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 (2D)
Ligand no: 1; Ligand: AMP NAD; Similar ligands found: 228
No: Ligand ECFP6 Tc MDL keys Tc
1 AMP NAD 1 1
2 NAD TDB 0.833333 0.985915
3 NAD IBO 0.833333 0.985915
4 A3D 0.745763 0.958904
5 NAD 0.74359 0.972222
6 N01 0.696721 0.972222
7 DND 0.689655 0.972603
8 NAJ 0.642276 0.972222
9 NA0 0.609023 0.945946
10 NHD 0.606299 0.945205
11 NAP 0.606061 0.958904
12 ZID 0.606061 0.958904
13 NAQ 0.598485 0.909091
14 GAP 0.59633 0.958904
15 ATP MG 0.592593 0.957747
16 ADP PO3 0.592593 0.957747
17 NAE 0.590909 0.933333
18 TAP 0.589552 0.896104
19 BEF ADP 0.587156 0.931507
20 VO4 ADP 0.585586 0.906667
21 ADP BEF 0.584906 0.957747
22 ADP MG 0.584906 0.957747
23 NFD 0.584615 0.921053
24 NDC 0.582734 0.909091
25 NAD BBN 0.576389 0.853659
26 ALF ADP 0.571429 0.883117
27 NAD CJ3 0.568493 0.823529
28 NDE 0.568345 0.945946
29 DAL AMP 0.556522 0.972222
30 NAD NDT 0.555556 0.736842
31 ANP MG 0.54386 0.918919
32 OOB 0.538462 0.972222
33 ADP BMA 0.537815 0.958904
34 MYR AMP 0.53719 0.875
35 CNA 0.530303 0.945946
36 ATP A 0.528455 0.971831
37 ATP A A A 0.528455 0.971831
38 AMP MG 0.528302 0.943662
39 AHZ 0.527559 0.875
40 NAJ PZO 0.522059 0.909091
41 ALF ADP 3PG 0.515385 0.897436
42 AR6 AR6 0.511811 0.985915
43 ARG AMP 0.511811 0.864198
44 LPA AMP 0.511628 0.875
45 CA0 0.508929 0.932432
46 APC MG 0.508772 0.931507
47 A 0.504673 0.90411
48 AMP 0.504673 0.90411
49 A2D 0.504587 0.931507
50 45A 0.504587 0.88
51 ABM 0.504587 0.88
52 ADP 0.504505 0.905405
53 KG4 0.504425 0.932432
54 00A 0.504132 0.921053
55 AF3 ADP 3PG 0.503817 0.897436
56 APC 0.5 0.87013
57 AN2 0.5 0.893333
58 NDO 0.496454 0.932432
59 9SN 0.496 0.909091
60 8LE 0.495726 0.907895
61 A12 0.495495 0.87013
62 AP2 0.495495 0.87013
63 BA3 0.495495 0.931507
64 B5M 0.492063 0.933333
65 DLL 0.491803 0.972222
66 8LQ 0.491667 0.92
67 ACP 0.491228 0.881579
68 AP5 0.491071 0.931507
69 B4P 0.491071 0.931507
70 3UK 0.487805 0.958904
71 8LH 0.487395 0.92
72 SON 0.486726 0.92
73 AT4 0.486726 0.87013
74 NAJ PYZ 0.485915 0.864198
75 AMP DBH 0.484375 0.932432
76 WAQ 0.483871 0.896104
77 B5V 0.483871 0.945946
78 V2G 0.483051 0.884615
79 5AL 0.483051 0.945205
80 M33 0.482456 0.893333
81 FA5 0.480315 0.945946
82 QA7 0.479339 0.907895
83 4TA 0.478261 0.864198
84 HEJ 0.478261 0.905405
85 ATP 0.478261 0.905405
86 SRP 0.475 0.92
87 ACQ 0.474576 0.881579
88 AR6 0.474138 0.931507
89 APR 0.474138 0.931507
90 AQP 0.474138 0.905405
91 5FA 0.474138 0.905405
92 SRA 0.472727 0.857143
93 4AD 0.471545 0.933333
94 RBY 0.470085 0.894737
95 ADV 0.470085 0.894737
96 AGS 0.470085 0.858974
97 AD9 0.470085 0.881579
98 ADX 0.469565 0.817073
99 AU1 0.469565 0.881579
100 1ZZ 0.468254 0.851852
101 3OD 0.468254 0.932432
102 8ID 0.466667 0.897436
103 NBP 0.465753 0.897436
104 50T 0.465517 0.868421
105 OAD 0.464 0.932432
106 8QN 0.463415 0.945205
107 9ZA 0.463415 0.896104
108 9ZD 0.463415 0.896104
109 6YZ 0.46281 0.881579
110 ANP 0.462185 0.881579
111 T99 0.462185 0.87013
112 TAT 0.462185 0.87013
113 DQV 0.462121 0.945205
114 M24 0.461538 0.886076
115 PRX 0.461538 0.857143
116 NJP 0.460432 0.933333
117 PR8 0.460317 0.8625
