Receptor
PDB id Resolution Class Description Source Keywords
1PNO 2.1 Å EC: 1.6.1.2 CRYSTAL STRUCTURE OF R. RUBRUM TRANSHYDROGENASE DOMAIN III BOUND TO NADP RHODOSPIRILLUM RUBRUM NUCLEOTIDE BINDING FOLD NADP OXIDOREDUCTASE
Ref.: CONFORMATIONAL CHANGE IN THE NADP(H) BINDING DOMAIN OF TRANSHYDROGENASE DEFINES FOUR STATES BIOCHEMISTRY V. 42 12143 2003
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
NAP A:500;
B:500;
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
1PNO 2.1 Å EC: 1.6.1.2 CRYSTAL STRUCTURE OF R. RUBRUM TRANSHYDROGENASE DOMAIN III BOUND TO NADP RHODOSPIRILLUM RUBRUM NUCLEOTIDE BINDING FOLD NADP OXIDOREDUCTASE
Ref.: CONFORMATIONAL CHANGE IN THE NADP(H) BINDING DOMAIN OF TRANSHYDROGENASE DEFINES FOUR STATES BIOCHEMISTRY V. 42 12143 2003
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 1PNQ - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
2 1PNO - 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 3 families.
1 1PNQ - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
2 1PNO - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
50% Homology Family (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 1PT9 - TAP C21 H28 N7 O16 P3 S c1cc(c[n+]....
2 1U31 - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
3 1DJL - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
4 1PNQ - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
5 1PNO - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
6 1D4O - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
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 : 1PNO; Ligand: NAP; Similar sites found: 171
This union binding pocket(no: 1) in the query (biounit: 1pno.bio2) has 31 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3MYZ TFX 0.0003385 0.50914 None
2 3W6X HZP 0.01808 0.41133 None
3 1L5Y BEF 0.01565 0.41123 None
4 2VWA PTY 0.02671 0.40673 None
5 4JLS 3ZE 0.04087 0.40588 None
6 3EVG SAH 0.01418 0.40185 None
7 3LLZ GAL NGA 0.04341 0.40063 None
8 1KYQ NAD 0.003572 0.43272 1.11111
9 5CB3 APR 0.002408 0.42286 1.66667
10 2PWY SAH 0.003502 0.41605 1.66667
11 3A25 SAM 0.007186 0.41525 1.66667
12 1L3I SAH 0.002328 0.41441 1.66667
13 3MB5 SAM 0.004374 0.41201 1.66667
14 5MF6 AR6 0.001338 0.41098 1.66667
15 5MF6 7M2 0.001338 0.41098 1.66667
16 5MX4 HPA 0.0462 0.40174 1.66667
17 1UAY ADN 0.001134 0.46478 2.22222
18 1G4U AF3 0.01746 0.42314 2.22222
19 4IF4 BEF 0.01984 0.41635 2.22222
20 4KRG SAH 0.01159 0.41247 2.22222
21 5LAU AR6 0.001141 0.40222 2.22222
22 3WUR O4B 0.02101 0.40023 2.33918
23 1R18 SAH 0.002341 0.42663 2.77778
24 3IID APR 0.001128 0.42387 2.77778
25 2DPM SAM 0.003686 0.41822 2.77778
