Receptor
PDB id Resolution Class Description Source Keywords
4M54 2.36 Å EC: 4.-.-.- THE STRUCTURE OF THE STAPHYLOFERRIN B PRECURSOR BIOSYNTHETIC SBNB BOUND TO N-(1-AMINO-1-CARBOXYL-2-ETHYL)-GLUTAMIC ACID STAPHYLOCOCCUS AUREUS SUBSP. AUREUS SIDEROPHORE IRON L-2 3-DIAMINOPROPIONIC ACID SYNTHESIS NBINDING ROSSMANN FOLD LYASE-LYASE INHIBITOR COMPLEX
Ref.: SYNTHESIS OF L-2,3-DIAMINOPROPIONIC ACID, A SIDEROP ANTIBIOTIC PRECURSOR. CHEM.BIOL. V. 21 379 2014
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CL A:402;
Invalid;
none;
submit data
35.453 Cl [Cl-]
NAI A:401;
Valid;
none;
submit data
665.441 C21 H29 N7 O14 P2 c1nc(...
AE5 A:403;
Valid;
none;
submit data
234.207 C8 H14 N2 O6 C(CC(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4MP8 1.85 Å EC: 4.-.-.- STAPHYLOFERRIN B PRECURSOR BIOSYNTHETIC ENZYME SBNB BOUND TO AND NAD+ STAPHYLOCOCCUS AUREUS SUBSP. AUREUS SIDEROPHORE L-DAP SYNTHESIS ACEGA DEHYDROGENASE OXIDOREDU
Ref.: SYNTHESIS OF L-2,3-DIAMINOPROPIONIC ACID, A SIDEROP ANTIBIOTIC PRECURSOR. CHEM.BIOL. V. 21 379 2014
Members (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 53 families.
1 4MP8 - MLI C3 H2 O4 C(C(=O)[O-....
2 4M54 - NAI C21 H29 N7 O14 P2 c1nc(c2c(n....
3 4MP6 - CIT C6 H8 O7 C(C(=O)O)C....
4 4MPD - NAJ C21 H27 N7 O14 P2 c1cc(c[n+]....
70% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 50 families.
1 4MP8 - MLI C3 H2 O4 C(C(=O)[O-....
2 4M54 - NAI C21 H29 N7 O14 P2 c1nc(c2c(n....
3 4MP6 - CIT C6 H8 O7 C(C(=O)O)C....
4 4MPD - NAJ C21 H27 N7 O14 P2 c1cc(c[n+]....
50% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 41 families.
1 4MP8 - MLI C3 H2 O4 C(C(=O)[O-....
2 4M54 - NAI C21 H29 N7 O14 P2 c1nc(c2c(n....
3 4MP6 - CIT C6 H8 O7 C(C(=O)O)C....
