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Receptor
PDB id Resolution Class Description Source Keywords
2BES 2.1 Å EC: 5.3.1.6 STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS RIBOSE-5-PHOSPHATE I RPIB, RV2465C, IN COMPLEX WITH 4-PHOSPHO-D-ERYTHRONOHYDROXA MYCOBACTERIUM TUBERCULOSIS RIBOSE 5-PHOSPHATE EPIMERASE PHOSPHOPENTOSISOMERASE PENTOSPHOSPHATE PATHWAY HIGH-ENERGY ENEDIOLATE INTERMEDIATE ISO
Ref.: COMPETITIVE INHIBITORS OF MYCOBACTERIUM TUBERCULOSI RIBOSE-5-PHOSPHATE ISOMERASE B REVEAL NEW INFORMATI THE REACTION MECHANISM. J.BIOL.CHEM. V. 280 6416 2005
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
RES A:200;
B:200;
C:200;
D:200;
E:200;
Valid;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
none;
Ki = 0.057 mM
231.098 C4 H10 N O8 P C([C@...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2BES 2.1 Å EC: 5.3.1.6 STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS RIBOSE-5-PHOSPHATE I RPIB, RV2465C, IN COMPLEX WITH 4-PHOSPHO-D-ERYTHRONOHYDROXA MYCOBACTERIUM TUBERCULOSIS RIBOSE 5-PHOSPHATE EPIMERASE PHOSPHOPENTOSISOMERASE PENTOSPHOSPHATE PATHWAY HIGH-ENERGY ENEDIOLATE INTERMEDIATE ISO
Ref.: COMPETITIVE INHIBITORS OF MYCOBACTERIUM TUBERCULOSI RIBOSE-5-PHOSPHATE ISOMERASE B REVEAL NEW INFORMATI THE REACTION MECHANISM. J.BIOL.CHEM. V. 280 6416 2005
Members (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 9 families.
1 2VVQ - R10 C5 H11 O9 P C([C@H]([C....
2 2VVO ic50 = 2 mM A6P C6 H13 O9 P C([C@@H]1[....
3 2VVP - R52 C5 H11 O8 P C([C@H]([C....
4 2BES Ki = 0.057 mM RES C4 H10 N O8 P C([C@H]([C....
5 2BET Ki = 1.7 mM DEZ C4 H9 O8 P C([C@H]([C....
70% Homology Family (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 7 families.
1 2VVQ - R10 C5 H11 O9 P C([C@H]([C....
2 2VVO ic50 = 2 mM A6P C6 H13 O9 P C([C@@H]1[....
3 2VVP - R52 C5 H11 O8 P C([C@H]([C....
4 2BES Ki = 0.057 mM RES C4 H10 N O8 P C([C@H]([C....
5 2BET Ki = 1.7 mM DEZ C4 H9 O8 P C([C@H]([C....
50% Homology Family (10)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 3PH3 - RB5 C5 H10 O5 C([C@H]([C....
2 3PH4 - AOS C6 H12 O6 C([C@H]([C....
3 2VVQ - R10 C5 H11 O9 P C([C@H]([C....
4 2VVO ic50 = 2 mM A6P C6 H13 O9 P C([C@@H]1[....
5 2VVP - R52 C5 H11 O8 P C([C@H]([C....
6 2BES Ki = 0.057 mM RES C4 H10 N O8 P C([C@H]([C....
7 2BET Ki = 1.7 mM DEZ C4 H9 O8 P C([C@H]([C....
8 3HEE - R5P C5 H11 O8 P C(C(C(C(C=....
9 3K8C - RES C4 H10 N O8 P C([C@H]([C....
