Receptor
PDB id Resolution Class Description Source Keywords
2NSY 2 Å EC: 6.3.5.1 CRYSTAL STRUCTURE OF NH3-DEPENDENT NAD+ SYNTHETASE FROM BACI SUBTILIS IN COMPLEX WITH NAD-ADENYLATE BACILLUS SUBTILIS LIGASE AMIDOTRANSFERASE NH3 DEPENDENT ATP PYROPHOSPHATASE
Ref.: A NOVEL DEAMIDO-NAD+-BINDING SITE REVEALED BY THE T NAD-ADENYLATE INTERMEDIATE IN THE NAD+ SYNTHETASE S STRUCTURE V. 6 1129 1998
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
AMP NAD A:300;
B:302;
Valid;
Valid;
none;
none;
submit data
991.607 n/a P(=O)...
GOL A:308;
B:309;
Invalid;
Invalid;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
MG A:304;
A:305;
B:306;
B:307;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
submit data
24.305 Mg [Mg+2...
POP A:863;
B:862;
Invalid;
Invalid;
none;
none;
submit data
175.959 H2 O7 P2 O[P@@...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1KQP 1.03 Å EC: 6.3.5.1 NH3-DEPENDENT NAD+ SYNTHETASE FROM BACILLUS SUBTILIS AT 1 A BACILLUS SUBTILIS LIGASE AMIDOTRANSFERASE ATP PYROPHOSPHATASE NAD-ADENYLATE
Ref.: NH3-DEPENDENT NAD+ SYNTHETASE FROM BACILLUS SUBTILI RESOLUTION. ACTA CRYSTALLOGR.,SECT.D V. 58 1138 2002
Members (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 1EE1 - DND C21 H27 N6 O15 P2 c1cc(c[n+]....
2 1IH8 - APC C11 H18 N5 O12 P3 c1nc(c2c(n....
3 2NSY - AMP NAD n/a n/a
4 1NSY - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
5 1IFX - DND C21 H27 N6 O15 P2 c1cc(c[n+]....
6 1FYD - AMP C10 H14 N5 O7 P c1nc(c2c(n....
7 1KQP - ADJ C31 H44 N11 O21 P3 c1nc(c2c(n....
70% 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 1EE1 - DND C21 H27 N6 O15 P2 c1cc(c[n+]....
2 1IH8 - APC C11 H18 N5 O12 P3 c1nc(c2c(n....
3 2NSY - AMP NAD n/a n/a
4 1NSY - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
5 1IFX - DND C21 H27 N6 O15 P2 c1cc(c[n+]....
6 1FYD - AMP C10 H14 N5 O7 P c1nc(c2c(n....
7 1KQP - ADJ C31 H44 N11 O21 P3 c1nc(c2c(n....
8 2PZA - AMP C10 H14 N5 O7 P c1nc(c2c(n....
9 2PZ8 - APC C11 H18 N5 O12 P3 c1nc(c2c(n....
50% Homology Family (13)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 1EE1 - DND C21 H27 N6 O15 P2 c1cc(c[n+]....
2 1IH8 - APC C11 H18 N5 O12 P3 c1nc(c2c(n....
3 2NSY - AMP NAD n/a n/a
4 1NSY - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
5 1IFX - DND C21 H27 N6 O15 P2 c1cc(c[n+]....
6 1FYD - AMP C10 H14 N5 O7 P c1nc(c2c(n....
7 1KQP - ADJ C31 H44 N11 O21 P3 c1nc(c2c(n....
8 1WXI - AMP C10 H14 N5 O7 P c1nc(c2c(n....
9 1WXG - DND C21 H27 N6 O15 P2 c1cc(c[n+]....
10 1WXH - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
11 1WXE - AMP C10 H14 N5 O7 P c1nc(c2c(n....
12 2PZA - AMP C10 H14 N5 O7 P c1nc(c2c(n....