4 4MPD - NAJ C21 H27 N7 O14 P2 c1cc(c[n+]....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: NAI; Similar ligands found: 279
No: Ligand ECFP6 Tc MDL keys Tc
1 NAI 1 1
2 0WD 0.814815 0.986842
3 NDP 0.803738 0.986842
4 AP0 0.743119 0.961039
5 NMN AMP PO4 0.704348 0.960526
6 NAX 0.663717 0.961538
7 A2D 0.659574 0.933333
8 80F 0.65 0.925926
9 6V0 0.649123 0.986842
10 TXE 0.62931 0.948052
11 BA3 0.628866 0.933333
12 AP5 0.622449 0.933333
13 B4P 0.622449 0.933333
14 TXD 0.62069 0.923077
15 APR 0.613861 0.907895
16 AR6 0.613861 0.907895
17 EAD 0.609375 0.961538
18 AGS 0.607843 0.8625
19 SAP 0.607843 0.8625
20 ADP 0.606061 0.907895
21 HEJ 0.60396 0.907895
22 50T 0.60396 0.871795
23 ATP 0.60396 0.907895
24 AT4 0.6 0.873418
25 AN2 0.6 0.896104
26 A22 0.598131 0.921053
27 AQP 0.598039 0.907895
28 5FA 0.598039 0.907895
29 M33 0.594059 0.896104
30 CA0 0.594059 0.909091
31 AD9 0.592233 0.884615
32 NAJ PZO 0.592 0.935897
33 P1H 0.590909 0.9375
34 KG4 0.588235 0.909091
35 ACP 0.588235 0.884615
36 A1R 0.587156 0.851852
37 4AD 0.587156 0.886076
38 PRX 0.582524 0.8375
39 ANP 0.580952 0.884615
40 3OD 0.580357 0.909091
41 SRP 0.579439 0.873418
42 ADX 0.578431 0.821429
43 OAD 0.576577 0.909091
44 5AL 0.575472 0.896104
45 HQG 0.574074 0.896104
46 NAJ PYZ 0.573643 0.890244
47 A3R 0.572727 0.851852
48 ADJ 0.569106 0.890244
49 8LQ 0.568807 0.873418
50 UP5 0.566667 0.960526
51 ACQ 0.566038 0.884615
52 8LH 0.564815 0.873418
53 9X8 0.5625 0.8625
54 A 0.561224 0.881579
55 AMP 0.561224 0.881579
56 8LE 0.560748 0.8625
57 ATF 0.555556 0.873418
58 6YZ 0.550459 0.884615
59 8QN 0.54955 0.896104
60 25L 0.547826 0.921053
61 4TC 0.544715 0.935897
62 AMO 0.544643 0.897436
63 ADQ 0.544643 0.909091
64 PAJ 0.544643 0.853659
65 ABM 0.544554 0.858974
66 45A 0.544554 0.858974
67 NPW 0.544 0.949367
68 PR8 0.54386 0.821429
69 WAQ 0.54386 0.851852
70 LAD 0.54386 0.831325
71 DQV 0.541667 0.946667
72 DG1 0.541353 0.986842
73 1DG 0.541353 0.986842
74 00A 0.539823 0.875
75 NZQ 0.539683 0.974026
76 1ZZ 0.53913 0.811765
77 BIS 0.53913 0.851852
78 APC 0.537736 0.873418
79 OMR 0.536585 0.823529
80 OOB 0.535714 0.921053
81 25A 0.535714 0.907895
82 5SV 0.535714 0.797619
83 3UK 0.535088 0.909091
84 A12 0.533981 0.873418
85 AP2 0.533981 0.873418
86 B5V 0.530435 0.897436
87 DND 0.528455 0.922078
88 NXX 0.528455 0.922078
89 CNA 0.527559 0.922078
90 AHX 0.526316 0.864198
91 DLL 0.526316 0.921053
92 FYA 0.525862 0.871795
93 NB8 0.525862 0.864198
94 PTJ 0.525862 0.841463
95 ME8 0.525862 0.811765
96 B5M 0.525424 0.886076
97 YAP 0.525424 0.886076
98 SRA 0.524752 0.8375
99 ADP MG 0.52381 0.881579
100 SON 0.52381 0.873418
101 TAT 0.522936 0.873418
102 T99 0.522936 0.873418
103 ADP VO4 0.522523 0.871795
104 VO4 ADP 0.522523 0.871795
105 OZV 0.522124 0.907895
106 48N 0.520325 0.864198
107 YLP 0.520325 0.793103
108 YLB 0.52 0.793103
