT5 NAD 0.0004648 0.41328 7.58294
138 5DN9 NAD 0.002043 0.43658 7.6087
139 2J8Z NAP 0.003602 0.42052 7.6087
140 3ICR FAD 0.007253 0.41681 7.6087
141 3ICS FAD 0.007701 0.41669 7.6087
142 5BSH PRO 0.008287 0.40863 7.6087
143 4JBI NDP 0.004084 0.4138 7.97101
144 3ABI NAD 0.000376 0.40926 7.97101
145 2G5C NAD 0.009058 0.40183 7.97101
146 1GV0 NAD 0.000008133 0.53677 8.33333
147 4BVA T3 0.0005751 0.46714 8.33333
148 4BVA NDP 0.0003792 0.46586 8.33333
149 1LDN NAD 0.000466 0.46195 8.33333
150 1PL6 572 0.0008347 0.45232 8.33333
151 1PL6 NAD 0.0004087 0.44885 8.33333
152 1D1T NAD 0.0000285 0.43801 8.33333
153 4RVU NDP 0.003516 0.42743 8.33333
154 1ZH8 NAP 0.007751 0.40476 8.33333
155 3ETG NDP 0.000635 0.47936 8.69565
156 3ETG GTP 0.0004346 0.47932 8.69565
157 3ETG GLU 0.0006932 0.47759 8.69565
158 1PZG A3D 0.00005898 0.40542 8.76133
159 3NJ4 NAD 0.0004512 0.51792 9.05797
160 3NJ4 AFX 0.001313 0.49455 9.05797
161 2AG8 NAP 0.00504 0.40334 9.12547
162 2F5Z FAD 0.02187 0.40077 9.375
163 2VVM FAD 0.01297 0.40843 9.42029
164 2VHW NAI 0.0001353 0.49262 9.78261
165 2FZW NAD 0.001293 0.45675 9.78261
166 4RQU NAD 0.0002371 0.42192 9.78261
167 2BRY FAD 0.009129 0.40796 10.1449
168 4GUT FAD 0.01808 0.40704 10.1449
169 4FWE FAD 0.01783 0.40484 10.1449
170 5O4J SAH 0.0108 0.40587 10.219
171 5O4J 9KH 0.0108 0.40587 10.219
172 5O4J PJL 0.01128 0.4039 10.219
173 4ZGS NAD 0.006613 0.40334 10.8696
174 4XYM COA 0.00658 0.42274 11.3043
175 4XZ3 COA 0.002811 0.41746 11.3043
176 1VM6 NAD 0.000681 0.44697 11.4035
177 3GGO NAI 0.01099 0.41355 11.5942
178 3GGO ENO 0.01099 0.41355 11.5942
179 1WDK NAD 0.002818 0.41742 11.9565
180 2FKA BEF 0.02633 0.40508 12.4031
181 1RSG FAD 0.01896 0.40275 13.0435
182 1YQD NAP 0.0003747 0.40017 13.0435
183 4MP8 NAD 0.0007322 0.46126 14.4928
184 2HK9 NAP 0.001453 0.43455 15.2174
185 1SAY PYR 0.00533 0.41944 16.3043
186 1EBF NAD 0.0002575 0.46314 16.6667
187 1T26 NAI 0.00002641 0.53226 19.5652
188 1J0X NAD 0.01291 0.41124 19.9275
189 1GR0 NAD 0.0008288 0.45513 20.6522
Pocket No.: 2; Query (leader) PDB : 3NGL; Ligand: NAP; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 3ngl.bio1) has 21 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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