13 2PZ8 - APC C11 H18 N5 O12 P3 c1nc(c2c(n....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: AMP NAD; Similar ligands found: 219
No: Ligand ECFP6 Tc MDL keys Tc
1 AMP NAD 1 1
2 A3D 0.745763 0.958904
3 NAD 0.74359 0.972222
4 N01 0.696721 0.972222
5 NXX 0.689655 0.972603
6 DND 0.689655 0.972603
7 NAJ 0.642276 0.972222
8 NA0 0.609023 0.945946
9 NHD 0.606299 0.945205
10 ZID 0.606061 0.958904
11 NAP 0.606061 0.958904
12 NAQ 0.598485 0.909091
13 GAP 0.59633 0.958904
14 ADP PO3 0.592593 0.957747
15 ATP MG 0.592593 0.957747
16 NAE 0.590909 0.933333
17 TAP 0.589552 0.896104
18 ADP MG 0.584906 0.957747
19 NFD 0.584615 0.921053
20 NDC 0.582734 0.909091
21 ALF ADP 0.571429 0.883117
22 ADP ALF 0.571429 0.883117
23 NDE 0.568345 0.945946
24 VO4 ADP 0.566372 0.918919
25 ADP VO4 0.566372 0.918919
26 DAL AMP 0.556522 0.972222
27 OOB 0.538462 0.972222
28 ADP BMA 0.537815 0.958904
29 MYR AMP 0.53719 0.875
30 TYR AMP 0.532258 0.959459
31 CNA 0.530303 0.945946
32 ATP A A A 0.528455 0.971831
33 ATP A 0.528455 0.971831
34 AHZ 0.527559 0.875
35 NAJ PZO 0.522059 0.909091
36 AR6 AR6 0.511811 0.985915
37 ARG AMP 0.511811 0.864198
38 LPA AMP 0.511628 0.875
39 CA0 0.508929 0.932432
40 APC MG 0.508772 0.931507
41 AMP 0.504673 0.90411
42 A 0.504673 0.90411
43 45A 0.504587 0.88
44 A2D 0.504587 0.931507
45 ABM 0.504587 0.88
46 ADP 0.504505 0.905405
47 KG4 0.504425 0.932432
48 00A 0.504132 0.921053
49 AF3 ADP 3PG 0.503817 0.897436
50 APC 0.5 0.87013
51 AN2 0.5 0.893333
52 NDO 0.496454 0.932432
53 9SN 0.496 0.909091
54 8LE 0.495726 0.907895
55 BA3 0.495495 0.931507
56 A12 0.495495 0.87013
57 AP2 0.495495 0.87013
58 B5M 0.492063 0.933333
59 DLL 0.491803 0.972222
60 8LQ 0.491667 0.92
61 ACP 0.491228 0.881579
62 AP5 0.491071 0.931507
63 B4P 0.491071 0.931507
64 3UK 0.487805 0.958904
65 8LH 0.487395 0.92
66 AT4 0.486726 0.87013
67 SON 0.486726 0.92
68 NAJ PYZ 0.485915 0.864198
69 AMP DBH 0.484375 0.932432
70 WAQ 0.483871 0.896104
71 A A 0.483871 0.931507
72 B5V 0.483871 0.945946
73 5AL 0.483051 0.945205
74 M33 0.482456 0.893333
75 FA5 0.480315 0.945946
76 ATP 0.478261 0.905405
77 HEJ 0.478261 0.905405
78 4TA 0.478261 0.864198
79 SRP 0.475 0.92
80 ACQ 0.474576 0.881579
81 5FA 0.474138 0.905405
82 AQP 0.474138 0.905405
83 APR 0.474138 0.931507
84 AR6 0.474138 0.931507
85 SRA 0.472727 0.857143
86 4AD 0.471545 0.933333
87 AD9 0.470085 0.881579
88 ADV 0.470085 0.894737
89 SAP 0.470085 0.858974
90 AGS 0.470085 0.858974
91 RBY 0.470085 0.894737
92 ADX 0.469565 0.817073
93 AU1 0.469565 0.881579
94 YAP 0.46875 0.933333
95 3OD 0.468254 0.932432
96 1ZZ 0.468254 0.851852
97 8ID 0.466667 0.897436
98 NBP 0.465753 0.897436
99 50T 0.465517 0.868421
100 OAD 0.464 0.932432
101 9ZA 0.463415 0.896104
102 8QN 0.463415 0.945205
103 9ZD 0.463415 0.896104
104 6YZ 0.46281 0.881579
105 T99 0.462185 0.87013
106 ANP 0.462185 0.881579
107 TAT 0.462185 0.87013
108 DQV 0.462121 0.945205
109 PRX 0.461538 0.857143
110 M24 0.461538 0.886076
111 NJP 0.460432 0.933333
112 PR8 0.460317 0.8625
113 NGD 0.459854 0.897436
114 PAJ 0.459677 0.873418
115 AMO 0.459677 0.92
116 A1R 0.459677 0.848101
117 B5Y 0.457364 0.933333
118 PTJ 0.456693 0.884615
119 ATF 0.454545 0.87013
120 DZD 0.453901 0.873418