109 AU1 0.518868 0.884615
110 ATP MG 0.518519 0.881579
111 ADP PO3 0.518519 0.881579
112 9SN 0.516949 0.864198
113 DAL AMP 0.513274 0.871795
114 TXA 0.512821 0.897436
115 B5Y 0.512605 0.886076
116 FA5 0.512605 0.897436
117 GAP 0.509091 0.860759
118 9ZD 0.508772 0.851852
119 9ZA 0.508772 0.851852
120 4UU 0.508197 0.960526
121 YLC 0.507937 0.833333
122 T5A 0.507812 0.925926
123 ADV 0.504587 0.873418
124 RBY 0.504587 0.873418
125 APC MG 0.504587 0.858974
126 TYR AMP 0.504132 0.8625
127 4UW 0.504 0.924051
128 TXP 0.503876 0.911392
129 F2R 0.5 0.813953
130 G3A 0.5 0.8875
131 ADP ALF 0.5 0.817073
132 LAQ 0.5 0.811765
133 TYM 0.5 0.897436
134 ALF ADP 0.5 0.817073
135 COD 0.496183 0.786517
136 YLA 0.496124 0.813953
137 139 0.496124 0.9125
138 G5P 0.495935 0.8875
139 AFH 0.495935 0.853659
140 XAH 0.495868 0.811765
141 BT5 0.492424 0.784091
142 AYB 0.492308 0.784091
143 A4P 0.492188 0.880952
144 GTA 0.491935 0.855422
145 4UV 0.491803 0.960526
146 A2R 0.491228 0.896104
147 MAP 0.486957 0.8625
148 XNP 0.484848 0.936709
149 NAD 0.484848 0.921053
150 UPA 0.484375 0.948052
151 ARG AMP 0.483871 0.781609
152 7MD 0.483871 0.833333
153 MYR AMP 0.483333 0.790698
154 NA7 0.483051 0.873418
155 YLY 0.477941 0.784091
156 ATR 0.477477 0.881579
157 AOC 0.47619 0.792208
158 ATP A 0.47541 0.894737
159 ATP A A A 0.47541 0.894737
160 BTX 0.473684 0.793103
161 5AS 0.472222 0.736264
162 GA7 0.472 0.873418
163 LMS 0.471154 0.77907
164 NAQ 0.471014 0.864198
165 ADP BMA 0.470588 0.884615
166 N0B 0.467626 0.835294
167 A3D 0.466667 0.909091
168 A A 0.466667 0.883117
169 NJP 0.466165 0.910256
170 IOT 0.465649 0.784091
171 AF3 ADP 3PG 0.465116 0.809524
172 PAP 0.464286 0.894737
173 NAE 0.463768 0.886076
174 7MC 0.461538 0.813953
175 H1Q 0.459459 0.846154
176 DZD 0.459259 0.876543
177 ZID 0.457143 0.909091
178 TAD 0.456693 0.853659
179 2A5 0.455357 0.8375
180 62F 0.453947 0.833333
181 AHZ 0.453125 0.790698
182 FB0 0.452055 0.76087
183 JB6 0.45082 0.851852
184 7D4 0.45045 0.825
185 ITT 0.45045 0.857143
186 LPA AMP 0.449612 0.790698
187 G5A 0.447368 0.755556
188 LEU LMS 0.446281 0.731183
189 M24 0.446043 0.843373
190 AVV 0.445378 0.841463
191 NDC 0.442177 0.864198
192 NSS 0.441667 0.775281
193 4TA 0.441176 0.890244
194 VMS 0.440678 0.764045
195 54H 0.440678 0.764045
196 7D3 0.440367 0.825
197 5CD 0.44 0.753247
198 PPS 0.439655 0.8
199 RAB 0.438776 0.789474
200 ADN 0.438776 0.789474
201 XYA 0.438776 0.789474
202 NDE 0.438356 0.897436
203 NVA LMS 0.438017 0.731183
204 AR6 AR6 0.4375 0.883117
205 53H 0.436975 0.755556
206 TSB 0.436975 0.793103
207 8X1 0.436975 0.731183
208 DTA 0.436893 0.759494
209 A2P 0.436364 0.868421
210 A3P 0.436364 0.881579
211 A5A 0.435897 0.781609
212 FNK 0.435065 0.840909
213 JSQ 0.434783 0.8625
214 HFD 0.434783 0.8625
215 ODP 0.433824 0.924051
216 SFG 0.433628 0.725
