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 62 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 59 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 47 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 (2D)
Ligand no: 1; Ligand: NAI; Similar ligands found: 287
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 ADP 0.606061 0.907895
20 50T 0.60396 0.871795
21 ATP 0.60396 0.907895
22 HEJ 0.60396 0.907895
23 AT4 0.6 0.873418
24 AN2 0.6 0.896104
25 A22 0.598131 0.921053
26 5FA 0.598039 0.907895
27 AQP 0.598039 0.907895
28 CA0 0.594059 0.909091
29 M33 0.594059 0.896104
30 AD9 0.592233 0.884615
31 NAJ PZO 0.592 0.935897
32 P1H 0.590909 0.9375
33 ACP 0.588235 0.884615
34 KG4 0.588235 0.909091
35 4AD 0.587156 0.886076
36 A1R 0.587156 0.851852
37 PRX 0.582524 0.8375
38 ANP 0.580952 0.884615
39 3OD 0.580357 0.909091
40 SRP 0.579439 0.873418
41 ADX 0.578431 0.821429
42 OAD 0.576577 0.909091
43 5AL 0.575472 0.896104
44 HQG 0.574074 0.896104
45 NAJ PYZ 0.573643 0.890244
46 A3R 0.572727 0.851852
47 ADJ 0.569106 0.890244
48 8LQ 0.568807 0.873418
49 UP5 0.566667 0.960526
50 ACQ 0.566038 0.884615
51 8LH 0.564815 0.873418
52 9X8 0.5625 0.8625
53 A 0.561224 0.881579
54 AMP 0.561224 0.881579
55 8LE 0.560748 0.8625
56 ATF 0.555556 0.873418
57 QA7 0.554545 0.8625
58 JNT 0.553571 0.884615
59 6YZ 0.550459 0.884615
60 8QN 0.54955 0.896104
61 25L 0.547826 0.921053
62 4TC 0.544715 0.935897
63 AMO 0.544643 0.897436
64 ADQ 0.544643 0.909091
65 PAJ 0.544643 0.853659
66 ABM 0.544554 0.858974
67 45A 0.544554 0.858974
68 NPW 0.544 0.949367
69 LAD 0.54386 0.831325
70 PR8 0.54386 0.821429
71 WAQ 0.54386 0.851852
72 DQV 0.541667 0.946667
73 DG1 0.541353 0.986842
74 1DG 0.541353 0.986842
75 AMP MG 0.54 0.868421
76 00A 0.539823 0.875
77 NZQ 0.539683 0.974026
78 1ZZ 0.53913 0.811765
79 BIS 0.53913 0.851852
80 APC 0.537736 0.873418
81 OMR 0.536585 0.823529
82 25A 0.535714 0.907895
83 5SV 0.535714 0.797619
84 OOB 0.535714 0.921053
85 3UK 0.535088 0.909091
86 A12 0.533981 0.873418
87 AP2 0.533981 0.873418
88 B5V 0.530435 0.897436
89 DND 0.528455 0.922078
90 CNA 0.527559 0.922078
91 AHX 0.526316 0.864198
92 DLL 0.526316 0.921053
93 NB8 0.525862 0.864198
94 ME8 0.525862 0.811765
95 PTJ 0.525862 0.841463
96 FYA 0.525862 0.871795
97 KMQ 0.525424 0.897436
98 B5M 0.525424 0.886076
99 SRA 0.524752 0.8375
100 ADP MG 0.52381 0.881579
101 ADP BEF 0.52381 0.881579
102 SON 0.52381 0.873418
103 TAT 0.522936 0.873418
104 T99 0.522936 0.873418
105 OZV 0.522124 0.907895
106 YLP 0.520325 0.793103
107 48N 0.520325 0.864198
108 L3W 0.52 0.973333
109 YLB 0.52 0.793103
110 AU1 0.518868 0.884615
111 ADP PO3 0.518519 0.881579
