Receptor
PDB id Resolution Class Description Source Keywords
2VVQ 2 Å EC: 5.3.1.6 CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS RIBOSE-5- PHOSPHATE ISOMERASE B IN COMPLEX WITH THE INHIBITOR 5- D EOXY-5-PHOSPHO-D-RIBONATE MYCOBACTERIUM TUBERCULOSIS PENTOSE PHOSPHATE PATHWAY RPIB RV2465C ISOMERASE CARBOHYDRATE METABOLISM
Ref.: D-RIBOSE-5-PHOSPHATE ISOMERASE B FROM ESCHERICHIA COLI IS ALSO A FUNCTIONAL D-ALLOSE-6-PHOSPHATE ISOMERASE, WHILE THE MYCOBACTERIUM TUBERCULOSIS ENZYME IS NOT. J.MOL.BIOL. V. 382 667 2008
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
R10 A:200;
B:200;
C:200;
D:200;
E:200;
Valid;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
none;
submit data
246.109 C5 H11 O9 P C([C@...
SO4 A:300;
C:300;
Invalid;
Invalid;
none;
none;
submit data
96.063 O4 S [O-]S...
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 (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 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 2BES Ki = 0.057 mM RES C4 H10 N O8 P C([C@H]([C....
4 2BET Ki = 1.7 mM DEZ C4 H9 O8 P C([C@H]([C....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: R10; Similar ligands found: 46
No: Ligand ECFP6 Tc MDL keys Tc
1 R10 1 1
2 PA5 1 1
3 LG6 0.72973 1
4 6PG 0.72973 1
5 F6R 0.641026 0.916667
6 TG6 0.641026 0.916667
7 DEZ 0.638889 1
8 DER 0.638889 1
9 P6F 0.609756 0.942857
10 PAN 0.609756 0.702128
11 P6T 0.609756 0.942857
12 2FP 0.609756 0.942857
13 M2P 0.588235 0.914286
14 KD0 0.55814 1
15 I22 0.534884 0.916667
16 LXP 0.526316 0.837838
17 DX5 0.526316 0.837838
18 LX1 0.526316 0.861111
19 A5P 0.526316 0.837838
20 4TP 0.525 0.829268
21 S6P 0.512821 0.861111
22 HMS 0.512195 0.891892
23 5RP 0.512195 0.891892
24 5SP 0.512195 0.891892
25 G6Q 0.5 0.970588
26 52L 0.5 0.755556
27 DXP 0.5 0.861111
28 TX4 0.487805 0.659574
29 R52 0.487805 0.970588
30 DG6 0.487805 0.815789
31 R5P 0.487805 0.970588
32 3PG 0.486486 0.941176
33 HG3 0.485714 0.882353
34 DG2 0.475 0.911765
35 AGP 0.465116 0.704545
36 RUB 0.465116 0.888889
37 XBP 0.465116 0.888889
38 RES 0.465116 0.702128
39 M6R 0.465116 0.704545
40 1NT 0.45098 1
41 LRY 0.44 0.75
42 H4P 0.4375 0.727273
43 SEP 0.425 0.707317
44 E4P 0.425 0.911765
45 22H 0.413793 0.693878
46 CAP 0.408163 0.918919
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2BES; Ligand: RES; Similar sites found: 131
This union binding pocket(no: 1) in the query (biounit: 2bes.bio1) has 17 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4X8O AP5 0.01361 0.42987 None
2 5A89 ADP 0.02133 0.41804 None
3 5A89 FMN 0.02133 0.41804 None
4 1I1D COA 0.009495 0.41569 None
5 1I1D 16G 0.01793 0.41166 None
6 3F81 STT 0.00133 0.47365 1.16279
7 1UPT GTP 0.01506 0.40283 1.16959
8 4HEQ FMN 0.01159 0.40475 2.05479
9 1JGS SAL 0.005837 0.41215 2.17391
10 2P8O BVA 0.0431 0.40048 2.29008
11 2V2V V12 0.03649 0.40511 2.32558
12 4ZGS NAD 0.02035 0.40256 2.32558
13 1TKB N1T 0.03366 0.40121 2.32558
14 1I9G SAM 0.00748 0.41735 2.90698
15 1R18 SAH 0.01124 0.41056 2.90698
16 4N82 FMN 0.009402 0.40712 2.90698
17 4HXY NDP 0.02439 0.40499 2.90698
18 4AG5 ADP 0.01566 0.4047 2.90698
19 1QB7 ADE 0.006441 0.40371 2.90698
