Receptor
PDB id Resolution Class Description Source Keywords
1PNQ 2.4 Å EC: 1.6.1.2 CRYSTAL STRUCTURE OF R. RUBRUM TRANSHYDROGENASE DOMAIN III BOUND TO NADPH RHODOSPIRILLUM RUBRUM NUCLEOTIDE BINDING FOLD NADPH 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
NDP A:500;
B:500;
Valid;
Valid;
none;
none;
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745.421 C21 H30 N7 O17 P3 c1nc(...
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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: NDP; Similar ligands found: 159
No: Ligand ECFP6 Tc MDL keys Tc
1 NDP 1 1
2 0WD 0.827273 1
3 NAI 0.803738 0.986842
4 NMN AMP PO4 0.794643 0.948052
5 NPW 0.692308 0.962025
6 NZQ 0.686441 0.987013
7 DG1 0.68 1
8 1DG 0.68 1
9 A2R 0.650943 0.909091
10 A22 0.64486 0.934211
11 TXP 0.644628 0.924051
12 ATR 0.640777 0.894737
13 NA7 0.636364 0.886076
14 XNP 0.620968 0.949367
15 AP0 0.598361 0.948718
16 A2P 0.598039 0.881579
17 NJP 0.574803 0.923077
18 25L 0.550847 0.934211
19 ODP 0.550388 0.936709
20 NAX 0.544 0.949367
21 25A 0.53913 0.921053
22 2AM 0.529412 0.87013
23 6V0 0.519685 0.974026
24 NAP 0.514493 0.922078
25 EAD 0.507143 0.949367
26 A2D 0.504673 0.921053
27 TXE 0.503876 0.935897
28 NA0 0.496454 0.910256
29 TXD 0.496124 0.911392
30 SAP 0.495575 0.875
31 AGS 0.495575 0.875
32 P1H 0.493056 0.925926
33 CO7 0.489796 0.791209
34 TAP 0.489362 0.864198
35 PAP 0.482456 0.907895
36 BA3 0.481818 0.921053
37 NAJ PZO 0.478261 0.924051
38 ATP 0.477876 0.921053
39 B4P 0.477477 0.921053
40 ADP 0.477477 0.921053
41 AP5 0.477477 0.921053
42 OAD 0.47541 0.897436
43 5FA 0.473684 0.921053
44 AR6 0.473684 0.896104
45 APR 0.473684 0.896104
46 AQP 0.473684 0.921053
47 AN2 0.473214 0.909091
48 3OD 0.467742 0.897436
49 50T 0.464912 0.884615
50 PO4 PO4 A A A A PO4 0.463415 0.857143
51 V3L 0.461538 0.896104
52 2A5 0.46087 0.85
53 A1R 0.459016 0.841463
54 ADQ 0.459016 0.897436
55 4AD 0.459016 0.875
56 OVE 0.458716 0.8375
57 OMR 0.458647 0.813953
58 PPS 0.457627 0.811765
59 AD9 0.456897 0.897436
60 CA0 0.45614 0.897436
61 M33 0.45614 0.884615
62 ADJ 0.455882 0.879518
63 A3P 0.455357 0.894737
64 ACP 0.452174 0.897436
65 ENP 0.451613 0.85
66 UP5 0.451128 0.948052
67 SRP 0.45 0.8625
68 ANP 0.449153 0.897436
69 ACQ 0.449153 0.897436
70 PRX 0.448276 0.82716
71 5AL 0.445378 0.884615
72 7D4 0.443478 0.8375
73 ADX 0.443478 0.811765
74 AMP 0.436364 0.894737
75 A 0.436364 0.894737
76 4TC 0.433824 0.924051
77 7D3 0.433628 0.8375
78 ETB 0.433566 0.797753
79 DCA 0.433566 0.788889
80 1ZZ 0.433071 0.802326
81 BIS 0.433071 0.864198
82 00A 0.432 0.864198
83 ATF 0.429752 0.886076
84 0T1 0.427586 0.788889
85 5SV 0.427419 0.788235
86 8QN 0.427419 0.884615
87 3AM 0.427273 0.857143
88 N01 0.426573 0.884615
89 PR8 0.425197 0.811765
90 WAQ 0.425197 0.841463
91 LAD 0.425197 0.821429
92 DTP 0.425 0.8375
93 AMO 0.424 0.886076
94 PAJ 0.424 0.843373
95 APC 0.423729 0.886076
96 UPA 0.423358 0.935897
97 48N 0.422222 0.853659
98 FYA 0.421875 0.860759
99 PTJ 0.421875 0.853659
100 CNA 0.421429 0.910256
101 PUA 0.42069 0.9125
102 NXX 0.419118 0.910256
103 DND 0.419118 0.910256
104 AV2 0.418033 0.848101
105 COA 0.417808 0.788889
106 3UK 0.417323 0.897436
107 OOB 0.416 0.909091
108 IVC 0.415584 0.78022
109 DAT 0.415254 0.8375
110 NDO 0.414966 0.897436
111 139 0.414286 0.901235
112 3AT 0.413223 0.896104
113 TAT 0.413223 0.886076
114 YLB 0.413043 0.784091
115 62F 0.4125 0.823529
116 ABM 0.412281 0.848101
117 YAP 0.412214 0.875
118 YLP 0.411765 0.784091
119 ME8 0.410853 0.802326
120 NB8 0.410853 0.853659
121 SON 0.410256 0.886076
122 DLL 0.409449 0.909091
123 AHX 0.409449 0.853659
124 COS 0.409396 0.771739
125 AMX 0.409396 0.797753
126 CAO 0.409396 0.763441
127 30N 0.409396 0.72449
128 7D5 0.409091 0.8125
129 4UW 0.408759 0.9125
130 APX 0.407692 0.841463
131 SRA 0.40708 0.85
132 CMX 0.406667 0.788889
133 SCO 0.406667 0.788889
134 TYM 0.405797 0.886076
135 COD 0.405594 0.777778
136 OXK 0.405229 0.771739
137 CA6 0.405229 0.70297
138 A12 0.405172 0.886076
139 AP2 0.405172 0.886076
140 9SN 0.40458 0.853659
141 LAQ 0.404412 0.802326
142 T5A 0.404255 0.914634
143 FAM 0.403974 0.771739
144 ACO 0.403974 0.763441
145 FCX 0.403974 0.763441
146 AMP MG 0.403509 0.825
147 VO4 ADP 0.403226 0.860759
148 ADP VO4 0.403226 0.860759
149 YLC 0.402878 0.823529
150 1VU 0.402597 0.763441
151 FA5 0.401515 0.886076
152 HAX 0.401316 0.771739
153 APU 0.4 0.923077
154 TXA 0.4 0.886076
155 A U 0.4 0.898734
156 4UU 0.4 0.948052
157 AFH 0.4 0.843373
158 CAJ 0.4 0.771739
159 AR6 AR6 0.4 0.871795
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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