10 3K7S - R52 C5 H11 O8 P C([C@H]([C....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: RES; Similar ligands found: 33
No: Ligand ECFP6 Tc MDL keys Tc
1 RES 1 1
2 PAN 0.634146 1
3 DER 0.578947 0.702128
4 DEZ 0.578947 0.702128
5 DXP 0.564103 0.645833
6 HMS 0.536585 0.673469
7 5RP 0.536585 0.673469
8 5SP 0.536585 0.673469
9 XBP 0.52381 0.666667
10 RUB 0.52381 0.666667
11 9C2 0.478261 0.897959
12 TX4 0.47619 0.956522
13 HG3 0.472222 0.617021
14 PA5 0.465116 0.702128
15 R10 0.465116 0.702128
16 GOS 0.447368 0.680851
17 EHM 0.447368 0.765957
18 M2P 0.447368 0.680851
19 6PG 0.444444 0.702128
20 LG6 0.444444 0.702128
21 TG6 0.444444 0.6875
22 F6R 0.444444 0.6875
23 4TP 0.44186 0.8125
24 2FP 0.425532 0.702128
25 P6T 0.425532 0.702128
26 I22 0.425532 0.6875
27 P6F 0.425532 0.702128
28 E4P 0.414634 0.673913
29 LX1 0.404762 0.645833
30 A5P 0.404762 0.632653
31 LXP 0.404762 0.632653
32 DX5 0.404762 0.632653
33 3PG 0.4 0.659574
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2BES; Ligand: RES; Similar sites found with APoc: 249
This union binding pocket(no: 1) in the query (biounit: 2bes.bio1) has 17 residues
No: Leader PDB Ligand Sequence Similarity
1 4X8O AP5 None
2 5A89 ADP None
3 5A89 FMN None
4 1I1D 16G None
5 1I1D COA None
6 4QAG F95 None
7 5GWT NAD 0.581395
8 3F81 STT 1.16279
9 1AKY AP5 1.16279
10 5KXE 6Y2 1.16279
11 1UPT GTP 1.16959
12 6BA2 7KM 1.74419
13 2YCH ATP 1.74419
14 6EDV COA 1.74419
15 6AR9 3L4 1.74419
16 2BQP GLC 1.74419
17 4HEQ FMN 2.05479
18 1JGS SAL 2.17391
19 4KFU ACP 2.32558
20 1DQN IMU 2.32558
21 4ZGS NAD 2.32558
22 4R2I ANP 2.32558
23 2V2V V12 2.32558
24 1TKB N1T 2.32558
25 1BZL FAD 2.90698
26 1I9G SAM 2.90698
27 1R18 SAH 2.90698
28 4N82 FMN 2.90698
29 4HXY NDP 2.90698
30 4AG5 ADP 2.90698
31 2PZE ATP 2.90698
32 1QB7 ADE 2.90698
33 4WZ6 ATP 2.90698
34 2A5F GTP 2.90698
35 1OBV FMN 2.95858
36 2CNT COA 3.125
37 2IMG MLT 3.48837
38 4MKG AP5 3.48837
39 1S3G AP5 3.48837
40 1BZY IMU 3.48837
41 5HV7 RBL 3.48837
42 4Y9J UCC 3.48837
43 4Y9J FAD 3.48837
44 5NM7 GLY 3.48837
45 4L2I FAD 3.48837
46 4L2I NAD 3.48837
47 5HSA FAS 3.48837
48 3UZO GLU 3.48837
49 6D6Y SAH 3.48837
50 1T5C ADP 3.48837
51 1DUB CAA 3.48837
52 3OZG SSI 3.48837
53 5M8T 0TR 3.48837
54 3HAZ FAD 3.48837
55 3LN9 FLC 3.59712
56 3RGQ 5P5 3.84615
57 4HE2 AMP 4.06977
58 2Q8M AMP 4.06977
59 5MW4 5JU 4.06977
60 5EZ7 FAD 4.06977
61 3LRE ADP 4.06977
