Receptor
PDB id Resolution Class Description Source Keywords
3R9V 1.9 Å NON-ENZYME: OTHER COCRYSTAL STRUCTURE OF PROTEOLYTICALLY TRUNCATED FORM OF IPA SHIGELLA FLEXNERI BOUND TO DEOXYCHOLATE SHIGELLA FLEXNERI TYPE III SECRETION SYSTEM TIP PROTEIN DEOXYCHOLATE CELL I
Ref.: IDENTIFICATION OF THE BILE SALT BINDING SITE ON IPA SHIGELLA FLEXNERI AND THE INFLUENCE OF LIGAND BINDI IPAD STRUCTURE. PROTEINS V. 80 935 2012
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
DXC B:1;
B:323;
Valid;
Valid;
none;
none;
submit data
392.572 C24 H40 O4 C[C@H...
GOL A:323;
A:324;
A:3968;
Invalid;
Invalid;
Invalid;
none;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3R9V 1.9 Å NON-ENZYME: OTHER COCRYSTAL STRUCTURE OF PROTEOLYTICALLY TRUNCATED FORM OF IPA SHIGELLA FLEXNERI BOUND TO DEOXYCHOLATE SHIGELLA FLEXNERI TYPE III SECRETION SYSTEM TIP PROTEIN DEOXYCHOLATE CELL I
Ref.: IDENTIFICATION OF THE BILE SALT BINDING SITE ON IPA SHIGELLA FLEXNERI AND THE INFLUENCE OF LIGAND BINDI IPAD STRUCTURE. PROTEINS V. 80 935 2012
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1256 families.
1 3R9V - DXC C24 H40 O4 C[C@H](CCC....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1068 families.
1 3R9V - DXC C24 H40 O4 C[C@H](CCC....
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 922 families.
1 3R9V - DXC C24 H40 O4 C[C@H](CCC....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: DXC; Similar ligands found: 11
No: Ligand ECFP6 Tc MDL keys Tc
1 DXC 1 1
2 4OA 0.619048 0.972222
3 CHD 0.609195 1
4 GCH 0.485149 0.714286
5 JN3 0.478261 1
6 82R 0.425743 0.767442
7 LOA 0.424242 0.868421
8 LHP 0.415842 0.846154
9 3KL 0.408163 0.891892
10 AOM 0.404762 0.857143
11 AON 0.404762 0.857143
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3R9V; Ligand: DXC; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 3r9v.bio2) has 6 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 3R9V; Ligand: DXC; Similar sites found: 71
This union binding pocket(no: 2) in the query (biounit: 3r9v.bio2) has 7 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1UO4 PIH 0.00003462 0.54128 None
2 1UO5 PIH 0.002875 0.43218 None
3 5UAV NDP 0.01157 0.41078 1.04895
4 5UAV TFB 0.01157 0.41078 1.04895
5 4DR9 BB2 0.0005505 0.47372 1.5625
6 5L4L 7OX 0.01765 0.40474 1.74825
7 1YY5 FAD 0.01082 0.4088 2.0979
8 5UR1 YY9 0.02533 0.40612 2.0979
9 4TWP AXI 0.001336 0.50261 2.21402
10 2UXI G50 0.007132 0.42049 2.38095
11 4XB4 45D 0.001965 0.41954 2.63158
12 1HN4 MJI 0.00723 0.44101 3.05344