118 NGD 0.459854 0.897436
119 AMO 0.459677 0.92
120 A1R 0.459677 0.848101
121 PAJ 0.459677 0.873418
122 B5Y 0.457364 0.933333
123 PTJ 0.456693 0.884615
124 ATF 0.454545 0.87013
125 DZD 0.453901 0.873418
126 9X8 0.452381 0.883117
127 9JJ 0.450617 0.875
128 IOT 0.449275 0.821429
129 Z5A 0.44898 0.833333
130 LAD 0.448819 0.873418
131 TYM 0.448529 0.945946
132 A3R 0.448 0.848101
133 LAQ 0.447761 0.851852
134 HQG 0.447154 0.918919
135 TXA 0.445312 0.92
136 ME8 0.445312 0.851852
137 FYA 0.445312 0.893333
138 NB8 0.445312 0.884615
139 JNT 0.444444 0.881579
140 AHX 0.444444 0.860759
141 MAP 0.443548 0.858974
142 A22 0.443548 0.918919
143 PO4 PO4 A A A A PO4 0.440945 0.943662
144 4UV 0.439394 0.933333
145 V47 0.439024 0.847222
146 TXE 0.437956 0.896104
147 LMS 0.4375 0.795181
148 ADQ 0.436508 0.932432
149 G3A 0.43609 0.884615
150 G5P 0.432836 0.884615
151 4UU 0.432836 0.933333
152 7MD 0.432836 0.851852
153 NAX 0.430657 0.8625
154 TXD 0.430657 0.896104
155 NAI 0.430657 0.896104
156 AOC 0.429825 0.810811
157 G5A 0.429752 0.770115
158 TAD 0.42963 0.85
159 F2R 0.429577 0.831325
160 OZV 0.428571 0.905405
161 25A 0.428571 0.931507
162 5SV 0.428571 0.814815
163 5AS 0.42735 0.75
164 NMN AMP PO4 0.426573 0.933333
165 139 0.425532 0.8625
166 DSZ 0.425197 0.790698
167 8PZ 0.424242 0.790698
168 54H 0.424 0.77907
169 VMS 0.424 0.77907
170 JB6 0.423077 0.871795
171 9K8 0.423077 0.764045
172 BIS 0.423077 0.848101
173 AFH 0.422222 0.873418
174 XAH 0.421053 0.829268
175 CNV FAD 0.420732 0.804598
176 TSB 0.420635 0.788235
177 8X1 0.420635 0.744444
178 5CA 0.420635 0.770115
179 4UW 0.42029 0.897436
180 6V0 0.42029 0.884615
181 25L 0.419847 0.918919
182 A5A 0.419355 0.797619
183 LEU LMS 0.418605 0.781609
184 OMR 0.417266 0.841463
185 H1Q 0.416667 0.891892
186 COA FLC 0.416107 0.802326
187 SSA 0.416 0.770115
188 NMN 0.415929 0.849315
189 ENQ 0.415385 0.930556
190 P5A 0.415385 0.736264
191 BT5 0.413793 0.821429
192 KMQ 0.413534 0.894737
193 YLP 0.413043 0.831325
194 48N 0.413043 0.884615
195 52H 0.412698 0.770115
196 NCN 0.412281 0.805556
197 GA7 0.411765 0.87013
198 YSA 0.410448 0.790698
199 B1U 0.410448 0.766667
200 NDP DTT 0.410256 0.853659
201 53H 0.409449 0.770115
202 D4F 0.409396 0.875
203 GTA 0.408759 0.875
204 A4D 0.407407 0.783784
205 5CD 0.407407 0.794521
206 FAD T2C 0.406977 0.78022
207 COD 0.406897 0.781609
208 XYA 0.40566 0.808219
209 ADN 0.40566 0.808219
210 RAB 0.40566 0.808219
211 YLA 0.405594 0.831325
212 T5A 0.405594 0.831325
213 GSU 0.40458 0.790698
214 4TC 0.404255 0.884615
215 AP0 0.404255 0.860759
216 YLB 0.404255 0.831325
217 YLC 0.404255 0.851852
218 L3W 0.404255 0.894737
219 7MC 0.404255 0.831325
220 DAL FAD PER 0.403509 0.797753
221 NSS 0.403101 0.790698
222 LSS 0.403101 0.752809
223 AYB 0.402778 0.821429
224 A4P 0.401408 0.811765
225 80F 0.401361 0.853659
226 FAD NBT 0.401198 0.76087
227 NVA LMS 0.4 0.764045
228 UP5 0.4 0.907895
Similar Ligands (3D)
Ligand no: 1; Ligand: AMP NAD; Similar ligands found: 1
No: Ligand Similarity coefficient
1 ADJ 0.9948
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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