26 1WUU GLA 0.0141 0.42991 3.33333
27 2VT3 ATP 0.008932 0.42546 3.33333
28 1I1N SAH 0.001216 0.40988 3.33333
29 2HMT NAI 0.006178 0.40865 3.47222
30 2C31 ADP 0.0009286 0.45678 3.88889
31 2C31 TZD 0.0009626 0.45678 3.88889
32 1JG3 ADN 0.001136 0.45149 3.88889
33 1NJR XYL 0.001228 0.42243 3.88889
34 1PL6 NAD 0.004659 0.41704 3.88889
35 1P4V GLY 0.02524 0.41546 3.88889
36 1EJ0 SAM 0.008963 0.4109 3.88889
37 1HGX 5GP 0.02625 0.40967 3.88889
38 2EJU SAH 0.01056 0.40767 3.88889
39 2Z48 NGA 0.03776 0.40747 3.88889
40 3SIG AR6 0.008081 0.40663 3.88889
41 1E1M FAD 0.01037 0.40277 3.88889
42 2Z48 A2G 0.03276 0.4015 3.88889
43 4ISS TAR 0.0409 0.40097 3.88889
44 1FP1 SAH 0.02059 0.40063 3.88889
45 3FGZ BEF 0.02792 0.40078 3.90625
46 3EGI ADP 0.001154 0.48597 4.44444
47 1T9D FAD 0.00002391 0.43255 4.44444
48 3SSO SAH 0.002982 0.42546 4.44444
49 1W73 NAP 0.003449 0.41332 4.44444
50 1W8D NAP 0.003789 0.41164 4.44444
51 1GZF NIR 0.03688 0.40582 4.44444
52 2ZIF SAM 0.0116 0.40272 4.44444
53 5FA8 SAM 0.006191 0.40569 4.96894
54 5DY5 5GR 0.00217 0.43512 5
55 2VDV SAM 0.006333 0.42876 5
56 2F5Z FAD 0.001632 0.42741 5
57 4MO2 FDA 0.003366 0.40878 5
58 1P1C SAH 0.006017 0.4062 5
59 2V6G NAP 0.002544 0.40088 5
60 3GPO APR 0.007158 0.40028 5.35714
61 2WPF FAD 0.004058 0.43997 5.55556
62 2WPF WPF 0.005286 0.43634 5.55556
63 2CDU ADP 0.01387 0.40546 5.55556
64 1VKF CIT 0.04329 0.40172 5.55556
65 5X62 SAH 0.01739 0.40089 5.55556
66 5DUS APR 0.0009765 0.44281 5.95238
67 3EWR APR 0.005041 0.40655 5.95238
68 2F6U CIT 0.02094 0.41903 6.11111
69 3G89 SAM 0.01262 0.41427 6.11111
70 1LVL NAD 0.006886 0.40965 6.11111
71 4HXY NDP 0.001498 0.40941 6.11111
72 2BFR ADP 0.005059 0.40936 6.11111
73 3CGD FAD 0.01863 0.4049 6.11111
74 3CGD COA 0.01863 0.4049 6.11111
75 1UA4 GLC 0.03521 0.40297 6.11111
76 1V5F FAD 0.0001699 0.48331 6.66667
77 3VYW SAM 0.00203 0.43271 6.66667
78 3M89 GSP 0.01781 0.41061 6.66667
79 4TQG NDP 0.002166 0.4101 6.66667
80 3IHB GLU 0.03714 0.40185 6.66667
81 4XFR CIT 0.04762 0.4012 6.66667
82 1M26 GAL A2G 0.007261 0.45098 6.76692
83 3ZG6 APR 0.0002165 0.47492 7.22222
84 2YX1 SFG 0.01184 0.41563 7.22222
85 4FC7 COA 0.006158 0.40358 7.22222
86 3EYA FAD 0.000353 0.44423 7.77778
87 3SQP FAD 0.01144 0.43793 7.77778
88 3HRD NIO 0.00933 0.43271 7.77778
89 2EG5 SAH 0.008448 0.42271 7.77778
90 1V59 NAD 0.01131 0.42039 7.77778
91 1ZQ9 SAM 0.00585 0.4193 7.77778
92 4I9B NAD 0.006484 0.41396 7.77778
93 4IQY AR6 0.005774 0.40696 7.77778
94 3PT9 SAH 0.01333 0.40307 7.77778
95 3AD8 NAD 0.002914 0.40774 8.08081
96 3ML1 MGD 0.01335 0.40788 8.14815
97 2B6N ALA PRO THR 0.005856 0.44377 8.33333