13 1IID NHM 0.005398 0.46312 3.14685
14 5JY6 NAD 0.01256 0.43402 3.14685
15 3G58 988 0.01045 0.42635 3.14685
16 2QYK NPV 0.02212 0.40776 3.14685
17 3B1M KRC 0.0002088 0.51573 3.18021
18 3G9E RO7 0.003186 0.42466 3.32103
19 5UV1 0FV 0.0003522 0.46192 3.4965
20 2D5Z L35 0.01209 0.46284 3.5461
21 4R38 RBF 0.01043 0.41632 3.57143
22 4BKJ STI 0.004459 0.44888 3.84615
23 3U1T MLI 0.002348 0.44788 3.84615
24 3VC1 GST 0.01807 0.40073 3.84615
25 1NTV ASN PHE ASP ASN PRO VAL TYR ARG LYS THR 0.01327 0.41478 3.94737
26 3G08 FEE 0.007707 0.43335 4.0404
27 3RDE OYP 0.0004035 0.45064 4.1958
28 3EE4 MYR 0.003228 0.44455 4.1958
29 2HJR APR 0.005501 0.41989 4.1958
30 4IAE 1DX 0.0226 0.41428 4.2328
31 3MBG FAD 0.0002723 0.46146 4.31655
32 3COW 52H 0.002825 0.42978 4.31894
33 5UC9 MYR 0.0001501 0.45808 4.42478
34 1LDN NAD 0.006111 0.40573 4.54545
35 1ZDT PEF 0.01739 0.41107 4.56432
36 1OQC FAD 0.0001786 0.47754 4.8
37 5X80 SAL 0.002153 0.41146 5
38 1XMU ROF 0.00735 0.45303 5.24476
39 1XMY ROL 0.008829 0.43043 5.24476
40 2XSU PIE 0.02691 0.40107 5.24476
41 5AZC PGT 0.02019 0.44874 5.59441
42 5LOF 70R 0.0009336 0.44724 5.59441
43 1SO2 666 0.01249 0.41254 5.59441
44 1RL4 BL5 0.002411 0.42876 5.85106
45 1YUC EPH 0.007478 0.46716 5.88235
46 3WCA FPS 0.003314 0.41155 5.94406
47 1YQZ FAD 0.04389 0.40063 5.94406
48 5XS3 VAL ARG SER ARG ARG CYS LEU ARG LEU 0.02279 0.43035 6.12245
49 5IKH 6BW 0.0004451 0.48483 6.29371
50 1N83 CLR 0.0004317 0.48816 6.2963
51 2BIF BOG 0.02219 0.42271 6.64336
52 5KJU 6TO 0.02047 0.41096 7.34266
53 4CRL C1I 0.002237 0.45611 7.36842
54 4OKZ 3E9 0.006559 0.40324 7.69231
55 1NE7 16G 0.003444 0.46093 9.44056
56 3G4G D71 0.02352 0.43017 9.44056
57 2YJD YJD 0.0224 0.40184 9.58333
58 1RSG FAD 0.007823 0.41733 9.79021
59 4PLG NAI 0.004314 0.46653 10.1399
60 4IN9 SER TRP PHE PRO 0.008201 0.42226 10.241
61 3LN0 52B 0.01065 0.4163 10.4895
62 1L6O SER LEU LYS LEU MET THR THR VAL 0.00883 0.43335 13.6842
63 1EZV UQ6 0.001595 0.43262 14.3357
64 2IBZ UQ6 0.002342 0.42598 14.3357
65 1JR8 FAD 0.0005933 0.42278 14.5299
66 1MFG GLU TYR LEU GLY LEU ASP VAL PRO VAL 0.01065 0.41804 14.7368
67 1MJH ATP 0.003693 0.40976 14.8148
68 2HJ3 FAD 0.0001758 0.49022 16.8
69 3V2Q PLM 0.0181 0.43967 17.7778
70 1Y75 NAG 0.01796 0.41271 18.6441
71 1RDT L79 0.01249 0.41061 32
72 3ET1 ET1 0.007874 0.44531 50
Pocket No.: 3; Query (leader) PDB : 3R9V; Ligand: DXC; Similar sites found: 124