62 2JK0 ASP 4.06977
63 2AWN ADP 4.06977
64 4QYS PLP SEP 4.06977
65 2BNF UTP 4.06977
66 6AM8 TRP 4.06977
67 6AM8 PLT 4.06977
68 1U3G THF 4.06977
69 6A0S HSE 4.06977
70 6A0S NDP 4.06977
71 6AMI TRP 4.06977
72 3LXK MI1 4.06977
73 2Q4W FAD 4.06977
74 4QYS PLR 4.06977
75 3MCT SAH 4.06977
76 1PVN MZP 4.06977
77 4CSD MFU 4.06977
78 2OEM 1AE 4.11622
79 4JEM C5P 4.11765
80 3T31 DCQ 4.65116
81 3T31 FAD 4.65116
82 4NU0 AP5 4.65116
83 6BKA FMN 4.65116
84 4WBD CIT 4.65116
85 2YFO GAL 4.65116
86 2YFO GLA 4.65116
87 4OTH DRN 4.65116
88 1QK3 5GP 4.65116
89 4WNP 3RJ 4.65116
90 4D52 GXL 4.65116
91 3GGF GVD 4.65116
92 3RNM FAD 4.65116
93 1MJH ATP 4.93827
94 2JJK R15 5.23256
95 3KC1 2T6 5.23256
96 6FP4 FAD 5.23256
97 1FNZ A2G 5.23256
98 5B3A 0JO 5.23256
99 6FP4 E1T 5.23256
100 3S1S SAH 5.23256
101 5EOU ATP 5.23256
102 5WS9 AMP 5.23256
103 4YHB FAD 5.23256
104 1OHE ACE ALA SEP PRO 5.23256
105 2JBH 5GP 5.23256
106 1GPM CIT 5.23256
107 4J56 FAD 5.23256
108 2JKY 5GP 5.23256
109 4BCN T9N 5.23256
110 4XFM THE 5.23256
111 3GE7 AFQ 5.23256
112 5V8E CIT 5.23256
113 4FRZ ADP 5.23256
114 4WOH 4NP 5.42169
115 3HGM ATP 5.44218
116 2C6Q NDP 5.81395
117 1GOJ ADP 5.81395
118 4D9M 0JO 5.81395
119 3B8I OXL 5.81395
120 2E5V FAD 5.81395
121 3RYC GTP 5.81395
122 3MB5 SAM 5.81395
123 6A20 ADP 5.81395
124 3TO7 COA 5.81395
125 1D6S MET PLP 5.81395
126 1Z83 AP5 5.81395
127 4A0S NAP 5.81395
128 4MKF AP5 5.99078
129 5UAO FAD 6.39535
130 5A5W GUO 6.39535
131 2ZXI FAD 6.39535
132 1T3D CYS 6.39535
133 4JB1 FAD 6.39535
134 4JB1 NAP 6.39535
135 2V7O DRN 6.39535
136 4U00 ADP 6.39535
137 3CEV ARG 6.39535
138 5Z21 NAI 6.39535
139 2F5X ASP 6.39535
140 1RP0 AHZ 6.39535
141 1T57 FMN 6.39535
142 5EE5 GTP 6.43275
143 1R4A GNP 6.66667
144 1CX9 NHP 6.80101
145 1WWZ ACO 6.91824
146 2WPF WPF 6.97674
147 2WPF FAD 6.97674
148 5LXT GTP 6.97674
149 1JG3 ADN 6.97674
150 4Q4K FMN 6.97674
151 5LXT GDP 6.97674
152 1G55 SAH 6.97674
153 5THY SAH 6.97674
154 4JZ8 CIT 6.97674
155 1XCL SAH 6.97674
156 3LAD FAD 6.97674
157 4CNK FAD 6.97674
158 3FJO FMN 6.97674
159 1J0D 5PA 6.97674
160 2VZZ SCA 6.97674
161 5THZ SAH 6.97674
162 5JIB OIA 7.55814
163 2FXV 5GP 7.55814
164 1NAA 6FA 7.55814
165 6HKE LMR 7.55814
166 2C49 ADN 7.55814
167 2ZIF SAM 7.55814
168 6HKE MLT 7.55814
169 1FEC FAD 8.13953
170 2D2F ADP 8.13953
171 3BP1 GUN 8.13953
172 3FB4 AP5 8.13953
173 3PVW QRX 8.13953
174 1QF5 RPL 8.13953
175 1QF5 GDP 8.13953