98 1I9G SAM 0.002849 0.42632 8.33333
99 2HNK SAH 0.003172 0.42429 8.33333
100 4NWJ 3PG 0.01523 0.42332 8.33333
101 3DXY SAM 0.01426 0.4154 8.33333
102 2PS1 ORO 0.02227 0.4134 8.33333
103 5JCA FAD 0.005651 0.40506 8.33333
104 1GUX ASP LEU TYR CYS TYR GLU GLN LEU ASN 0.004154 0.43354 8.55263
105 1P77 ATR 0.02783 0.41241 8.88889
106 3CBG SAH 0.01266 0.40729 8.88889
107 3EGV SAH 0.01405 0.40519 8.88889
108 2NXE SAM 0.01469 0.40116 8.88889
109 1G8K MGD 0.0004837 0.40196 9.02256
110 4YDD MGD 0.001254 0.45193 9.44444
111 4YDD MD1 0.001254 0.45193 9.44444
112 4DMG SAM 0.005053 0.43769 9.44444
113 1YBH FAD 0.00008007 0.41918 9.44444
114 2POC UD1 0.01852 0.41758 9.44444
115 1DL5 SAH 0.00334 0.4082 9.44444
116 4YSX FAD 0.007038 0.40033 9.44444
117 2PZM UDP 0.007757 0.40052 9.69697
118 3U31 NAD 0.00002887 0.50792 10
119 5U8U FAD 0.004368 0.42525 10.5556
120 5J60 FAD 0.005146 0.40472 10.5556
121 3EWP APR 0.004412 0.4034 10.7345
122 2VOH CIT 0.04513 0.40115 10.828
123 2V3V MGD 0.004727 0.42755 11.1111
124 3ICS ADP 0.009527 0.42408 11.1111
125 3ICT ADP 0.01083 0.42132 11.1111
126 3LST SAH 0.01208 0.4152 11.1111
127 1DJN ADP 0.003806 0.41454 11.1111
128 1MO9 FAD 0.01449 0.41011 11.1111
129 1MO9 KPC 0.01738 0.40721 11.1111
130 1O94 ADP 0.005599 0.40467 11.1111
131 4WCX MET 0.04202 0.4036 11.1111
132 2Q28 ADP 0.000009173 0.54012 11.6667
133 2NYR SVR 0.001793 0.45013 11.6667
134 3RIY NAD 0.000274 0.44126 11.6667
135 3GU3 SAH 0.007434 0.43366 11.6667
136 2V7Y ADP 0.01431 0.40483 11.6667
137 1LSS NAD 0.0005688 0.45671 12.1429
138 3G2O SAM 0.004796 0.42321 12.2222
139 2AE2 NAP 0.003882 0.40953 12.2222
140 2AE2 PTO 0.003882 0.40953 12.2222
141 1M2K APR 0.00006369 0.47245 12.7778
142 1X87 NAD 0.003264 0.41733 12.7778
143 5EB4 FAD 0.002716 0.41563 12.7778
144 4YNU FAD 0.004153 0.41224 12.7778
145 4YNU LGC 0.005418 0.4111 12.7778
146 3DUW SAH 0.0119 0.40224 12.7778
147 1UWK NAD 0.001346 0.43269 13.3333
148 3FUU ADN 0.003397 0.42641 13.3333
149 4J1Q NDP 0.00228 0.40116 13.8889
150 4I5I NAD 0.0008023 0.42962 14.4444
151 1XDS SAM 0.007844 0.42427 14.4444
152 4KXQ APR 0.0001993 0.4722 15
153 1QZZ SAM 0.01983 0.40476 15
154 1FEC FAD 0.0009273 0.44012 15.5556
155 3A27 SAM 0.009129 0.41054 15.5556
156 5A3B APR 0.0001086 0.44464 16.1111
157 5HJM MTA 0.01099 0.40378 16.1111
158 1E5Q NDP 0.001644 0.41468 16.6667
159 5KMS FAD 0.004476 0.40287 17.2222
160 2QQF A1R 0.0005656 0.41512 17.7778
161 2OD9 A1R NCA 0.001491 0.41356 17.7778
162 4BUZ NAD 0.0006055 0.43438 18.3333
163 1YC5 NCA 0.0007528 0.4181 18.3333
164 4BUZ OCZ 0.001046 0.41483 18.3333
165 4BUZ OAD 0.001061 0.41459 18.3333