This union binding pocket(no: 3) in the query (biounit: 3r9v.bio3) has 13 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1UVC STE 0.01306 0.43049 None
2 3RET PYR 0.01333 0.40889 None
3 3RET SAL 0.01333 0.40889 None
4 2GTE VA 0.02473 0.40555 None
5 1DB1 VDX 0.03429 0.41254 1.5444
6 5N87 N66 0.01634 0.43216 1.74825
7 1BGQ RDC 0.02225 0.41401 1.77778
8 5APJ 76E 0.004181 0.45812 1.8797
9 3KMZ EQO 0.04038 0.40294 1.8797
10 5X8Q 82R 0.005732 0.44201 1.93798
11 5NTW 98N 0.02371 0.41903 1.94553
12 3SVJ 4LI 0.01397 0.41954 1.97044
13 4QWT ACD 0.01995 0.41672 2.0979
14 4ZW3 4S9 0.03916 0.41123 2.0979
15 1N20 3AG 0.03133 0.40126 2.0979
16 5G5W R8C 0.02471 0.4138 2.14286
17 5IXK 6EW 0.008902 0.4432 2.19298
18 4ZOM 4Q3 0.01354 0.43949 2.22222
19 2LBD REA 0.01737 0.41836 2.24719
20 4RC8 STE 0.01755 0.41667 2.25225
21 4P6X HCY 0.02784 0.40203 2.35294
22 5B4B LP5 0.002818 0.46805 2.41935
23 2C3Q GTX 0.009319 0.41835 2.42915
24 2PX6 DH9 0.01926 0.40483 2.44755
25 4H6Q TFB 0.03436 0.40472 2.44755
26 4BXK 1IU 0.01438 0.43603 2.7972
27 3Q2H QHF 0.01023 0.42158 2.7972
28 1TV5 N8E 0.01032 0.41336 2.7972
29 3GWT 066 0.04091 0.40646 2.7972
30 4KIB SAH 0.021 0.4052 2.7972
31 1W96 S1A 0.02296 0.4039 2.7972
32 1GHE ACO 0.03652 0.40015 2.82486
33 2E2R 2OH 0.01022 0.44408 2.86885
34 4XVX P33 FDA 0.02366 0.42271 3.14685
35 3T03 3T0 0.01877 0.40316 3.16901
36 3I51 6PL 0.005865 0.44668 3.33333
37 3D78 NBB 0.02593 0.42001 3.36134
38 5CUQ NSC 0.03729 0.40999 3.37079
39 5K53 STE 0.01583 0.41573 3.43511
40 3H2B SAH 0.02451 0.40398 3.44828
41 5IR4 ZPE 0.03857 0.41798 3.4965
42 3JRX S1A 0.02079 0.40624 3.4965
43 3HY9 098 0.007401 0.4303 3.61991
44 2ZFU SAH 0.02511 0.40533 3.72093
45 2FV5 541 0.009223 0.44092 3.83142
46 1FCH TYR GLN SER LYS LEU 0.0302 0.40796 3.84615
47 1C7O PPG 0.02606 0.40406 3.84615
48 4EUU BX7 0.03817 0.40091 3.84615
49 3KDU NKS 0.02472 0.42528 3.97112
50 5GK9 ACO 0.01882 0.4201 4
51 1MHC FME TYR PHE ILE ASN ILE LEU THR LEU 0.02867 0.41849 4.0404
52 1BII ARG GLY PRO GLY ARG ALA PHE VAL THR ILE 0.02428 0.41569 4.1958
53 3G5K BB2 0.001516 0.46162 4.37158
54 1NLI ADE 0.02792 0.40565 4.43548
55 1YMT DR9 0.03302 0.40763 4.47154
56 2BJ4 OHT 0.02158 0.40866 4.7619
57 2QE4 JJ3 0.0258 0.43304 4.83871
58 5E7V M7E 0.04493 0.40228 4.8951
59 1KJM ALA GLN PHE SER ALA SER ALA SER ARG 0.0234 0.418 5
60 4DOO DAO 0.01258 0.41782 5.36585
61 4GFD 0YB 0.03403 0.40035 5.36585
62 3FAL LO2 0.01649 0.42888 5.3719
63 5G3N X28 0.009592 0.42846 5.51181
64 5EUD 5S6 0.01392 0.41283 5.59441
65 2FHK MFN 0.02836 0.4019 5.59441