176 2WET FAD 8.13953
177 5G41 AP5 8.13953
178 3V0H I3P 8.13953
179 1ZIN AP5 8.13953
180 1JJ7 ADP 8.13953
181 1OYB FMN 8.13953
182 1OYB HBA 8.13953
183 6C2Z P1T 8.72093
184 3VC3 C6P 8.72093
185 3QFA FAD 8.72093
186 4PPF FLC 8.72093
187 4LNU GTP 8.72093
188 1G6H ADP 8.72093
189 5EIB GTP 8.72093
190 4DEC 3PG 8.72093
191 4DEC UDP 8.72093
192 5DOZ NDP 8.72093
193 3VPB GLU 8.92857
194 2OG2 MLI 9.30233
195 3B9Q MLI 9.30233
196 3BW2 FMN 9.30233
197 2VVG ADP 9.30233
198 5GVR LMR 9.30233
199 1GHE ACO 9.30233
200 2WSB NAD 9.30233
201 1WUR 8DG 9.54545
202 3ZEI AWH 9.67742
203 2A8X FAD 9.88372
204 1IWE IMP 9.88372
205 1WPQ 13P 9.88372
206 3PC3 P1T 9.88372
207 6H3O FAD 9.88372
208 2XN2 GLA 9.88372
209 5KF9 NAG 9.88372
210 5KF9 COA 9.88372
211 5GK9 ACO 10
212 2RGX AP5 10.4651
213 5BUK FAD 10.4651
214 3WQT ANP 10.4651
215 1BOB ACO 10.4651
216 3CTY FAD 10.4651
217 4EIL NDP 10.4651
218 1I1N SAH 10.4651
219 2ZQO NGA 10.7692
220 1DL5 SAH 11.0465
221 5ZI9 FLC 11.0465
222 3HQP OXL 11.0465
223 6BYF CIT 11.1765
224 3IAE D7K 11.6279
225 3VC1 GST 11.6279
226 2UZ1 TPP 11.6279
227 2B3D FAD 12.2093
228 3MBI HSX 12.7907
229 1U7Z PMT 13.3721
230 1TLL FMN 13.3721
231 5OVX AY5 13.3721
232 2CK3 ADP 13.6986
233 4P83 U5P 13.9535
234 5AOA PPI 13.9535
235 4CRZ ACO 14.6853
236 4P86 5GP 15.1163
237 1O5O U5P 15.1163
238 4JLS 3ZE 15.1316
239 2BNE U5P 16.2791
240 2A2C ADP 17.4419
241 2A2C NG1 17.4419
242 1ADO 13P 17.4419
243 2PWY SAH 18.6047
244 1YQT ADP 19.7674
245 2GAG NAD 20.202
246 5LS7 ACO 20.5882
247 1US5 GLU 26.1628
248 4WG0 CHD 33.3333
249 4LFL TG6 43.8272
Pocket No.: 2; Query (leader) PDB : 2BES; Ligand: RES; Similar sites found with APoc: 49
This union binding pocket(no: 2) in the query (biounit: 2bes.bio1) has 17 residues
No: Leader PDB Ligand Sequence Similarity
1 5GWT SIN 0.581395
2 3R96 AMP 1.74419
3 3R96 ACO 1.74419
4 1C3M MAN MAN 2.04082
5 3A4T SFG 2.32558
6 5Z2F PDC 2.90698
7 2WPB ZZI 3.48837
8 5MPT SAH 3.48837
9 4YDD MGD 4.06977
10 4YDD MD1 4.06977
11 1YQZ FAD 4.06977
12 5UY8 AMZ 4.06977
13 5JWC FAD 4.65116
14 2HQM FAD 4.65116
15 5A1S FLC 4.65116
16 6HOY TSN 4.65116
17 5IDM ANP 4.65116
18 1L5Y BEF 5.16129
19 3U6W KIV 5.23256
20 3NKS FAD 5.23256
21 1LLU NAD 5.23256
22 4JK3 NAD 5.81395
23 4J4H 1J1 5.81395
24 4J4H NAI 5.81395
25 1V0C ACO 5.81395
26 1V0C KNC 5.81395
27 4U36 TNR 5.81395
28 1D6S PLP MET 5.81395
29 3OIX FMN 5.81395
30 4NW6 2NS 5.81395
31 5OF9 ANP 6.39535