166 2D24 XYS XYS 0.01666 0.41874 18.8889
167 1S7G NAD 0.0003045 0.43466 19.4444
168 1S7G APR 0.0002954 0.42637 19.4444
169 3LAD FAD 0.0006987 0.44097 20
170 1AE1 NAP 0.003636 0.40284 25.5556
171 4JCA CIT 0.02356 0.41722 28.7425
Pocket No.: 2; Query (leader) PDB : 1PNO; Ligand: NAP; Similar sites found: 60
This union binding pocket(no: 2) in the query (biounit: 1pno.bio1) has 32 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4NCW 2KN 0.003311 0.43548 None
2 1XE7 GUN 0.02605 0.42619 None
3 2PT9 S4M 0.004378 0.40756 None
4 1BDB NAD 0.00198 0.40105 1.11111
5 4NBW NAD 0.004907 0.40029 1.11111
6 4BQS K2Q 0.03782 0.40248 1.13636
7 2WPB ZZI 0.02039 0.42084 1.66667
8 5E5U MLI 0.005447 0.40506 1.66667
9 5N9X THR 0.02781 0.41423 2.22222
10 1ZEM NAD 0.003773 0.40742 2.22222
11 3LU1 NAD 0.003133 0.4003 2.22222
12 3IWD M2T 0.01739 0.43092 2.94118
13 3AQT RCO 0.01272 0.43098 3.33333
14 2YY7 NAD 0.002165 0.40627 3.33333
15 2IV2 MGD 0.0007087 0.4043 3.33333
16 1G0N PHH 0.0061 0.40051 3.33333
17 2YYY NAP 0.004263 0.40014 3.33333
18 3IWJ NAD 0.008676 0.41616 3.88889
19 5EOO CIT 0.02644 0.41411 3.88889
20 3GON PMV 0.03799 0.40625 3.88889
21 4HNN LYS 0.04287 0.40564 3.88889
22 1SQK ADP 0.01761 0.40506 3.88889
23 2Z49 AMG 0.03469 0.4029 3.88889
24 1PTR PRB 0.02901 0.40226 4
25 1H3F TYE 0.02575 0.41973 4.16667
26 3MJE NDP 0.00194 0.41063 4.23387
27 1IM8 SAI 0.00908 0.40567 4.44444
28 5LD5 NAD 0.006924 0.40492 4.44444
29 1VL8 NAP 0.00166 0.40411 4.44444
30 3U4C NDP 0.001757 0.41496 5
31 1ZMD NAI 0.004598 0.4067 5
32 5BUK FAD 0.006966 0.40104 5
33 3LRE ADP 0.04363 0.40065 5
34 4YAG NAI 0.005632 0.40281 5.55556
35 4DC2 ADE 0.04691 0.40205 5.55556
36 1VBO MAN 0.008433 0.43638 6.04027
37 4RSL FAD 0.002806 0.40824 6.11111
38 2FR1 NDP 0.002287 0.4015 6.11111
39 2XYQ SAH 0.01603 0.40064 6.11111
40 3WMX NAD 0.00447 0.40449 6.66667
41 2D7D ADP 0.03468 0.40078 6.66667
42 4RW3 DKA 0.02127 0.42609 7.77778
43 4EZW ASN ARG LEU LEU LEU THR GLY 0.008623 0.41981 7.77778
44 2WSB NAD 0.003817 0.40742 8.33333
45 1F3L SAH 0.006347 0.40943 8.88889
46 1ZOS MTM 0.01746 0.40201 8.88889
47 3SJU NDP 0.003053 0.40072 8.88889
48 2ZAT NAP 0.003415 0.40134 9.44444
49 4N49 SAM 0.007363 0.40965 10.5556
50 3L9W GSH 0.003429 0.40379 10.5556
51 1RYD GLC 0.04335 0.4035 10.5556
52 2IDO TMP 0.04833 0.40287 10.8434
53 3HQP FDP 0.0284 0.40167 11.1111
54 1FQJ ALF 0.04212 0.40502 14.2857
55 2PZE ATP 0.03418 0.41002 14.4444
56 4WZ6 ATP 0.04385 0.40459 14.4444
57 4UHO PLP 0.03932 0.40544 15
58 1H5Q NAP 0.002207 0.40597 16.6667
59 2CCV A2G 0.04765 0.4086 16.8317
60 1XHL NDP 0.00315 0.4015 17.8451
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