66 4M8E 29V 0.01831 0.41629 5.62771
67 4POJ 2VP 0.01983 0.41601 5.62771
68 3H0A D30 0.01628 0.42255 5.70175
69 4OIV XX9 0.03329 0.41807 5.75221
70 1YOK P6L 0.03184 0.41551 5.85938
71 5UWA 8ND 0.01811 0.42386 5.91133
72 4WUJ FMN 0.01509 0.4121 6.12245
73 5UNJ RJW 0.01389 0.41092 6.12245
74 4P3H 25G 0.01897 0.40813 6.21762
75 3WYJ H78 0.04652 0.42332 6.32411
76 3ND6 ATP 0.04483 0.40431 6.43275
77 4H07 IPH 0.0165 0.42626 6.49351
78 4S15 4D8 0.0185 0.4141 6.64062
79 4OYA 1VE 0.04425 0.42655 6.64336
80 3P5P A3C 0.02687 0.40312 6.64336
81 5BYZ 4WE 0.02245 0.41991 6.99301
82 4ZM4 P3B 0.02904 0.40035 6.99301
83 1JGS SAL 0.005857 0.41738 7.24638
84 4G31 0WH 0.009949 0.44037 7.34266
85 1RQJ RIS 0.02888 0.407 7.34266
86 4UDB CV7 0.02882 0.4076 7.35294
87 1XON PIL 0.03454 0.40724 7.69231
88 5HCV 60R 0.01645 0.41912 7.7821
89 2A3I C0R 0.01023 0.42717 7.90514
90 2OKL BB2 0.01056 0.42073 8.10811
91 5JF2 SF7 0.01326 0.41714 8.33333
92 2GU8 796 0.02381 0.43679 8.39161
93 1VR0 3SL 0.009067 0.41364 8.50202
94 1YKD CMP 0.01637 0.41052 8.74126
95 1S17 GNR 0.003028 0.44911 8.88889
96 3V49 PK0 0.03014 0.40714 9.02256
97 3NMV PYV 0.02252 0.40209 9.55056
98 3OLL EST 0.02221 0.40255 9.58333
99 3E3U NVC 0.0002684 0.42885 9.64467
100 4O4K 2PK 0.009935 0.42996 10.1399
101 2DYS PGV 0.01865 0.42851 10.8392
102 2DYR PGV 0.04964 0.40833 10.8392
103 2DYR PSC 0.04426 0.4007 10.8392
104 3CLH NAD 0.03177 0.40183 11.5385
105 5HCN DAO 0.01095 0.40618 11.8774
106 5CHR 4NC 0.006382 0.41465 12.4088
107 3I6I NDP 0.01326 0.44181 12.5874
108 3KRO DST 0.02427 0.41276 12.5874
109 3KRO IPE 0.02427 0.41276 12.5874
110 1N4H REA 0.004439 0.44742 13.1274
111 1PZL MYR 0.01156 0.41974 13.9241
112 1EZV SMA 0.01461 0.42544 14.3357
113 4COL DTP 0.002517 0.45044 16.0839
114 4X6F 3XU 0.03365 0.41781 16.1905
115 5JHD GLY ILE LEU GLY PHE VAL PHE THR LEU 0.03618 0.41737 17
116 5ISZ GLY ILE LEU GLY PHE VAL PHE THR LEU 0.04693 0.40933 17.3469
117 3BZF VAL MET ALA PRO ARG ALA LEU LEU LEU 0.01525 0.4327 17.5258
118 2FYU FDN 0.02654 0.40014 17.9487
119 3GST GPR 0.01041 0.43288 22.5806
120 3R1V AZB 0.02752 0.40817 29.1339
121 1NRL SRL 0.003847 0.44775 32
122 3IPQ 965 0.03698 0.40794 32
123 4DM8 REA 0.02583 0.40557 32
124 4C2V YJA 0.008348 0.44207 34.0909
125 3ET3 ET1 0.0282 0.40271 50
Pocket No.: 4; Query (leader) PDB : 3R9V; Ligand: DXC; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 3r9v.bio3) has 8 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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