32 5E9G GLV 6.39535
33 5LXT 7AK 6.97674
34 4ZCC FAD 6.97674
35 2X2T GAL NGA 7.18954
36 2Z48 A2G 7.55814
37 1W62 PYC 7.55814
38 1SR9 KIV 8.13953
39 1UWK NAD 8.72093
40 1UWK URO 8.72093
41 5EO8 TFU 9.30233
42 2OGA PGU 9.30233
43 3UDG TMP 9.30233
44 1QM5 GLC GLC GLC PO4 SGC GLC 10.4651
45 3VC1 SAH 11.6279
46 4RLQ 3SK 12.2093
47 1AKV FMN 12.2449
48 5YX4 HCC 12.5
49 2Y88 2ER 15.6977
Pocket No.: 3; Query (leader) PDB : 2BES; Ligand: RES; Similar sites found with APoc: 4
This union binding pocket(no: 3) in the query (biounit: 2bes.bio3) has 17 residues
No: Leader PDB Ligand Sequence Similarity
1 1IZC PYR 4.65116
2 4S00 AKR 5.23256
3 3ITJ CIT 6.39535
4 5E5U MLI 7.55814
Pocket No.: 4; Query (leader) PDB : 2BES; Ligand: RES; 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: 2bes.bio3) has 17 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 2BES; Ligand: RES; Similar sites found with APoc: 24
This union binding pocket(no: 5) in the query (biounit: 2bes.bio2) has 17 residues
No: Leader PDB Ligand Sequence Similarity
1 1DR1 HBI 2.32558
2 1DR1 NAP 2.32558
3 6BJ0 G6P 3.48837
4 4TWP AXI 3.48837
5 3WXL ADP 3.48837
6 3QH2 3NM 4.06977
7 4MZU COA 4.65116
8 5XLS URA 5.23256
9 5A3B APR 5.23256
10 1KYQ NAD 5.23256
11 5M67 NAD 5.81395
12 3GDH SAH 5.81395
13 2WCI GSH 5.92593
14 5OC1 FAD 6.39535
15 2KCE D16 6.39535
16 4UCF GLA 6.97674
17 4YSX MLI 6.97674
18 4YNU FAD 6.97674
19 1TD2 PXL 7.55814
20 4IVG ANP 7.55814
21 6F7X MFU 7.77778
22 5FJN FAD 8.13953
23 1ZXM ANP 8.13953
24 3OU2 SAH 11.0465
Pocket No.: 6; Query (leader) PDB : 2BES; Ligand: RES; Similar sites found with APoc: 30
This union binding pocket(no: 6) in the query (biounit: 2bes.bio2) has 17 residues
No: Leader PDB Ligand Sequence Similarity
1 3QIN P1Y None
2 1QZR ANP 1.74419
3 1G8S MET 3.48837
4 4BQS K2Q 3.48837
5 2UVO NDG 3.50877
6 4X9M FAD 4.06977
7 2VYN NAD 4.65116
8 1DJN ADP 4.65116
9 1BVY FMN 5.23256
10 5J60 FAD 5.23256
11 2D24 XYS XYS 5.81395
12 5M67 3D1 5.81395
13 5M67 ADE 5.81395
14 2CNE DFJ 5.81395
15 2GMH FAD 5.81395
16 1ZGS XMM 5.81395
17 1ME8 RVP 5.81395
18 6F97 FAD 6.39535
19 3ITJ FAD 6.39535
20 2NPX FAD 6.39535
21 2Y69 CHD 6.75676
22 4CNK MEU 6.97674
23 2W8Q SIN 6.97674
24 1QNF FAD 6.97674
25 4IPE ANP 7.55814
26 3C1O NAP 8.72093
27 4FZV SAM 8.72093
28 4NMC FAD 11.0465
29 4P5Z Q7M 12.2093
30 1XRO LEU 13.9535
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