112 ATP MG 0.518519 0.881579
113 V2G 0.518182 0.841463
114 9SN 0.516949 0.864198
115 BEF ADP 0.513761 0.858974
116 DAL AMP 0.513274 0.871795
117 TXA 0.512821 0.897436
118 FA5 0.512605 0.897436
119 B5Y 0.512605 0.886076
120 GAP 0.509091 0.860759
121 9ZA 0.508772 0.851852
122 9ZD 0.508772 0.851852
123 4UU 0.508197 0.960526
124 YLC 0.507937 0.833333
125 T5A 0.507812 0.925926
126 RBY 0.504587 0.873418
127 APC MG 0.504587 0.858974
128 ADV 0.504587 0.873418
129 4UW 0.504 0.924051
130 TXP 0.503876 0.911392
131 VO4 ADP 0.5 0.860759
132 LAQ 0.5 0.811765
133 TYM 0.5 0.897436
134 G3A 0.5 0.8875
135 F2R 0.5 0.813953
136 ANP MG 0.5 0.871795
137 ALF ADP 0.5 0.817073
138 COD 0.496183 0.786517
139 YLA 0.496124 0.813953
140 139 0.496124 0.9125
141 AFH 0.495935 0.853659
142 G5P 0.495935 0.8875
143 XAH 0.495868 0.811765
144 BT5 0.492424 0.784091
145 AYB 0.492308 0.784091
146 A4P 0.492188 0.880952
147 GTA 0.491935 0.855422
148 4UV 0.491803 0.960526
149 A2R 0.491228 0.896104
150 MAP 0.486957 0.8625
151 XNP 0.484848 0.936709
152 NAD 0.484848 0.921053
153 UPA 0.484375 0.948052
154 7MD 0.483871 0.833333
155 ARG AMP 0.483871 0.781609
156 MYR AMP 0.483333 0.790698
157 NA7 0.483051 0.873418
158 YLY 0.477941 0.784091
159 ATR 0.477477 0.881579
160 ALF ADP 3PG 0.476562 0.809524
161 AOC 0.47619 0.792208
162 ATP A 0.47541 0.894737
163 ATP A A A 0.47541 0.894737
164 BTX 0.473684 0.793103
165 NDP DTT 0.472222 0.902439
166 5AS 0.472222 0.736264
167 GA7 0.472 0.873418
168 LMS 0.471154 0.77907
169 NAQ 0.471014 0.864198
170 LEU LMS 0.470588 0.709677
171 ADP BMA 0.470588 0.884615
172 N0B 0.467626 0.835294
173 A3D 0.466667 0.909091
174 NJP 0.466165 0.910256
175 IOT 0.465649 0.784091
176 AF3 ADP 3PG 0.465116 0.809524
177 PAP 0.464286 0.894737
178 D4F 0.463768 0.833333
179 NAE 0.463768 0.886076
180 NAD TDB 0.461538 0.907895
181 NAD IBO 0.461538 0.907895
182 7MC 0.461538 0.813953
183 H1Q 0.459459 0.846154
184 DZD 0.459259 0.876543
185 ZID 0.457143 0.909091
186 TAD 0.456693 0.853659
187 2A5 0.455357 0.8375
188 62F 0.453947 0.833333
189 AHZ 0.453125 0.790698
190 FB0 0.452055 0.76087
191 JB6 0.45082 0.851852
192 7D4 0.45045 0.825
193 ITT 0.45045 0.857143
194 LPA AMP 0.449612 0.790698
195 G5A 0.447368 0.755556
196 M24 0.446043 0.843373
197 AVV 0.445378 0.841463
198 NDC 0.442177 0.864198
199 NSS 0.441667 0.775281
200 4TA 0.441176 0.890244
201 54H 0.440678 0.764045
202 VMS 0.440678 0.764045
203 7D3 0.440367 0.825
204 5CD 0.44 0.753247
205 PPS 0.439655 0.8
206 XYA 0.438776 0.789474
207 RAB 0.438776 0.789474
208 ADN 0.438776 0.789474
209 NDE 0.438356 0.897436
210 NVA LMS 0.438017 0.731183
211 AR6 AR6 0.4375 0.883117
212 8X1 0.436975 0.731183