217 Z5A 0.433566 0.858824
218 6FA 0.433333 0.835294
219 SSA 0.432203 0.775281
220 J7C 0.431193 0.702381
221 DTP 0.431034 0.825
222 P5A 0.430894 0.723404
223 AMP NAD 0.430657 0.896104
224 5N5 0.43 0.766234
225 DSZ 0.429752 0.775281
226 LSS 0.429752 0.73913
227 52H 0.428571 0.755556
228 NO7 0.428571 0.873418
229 SFD 0.427632 0.731959
230 9K8 0.427419 0.712766
231 6AD 0.42735 0.831325
232 EP4 0.427184 0.707317
233 FDA 0.426667 0.870588
234 ARU 0.42623 0.788235
235 6RE 0.425926 0.694118
236 A4D 0.425743 0.766234
237 5CA 0.425 0.775281
238 3DH 0.424528 0.725
239 AV2 0.423729 0.835443
240 AMP DBH 0.421875 0.860759
241 U A 0.421429 0.923077
242 DAT 0.421053 0.825
243 5X8 0.421053 0.7375
244 GSU 0.419355 0.755556
245 MTA 0.419048 0.725
246 3AT 0.418803 0.883117
247 ETB 0.41844 0.786517
248 DCA 0.41844 0.777778
249 FAD 0.418301 0.845238
250 FAS 0.418301 0.845238
251 A3N 0.418182 0.759494
252 F2N 0.417178 0.850575
253 7D5 0.415094 0.8
254 A U 0.414815 0.910256
255 YSA 0.414062 0.775281
256 B1U 0.414062 0.734043
257 0T1 0.412587 0.777778
258 A C A C 0.411348 0.8875
259 2AM 0.411215 0.857143
260 9JJ 0.409938 0.855422
261 M2T 0.409524 0.690476
262 KAA 0.408 0.731183
263 7C5 0.407692 0.790123
264 3AM 0.407407 0.844156
265 NAP 0.406897 0.909091
266 8PZ 0.40625 0.795455
267 KOY 0.406015 0.797468
268 PUA 0.405594 0.9
269 FAY 0.405063 0.855422
270 P5F 0.404908 0.83908
271 EEM 0.403361 0.670455
272 COA 0.402778 0.777778
273 RFL 0.402516 0.816092
274 6MZ 0.401786 0.846154
275 GJV 0.401786 0.686047
276 SA8 0.401709 0.686047
277 U A C C 0.401408 0.898734
278 G A A A 0.4 0.841463
279 WSA 0.4 0.784091
Ligand no: 2; Ligand: AE5; Similar ligands found: 10
No: Ligand ECFP6 Tc MDL keys Tc
1 AE5 1 1
2 3O3 0.595238 0.885714
3 TNA 0.543478 0.837838
4 SHR 0.520833 0.882353
5 KSN 0.458333 0.684211
6 GGL 0.447368 0.727273
7 DGL 0.447368 0.727273
8 GLU 0.447368 0.727273
9 NLG 0.428571 0.605263
10 NIG 0.409091 0.648649
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4MP8; Ligand: MLI; Similar sites found with APoc: 2
This union binding pocket(no: 1) in the query (biounit: 4mp8.bio1) has 38 residues
No: Leader PDB Ligand Sequence Similarity
1 4BVA NDP 36.7164
2 4BVA NDP 36.7164
Pocket No.: 2; Query (leader) PDB : 4MP8; Ligand: MLI; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 4mp8.bio1) has 38 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 4MP8; Ligand: NAD; Similar sites found with APoc: 2
This union binding pocket(no: 3) in the query (biounit: 4mp8.bio1) has 38 residues
No: Leader PDB Ligand Sequence Similarity
1 4BVA NDP 36.7164
2 4BVA NDP 36.7164
Pocket No.: 4; Query (leader) PDB : 4MP8; Ligand: NAD; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 4mp8.bio1) has 38 residues
No: Leader PDB Ligand Sequence Similarity
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