20 2A5F GTP 0.01996 0.40008 2.90698
21 1OBV FMN 0.01426 0.40226 2.95858
22 2CNT COA 0.007956 0.41939 3.125
23 4MKG AP5 0.008491 0.43564 3.48837
24 1S3G AP5 0.01186 0.42826 3.48837
25 3OZG SSI 0.004703 0.41911 3.48837
26 1N4W FAD 0.03648 0.40766 3.48837
27 4L2I NAD 0.0417 0.40542 3.48837
28 4L2I FAD 0.02914 0.40542 3.48837
29 3UZO GLU 0.01801 0.40515 3.48837
30 5W8V 9YP 0.01677 0.40376 3.48837
31 3RGQ 5P5 0.005357 0.4299 3.84615
32 2Q8M AMP 0.001588 0.43616 4.06977
33 5MW4 5JU 0.01721 0.42193 4.06977
34 5EZ7 FAD 0.02001 0.41764 4.06977
35 4QYS PLP SEP 0.01289 0.41079 4.06977
36 1U3G THF 0.01326 0.40711 4.06977
37 2IDX ATP 0.008134 0.40588 4.06977
38 2BNF UTP 0.01726 0.40464 4.06977
39 3LXK MI1 0.02005 0.40424 4.06977
40 2Q4W FAD 0.03295 0.40168 4.06977
41 4B1Y ATP 0.01738 0.40146 4.06977
42 4QYS PLR 0.009064 0.40145 4.06977
43 4JEM C5P 0.01243 0.4051 4.11765
44 3T31 DCQ 0.0149 0.43704 4.65116
45 3T31 FAD 0.01402 0.43704 4.65116
46 4DQ2 BTX 0.04202 0.41548 4.65116
47 4OTH DRN 0.008532 0.41463 4.65116
48 3CIP ATP 0.031 0.41051 4.65116
49 4WNP 3RJ 0.008871 0.40627 4.65116
50 3GGF GVD 0.009664 0.40241 4.65116
51 1MJH ATP 0.008675 0.41428 4.93827
52 3KC1 2T6 0.0005046 0.46883 5.23256
53 1FNZ A2G 0.006032 0.42281 5.23256
54 5B3A 0JO 0.007303 0.41955 5.23256
55 3S1S SAH 0.008409 0.41823 5.23256
56 5EOU ATP 0.007945 0.41611 5.23256
57 4YHB FAD 0.01472 0.40943 5.23256
58 4J56 FAD 0.03906 0.40691 5.23256
59 2JKY 5GP 0.008102 0.40596 5.23256
60 2WUF KEM 0.0481 0.40587 5.23256
61 3HGM ATP 0.007196 0.41816 5.44218
62 1GOJ ADP 0.0115 0.41823 5.81395
63 4JK3 NAD 0.04568 0.41351 5.81395
64 2E5V FAD 0.03354 0.41116 5.81395
65 3RYC GTP 0.0186 0.41087 5.81395
66 3MB5 SAM 0.01197 0.41084 5.81395
67 3TO7 COA 0.01688 0.4051 5.81395
68 1D6S MET PLP 0.01637 0.40427 5.81395
69 4A0S NAP 0.0297 0.4007 5.81395
70 4MKF AP5 0.01253 0.42804 5.99078
71 5UAO FAD 0.01793 0.42101 6.39535
72 5A5W GUO 0.02762 0.41046 6.39535
73 4JB1 FAD 0.04812 0.40515 6.39535
74 4JB1 NAP 0.04662 0.40515 6.39535
75 2F5X ASP 0.01668 0.40154 6.39535
76 1RP0 AHZ 0.03184 0.4003 6.39535
77 1ECC PCP 0.01987 0.40018 6.39535
78 5EE5 GTP 0.0151 0.40278 6.43275
79 1WWZ ACO 0.02423 0.40149 6.91824
80 2WPF WPF 0.02624 0.44142 6.97674
81 5LXT GTP 0.02826 0.42881 6.97674
82 4Q4K FMN 0.008401 0.4213 6.97674
83 5THY SAH 0.008755 0.41409 6.97674
84 4JZ8 CIT 0.01276 0.41135 6.97674
85 3LAD FAD 0.03952 0.40501 6.97674
86 4CNK FAD 0.03835 0.40486 6.97674
87 3FJO FMN 0.01287 0.40438 6.97674
88 4NTD FAD 0.03643 0.40335 6.97674
89 1J0D 5PA 0.02128 0.40297 6.97674
90 5THZ SAH 0.01523 0.4009 6.97674
91 2ZIF SAM 0.004976 0.42397 7.55814
92 2FXV 5GP 0.009881 0.41485 7.55814
93 2C49 ADN 0.007851 0.41079 7.55814
94 5JSQ 6MS 0.009138 0.40129 7.55814
95 1FEC FAD 0.009689 0.44006 8.13953
96 3FB4 AP5 0.01339 0.42559 8.13953
97 1QF5 GDP 0.02733 0.41738 8.13953
98 5G41 AP5 0.04102 0.40499 8.13953
99 1ZIN AP5 0.04012 0.40119 8.13953
100 1JJ7 ADP 0.02248 0.40053 8.13953
101 3VC3 C6P 0.007381 0.42404 8.72093
102 4LNU GTP 0.01676 0.40806 8.72093
103 5EIB GTP 0.02167 0.40258 8.72093
104 3B9Q MLI 0.004627 0.42978 9.30233