213 TSB 0.436975 0.793103
214 53H 0.436975 0.755556
215 DTA 0.436893 0.759494
216 A3P 0.436364 0.881579
217 A2P 0.436364 0.868421
218 A5A 0.435897 0.781609
219 FNK 0.435065 0.840909
220 HFD 0.434783 0.8625
221 JSQ 0.434783 0.8625
222 ODP 0.433824 0.924051
223 SFG 0.433628 0.725
224 Z5A 0.433566 0.858824
225 6FA 0.433333 0.835294
226 SSA 0.432203 0.775281
227 J7C 0.431193 0.702381
228 DTP 0.431034 0.825
229 P5A 0.430894 0.723404
230 AMP NAD 0.430657 0.896104
231 5N5 0.43 0.766234
232 DSZ 0.429752 0.775281
233 LSS 0.429752 0.73913
234 NO7 0.428571 0.873418
235 52H 0.428571 0.755556
236 SFD 0.427632 0.731959
237 9K8 0.427419 0.712766
238 6AD 0.42735 0.831325
239 EP4 0.427184 0.707317
240 FDA 0.426667 0.870588
241 ARU 0.42623 0.788235
242 6RE 0.425926 0.694118
243 A4D 0.425743 0.766234
244 5CA 0.425 0.775281
245 3DH 0.424528 0.725
246 AV2 0.423729 0.835443
247 AMP DBH 0.421875 0.860759
248 5X8 0.421053 0.7375
249 DAT 0.421053 0.825
250 GSU 0.419355 0.755556
251 MTA 0.419048 0.725
252 3AT 0.418803 0.883117
253 ETB 0.41844 0.786517
254 DCA 0.41844 0.777778
255 FAS 0.418301 0.845238
256 FAD 0.418301 0.845238
257 A3N 0.418182 0.759494
258 K3K 0.417323 0.797468
259 F2N 0.417178 0.850575
260 38V 0.416667 0.855422
261 7D5 0.415094 0.8
262 B1U 0.414062 0.734043
263 YSA 0.414062 0.775281
264 NAD BBN 0.412903 0.835294
265 0T1 0.412587 0.777778
266 2AM 0.411215 0.857143
267 K3E 0.410853 0.7875
268 9JJ 0.409938 0.855422
269 M2T 0.409524 0.690476
270 CUU 0.408696 0.883117
271 V47 0.408333 0.779221
272 KAA 0.408 0.731183
273 7C5 0.407692 0.790123
274 3AM 0.407407 0.844156
275 NAP 0.406897 0.909091
276 8PZ 0.40625 0.795455
277 KOY 0.406015 0.797468
278 PUA 0.405594 0.9
279 FAY 0.405063 0.855422
280 P5F 0.404908 0.83908
281 EEM 0.403361 0.670455
282 COA 0.402778 0.777778
283 RFL 0.402516 0.816092
284 GJV 0.401786 0.686047
285 6MZ 0.401786 0.846154
286 SA8 0.401709 0.686047
287 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 GLU 0.447368 0.727273
7 GGL 0.447368 0.727273
8 DGL 0.447368 0.727273
9 NLG 0.428571 0.605263
10 NIG 0.409091 0.648649
Similar Ligands (3D)
Ligand no: 1; Ligand: NAI; Similar ligands found: 4
No: Ligand Similarity coefficient
1 NAJ 0.9967
2 8ID 0.9651
3 NHD 0.9450
4 A7R 0.8646
Ligand no: 2; Ligand: AE5; Similar ligands found: 15
No: Ligand Similarity coefficient
1 ALA GLN 0.9030
2 HKK 0.8898
3 CIL 0.8877
4 ALA DGL 0.8850
5 ALA LYS 0.8838
6 ALA GLU 0.8746
7 ALA PHE 0.8617
8 BN1 0.8608
9 29B 0.8607
10 6NZ 0.8588
11 VAL LYS 0.8578
12 F6R 0.8565
13 I46 0.8554
14 AQK 0.8552
15 583 0.8503
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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