Receptor
PDB id Resolution Class Description Source Keywords
6VDF 1.92 Å NON-ENZYME: TRANSPORT STRUCTURE OF THE PERIPLASMIC DOMAIN OF YEJM FROM SALMONELLA TYPHIMURIUM (TWINNED) SALMONELLA TYPHIMURIUM YEJM MEMBRANE PROTEIN HYDROLASE PHOSPHATASE CARDIOLIPINTRANSPORT PROTEIN
Ref.: THE ESSENTIAL INNER MEMBRANE PROTEIN YEJM IS A METALLOENZYME. SCI REP V. 10 17794 2020
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
PEG D:702;
A:602;
 Invalid;
Invalid;
 none;
none;
 submit data
106.12 C4 H10 O3 C(COC...
PO4 D:703;
A:603;
 Invalid;
Invalid;
 none;
none;
 submit data
94.971 O4 P [O-]P...
PSE D:701;
C:601;
 Valid;
Valid;
 none;
none;
 submit data
171.089 C3 H10 N O5 P C([C@...
MN A:604;
D:704;
B:602;
 Invalid;
Invalid;
Invalid;
 none;
none;
none;
 submit data
54.938 Mn [Mn+2...
EDO B:601;
 Invalid;
 none;
 submit data
62.068 C2 H6 O2 C(CO)...
PGE A:601;
 Invalid;
 none;
 submit data
150.173 C6 H14 O4 C(COC...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
6VDF 1.92 Å NON-ENZYME: TRANSPORT STRUCTURE OF THE PERIPLASMIC DOMAIN OF YEJM FROM SALMONELLA TYPHIMURIUM (TWINNED) SALMONELLA TYPHIMURIUM YEJM MEMBRANE PROTEIN HYDROLASE PHOSPHATASE CARDIOLIPINTRANSPORT PROTEIN
Ref.: THE ESSENTIAL INNER MEMBRANE PROTEIN YEJM IS A METALLOENZYME. SCI REP V. 10 17794 2020
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 232 families.
1 6VDF - PSE C3 H10 N O5 P C([C@H](CO....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 197 families.
1 6VDF - PSE C3 H10 N O5 P C([C@H](CO....
50% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 322 families.
1 6VDF - PSE C3 H10 N O5 P C([C@H](CO....
2 6XLP - VJ4 KDO VJ1 n/a n/a
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: PSE; Similar ligands found: 15
No: Ligand ECFP6 Tc MDL keys Tc
1 PSE 1 1
2 1GP 0.483871 0.736842
3 G3P 0.483871 0.736842
4 HSA 0.47619 0.632653
5 AGP 0.435897 0.853659
6 M6R 0.435897 0.853659
7 SEP 0.428571 0.868421
8 GOS 0.424242 0.658537
9 M2P 0.424242 0.658537
10 LXP 0.416667 0.682927
11 A5P 0.416667 0.682927
12 DX5 0.416667 0.682927
13 G3H 0.411765 0.625
14 HG3 0.40625 0.666667
15 S6P 0.405405 0.7
Similar Ligands (3D)
Ligand no: 1; Ligand: PSE; Similar ligands found: 264
No: Ligand Similarity coefficient
1 13P 0.9932
2 GP9 0.9834
3 CYX 0.9738
4 PGH 0.9706
5 LLQ 0.9645
6 PGA 0.9638
7 X1S 0.9582
8 129 0.9562
9 3PP 0.9558
10 3PG 0.9551
11 LTL 0.9523
12 OSE 0.9488
13 PEP 0.9431
14 MSL 0.9400
15 PMB 0.9392
16 KVV 0.9390
17 AKG 0.9375
18 PAH 0.9369
19 OGA 0.9367
20 FUM 0.9366
21 FB2 0.9366
22 PPR 0.9356
23 SPV 0.9346
24 3SL 0.9344
25 GLU 0.9343
26 GZ3 0.9329
27 GLN 0.9292
28 NF3 0.9284
29 MEQ 0.9280
30 HPV 0.9276
31 SIN 0.9267
32 GPJ 0.9266
33 GPF 0.9266
34 DQY 0.9265
35 QMP 0.9261
36 2PG 0.9237
37 9ON 0.9230
38 1SA 0.9229
39 2HG 0.9228
40 PPV 0.9226
41 CCD 0.9225
42 EOU 0.9219
43 IP8 0.9212
44 MHO 0.9210
45 ONL 0.9195
46 0V5 0.9187
47 BEZ 0.9185
48 4MV 0.9163
49 DIR 0.9154
50 GLY GLY 0.9153
51 AL0 0.9153
52 FOM 0.9149
53 CCE 0.9141
54 SD4 0.9139
55 A20 0.9138
56 HL5 0.9136
57 7OD 0.9124
58 2PN 0.9111
59 4CS 0.9108
60 8K2 0.9103
61 PLU 0.9094
62 GGL 0.9090
63 2IT 0.9090
64 PAC 0.9085
65 G2H 0.9078
66 OKG 0.9077
67 MDN 0.9076
68 OAA 0.9075
69 51R 0.9074
70 AT3 0.9071
71 S2G 0.9066
72 RTK 0.9063
73 HSO 0.9062