121 9X8 0.452381 0.883117
122 9JJ 0.450617 0.875
123 IOT 0.449275 0.821429
124 Z5A 0.44898 0.833333
125 LAD 0.448819 0.873418
126 TYM 0.448529 0.945946
127 A3R 0.448 0.848101
128 LAQ 0.447761 0.851852
129 HQG 0.447154 0.918919
130 G A A A 0.446809 0.909091
131 A G 0.446809 0.921053
132 FYA 0.445312 0.893333
133 TXA 0.445312 0.92
134 ME8 0.445312 0.851852
135 NB8 0.445312 0.884615
136 AHX 0.444444 0.860759
137 U A G G 0.443662 0.921053
138 A22 0.443548 0.918919
139 MAP 0.443548 0.858974
140 PO4 PO4 A A A A PO4 0.440945 0.943662
141 4UV 0.439394 0.933333
142 TXE 0.437956 0.896104
143 LMS 0.4375 0.795181
144 ADQ 0.436508 0.932432
145 G3A 0.43609 0.884615
146 7MD 0.432836 0.851852
147 G5P 0.432836 0.884615
148 4UU 0.432836 0.933333
149 NAI 0.430657 0.896104
150 NAX 0.430657 0.8625
151 TXD 0.430657 0.896104
152 AOC 0.429825 0.810811
153 G5A 0.429752 0.770115
154 TAD 0.42963 0.85
155 F2R 0.429577 0.831325
156 OZV 0.428571 0.905405
157 25A 0.428571 0.931507
158 5SV 0.428571 0.814815
159 U A 0.427586 0.921053
160 5AS 0.42735 0.75
161 NMN AMP PO4 0.426573 0.933333
162 139 0.425532 0.8625
163 DSZ 0.425197 0.790698
164 8PZ 0.424242 0.790698
165 VMS 0.424 0.77907
166 54H 0.424 0.77907
167 JB6 0.423077 0.871795
168 BIS 0.423077 0.848101
169 9K8 0.423077 0.764045
170 AFH 0.422222 0.873418
171 XAH 0.421053 0.829268
172 TSB 0.420635 0.788235
173 5CA 0.420635 0.770115
174 8X1 0.420635 0.744444
175 6V0 0.42029 0.884615
176 4UW 0.42029 0.897436
177 25L 0.419847 0.918919
178 A5A 0.419355 0.797619
179 A A A 0.418605 0.918919
180 OMR 0.417266 0.841463
181 H1Q 0.416667 0.891892
182 COA FLC 0.416107 0.802326
183 SSA 0.416 0.770115
184 NMN 0.415929 0.849315
185 P5A 0.415385 0.736264
186 ENQ 0.415385 0.930556
187 BT5 0.413793 0.821429
188 YLP 0.413043 0.831325
189 48N 0.413043 0.884615
190 52H 0.412698 0.770115
191 NCN 0.412281 0.805556
192 GA7 0.411765 0.87013
193 YSA 0.410448 0.790698
194 B1U 0.410448 0.766667
195 53H 0.409449 0.770115
196 GTA 0.408759 0.875
197 5CD 0.407407 0.794521
198 A4D 0.407407 0.783784
199 COD 0.406897 0.781609
200 RAB 0.40566 0.808219
201 ADN 0.40566 0.808219
202 XYA 0.40566 0.808219
203 T5A 0.405594 0.831325
204 YLA 0.405594 0.831325
205 GSU 0.40458 0.790698
206 7MC 0.404255 0.831325
207 4TC 0.404255 0.884615
208 AP0 0.404255 0.860759
209 YLC 0.404255 0.851852
210 YLB 0.404255 0.831325
211 CNV FAD 0.403614 0.833333
212 NSS 0.403101 0.790698
213 LSS 0.403101 0.752809
214 AYB 0.402778 0.821429
215 A4P 0.401408 0.811765
216 80F 0.401361 0.853659
217 FAD NBT 0.401198 0.76087
218 UP5 0.4 0.907895
219 NVA LMS 0.4 0.764045
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1KQP; Ligand: ADJ; Similar sites found with APoc: 3
This union binding pocket(no: 1) in the query (biounit: 1kqp.bio1) has 40 residues
No: Leader PDB Ligand Sequence Similarity
1 1XNG ATP 38.806
2 1XNG ATP 38.806
3 1XNG DND 38.806
Pocket No.: 2; Query (leader) PDB : 1KQP; Ligand: ADJ; Similar sites found with APoc: 4
This union binding pocket(no: 2) in the query (biounit: 1kqp.bio1) has 45 residues
No: Leader PDB Ligand Sequence Similarity
1 1XNG ATP 38.806
2 1XNG ATP 38.806
3 1XNG DND 38.806
4 1XNG DND 38.806
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