74 HX2 0.9060
75 4LR 0.9060
76 3S5 0.9060
77 DHM 0.9059
78 QY9 0.9058
79 DE5 0.9055
80 1DV 0.9053
81 A09 0.9046
82 TPO 0.9042
83 DS0 0.9038
84 PEQ 0.9034
85 RNS 0.9031
86 FBW 0.9029
87 TLA 0.9029
88 MJ2 0.9026
89 PMF 0.9024
90 IZC 0.9020
91 ZGL 0.9017
92 CFI 0.9012
93 TSU 0.9011
94 SHV 0.9008
95 DGL 0.9007
96 XCZ 0.9001
97 LMR 0.9000
98 SPA 0.8997
99 SHF 0.8995
100 DGN 0.8994
101 3OM 0.8993
102 H95 0.8989
103 BNS 0.8989
104 FCR 0.8988
105 NLE 0.8977
106 N6C 0.8976
107 SAN 0.8973
108 RSO 0.8972
109 CHH 0.8968
110 GUA 0.8967
111 MLT 0.8962
112 HPS 0.8956
113 6NA 0.8951
114 OPE 0.8946
115 4SX 0.8945
116 FB1 0.8930
117 HIS 0.8929
118 0VT 0.8929
119 SRT 0.8927
120 LEU 0.8924
121 NMG 0.8923
122 CRN 0.8919
123 7N0 0.8913
124 XYL 0.8912
125 2CO 0.8903
126 FQI 0.8902
127 PC 0.8901
128 MUC 0.8901
129 HGA 0.8897
130 HQJ 0.8897
131 KVP 0.8893
132 PIS 0.8888
133 K34 0.8888
134 ITN 0.8884
135 TEO 0.8876
136 DZA 0.8874
137 8GL 0.8872
138 ASN 0.8868
139 LYS 0.8867
140 DA4 0.8867
141 KTA 0.8866
142 98J 0.8863
143 9X6 0.8857
144 VKC 0.8854
145 ASP 0.8852
146 0OC 0.8851
147 3LR 0.8849
148 B85 0.8846
149 LUQ 0.8846
150 OEG 0.8844
151 RNT 0.8841
152 CXF 0.8838
153 MNN 0.8838
154 TIH 0.8836
155 K5W 0.8828
156 4FH 0.8827
157 J9N 0.8827
158 XRG 0.8823
159 UN1 0.8822
160 FOC 0.8822
161 RAT 0.8819
162 ACA 0.8818
163 2RH 0.8817
164 EDR 0.8816
165 GJZ 0.8813
166 P22 0.8812
167 NSB 0.8809
168 4J8 0.8808
169 KMH 0.8806
170 FBS 0.8802
171 PHU 0.8802
172 ACH 0.8801
173 K7M 0.8798
174 GAB 0.8791
175 GWM 0.8791
176 BHH 0.8790
177 R20 0.8789
178 S7A 0.8787
179 FBJ 0.8787
180 7WG 0.8784
181 JYD 0.8784
182 KPC 0.8782
183 HHI 0.8782
184 2EH 0.8781
185 IOM 0.8781
186 ORN 0.8780
187 SOR 0.8777
188 IXW 0.8776
189 FK8 0.8775
190 AAS 0.8774
191 ISZ 0.8773
192 GOJ 0.8773
193 9GB 0.8770
194 SYM 0.8770
195 OK7 0.8762
196 FEH 0.8762
197 AMS 0.8760
198 CXP 0.8756
199 2FT 0.8749
200 SYC 0.8748
201 PG3 0.8745
202 EKZ 0.8743
203 URO 0.8741
204 1SH 0.8740
205 DAS 0.8733
206 URP 0.8725
207 RMN 0.8723
208 6TZ 0.8721
209 I4B 0.8718
210 DAV 0.8717
211 DAR 0.8715
212 SMN 0.8707
213 OCT 0.8705
214 MET 0.8705
215 3HG 0.8702
216 MED 0.8701
217 0L1 0.8693
218 DHI 0.8693
219 X0V 0.8691
220 S8V 0.8690
221 TZL 0.8688
222 1X4 0.8685
223 DER 0.8684
224 TAG 0.8683
225 173 0.8679
226 GRO 0.8667
227 DHS 0.8650
228 S2P 0.8649
229 NM2 0.8649
230 SHI 0.8647
231 SVD 0.8646
232 NIZ 0.8645
233 16D 0.8645
234 3QM 0.8643
235 PKU 0.8643
236 XBT 0.8640
237 ZBT 0.8632
238 B40 0.8629
239 DXP 0.8627
240 AOS 0.8626
241 E4P 0.8623
242 IWT 0.8619
243 HF2 0.8614
244 LEA 0.8614
245 4P5 0.8608
246 M4S 0.8605
247 PHE 0.8605
248 ARG 0.8598
249 FUD 0.8594
250 M3H 0.8588
251 4WL 0.8586
252 4ZA 0.8582
253 HDH 0.8581
254 MPV 0.8581
255 BHL 0.8579
256 650 0.8570
257 DAL DAL 0.8566
258 LFC 0.8555
259 NCT 0.8545
260 SDD 0.8544
261 PO6 0.8542
262 152 0.8533
263 36E 0.8526
264 8OZ 0.8524
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 6VDF; Ligand: PSE; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 6vdf.bio4) has 6 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 6VDF; Ligand: PSE; 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: 6vdf.bio3) has 7 residues
No: Leader PDB Ligand Sequence Similarity
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