105 1GHE ACO 0.0192 0.4009 9.30233
106 2WSB NAD 0.04551 0.40013 9.30233
107 1WUR 8DG 0.01727 0.40159 9.54545
108 3ZEI AWH 0.009321 0.42326 9.67742
109 3PC3 P1T 0.0104 0.41052 9.88372
110 5GK9 ACO 0.007558 0.42499 10
111 1AX2 NDG GAL 0.003911 0.43288 10.4651
112 2RGX AP5 0.0155 0.42426 10.4651
113 5BUK FAD 0.02324 0.41868 10.4651
114 3WQT ANP 0.01161 0.40823 10.4651
115 3CTY FAD 0.04748 0.40245 10.4651
116 1I1N SAH 0.02436 0.40138 10.4651
117 2ZQO NGA 0.01476 0.40627 10.7692
118 1DL5 SAH 0.01256 0.41421 11.0465
119 3IAE D7K 0.02107 0.40816 11.6279
120 2B3D FAD 0.003137 0.4405 12.2093
121 3MBI HSX 0.008326 0.41181 12.7907
122 1U7Z PMT 0.0149 0.41799 13.3721
123 1TLL FMN 0.01229 0.41029 13.3721
124 3B8X G4M 0.02464 0.40808 13.3721
125 5AOA PPI 0.003063 0.42582 13.9535
126 4P83 U5P 0.003469 0.42525 13.9535
127 2BNE U5P 0.004563 0.42759 16.2791
128 2PWY SAH 0.01656 0.40403 18.6047
129 2GAG NAD 0.03567 0.40289 20.202
130 1US5 GLU 0.004642 0.4148 26.1628
131 4LFL TG6 0.000000001097 0.70233 43.8272
Pocket No.: 2; Query (leader) PDB : 2BES; Ligand: RES; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 2bes.bio1) has 17 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 2BES; Ligand: RES; Similar sites found: 114
This union binding pocket(no: 3) in the query (biounit: 2bes.bio3) has 17 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2XBP ATP 0.002209 0.44694 None
2 4CO3 ATP 0.009046 0.41705 None
3 1LNX URI 0.004592 0.40652 None
4 3H86 AP5 0.02711 0.4008 None
5 1UWZ THU 0.003686 0.40022 1.47059
6 4K5S PM0 0.004777 0.43494 2.32558
7 2NCD ADP 0.00254 0.42272 2.32558
8 4K5S FAD 0.006716 0.41395 2.32558
9 2CFA FAD 0.006371 0.40083 2.32558
10 4NAT ADP 0.02058 0.42427 2.5
11 2OD9 A1R NCA 0.001574 0.43537 2.90698
12 2QQF A1R 0.003479 0.41586 2.90698
13 4Q0P 0MK 0.04955 0.41116 2.90698
14 4KXV TDP DX5 0.01139 0.40999 2.90698
15 4PVV HO4 0.01218 0.40879 2.90698
16 2F3R G5P 0.01936 0.40823 2.90698
17 4LTN FMN 0.01799 0.4063 2.90698
18 1SOW NAD 0.01086 0.40432 2.90698
19 2HW1 ANP 0.00551 0.40152 2.90698
20 2XD9 XD9 0.04009 0.42675 2.99401
21 2Q28 TPP 0.002268 0.42312 3.48837
22 1MVN PCO 0.01404 0.41976 3.48837
23 2QA1 FAD 0.007859 0.41346 3.48837
24 3NYQ AMP 0.01161 0.40432 3.48837
25 3NYQ MCA 0.01095 0.40419 3.48837
26 1Y52 BTN 0.005777 0.42517 3.96825
27 1W7J ADP BEF 0.0001374 0.4192 3.97351
28 3P0F BAU 0.0001344 0.45348 4.06977
29 1XVV CCQ 0.004979 0.42587 4.06977
30 3ICC NAP 0.004565 0.41951 4.06977
31 4HE2 AMP 0.00555 0.41484 4.06977
32 1VPM COA 0.003478 0.41265 4.06977
33 1K6M AGS 0.003342 0.4116 4.06977
34 1PL6 NAD 0.003457 0.41104 4.06977
35 1MOQ GLP 0.002863 0.40853 4.06977
36 1G79 PLP 0.007466 0.41547 4.12844
37 1G79 FMN 0.007629 0.41171 4.12844
38 3BY8 MLT 0.000666 0.462 4.22535
39 1R37 NAD 0.01496 0.40095 4.32277
40 1V6A TRE 0.003147 0.41884 4.65116
41 1VBH PEP 0.0001387 0.41822 4.65116
42 2NP9 YE1 0.005893 0.41504 4.65116
43 1SBZ FMN 0.007661 0.41045 4.65116
44 4PLG OXM 0.0139 0.4054 4.65116
45 4PLG NAI 0.0139 0.4054 4.65116
46 1HV9 COA 0.02895 0.40074 4.65116
47 4AAW R84 0.01675 0.41092 4.79303
48 2V6O FAD 0.001149 0.47717 5.23256
49 3ZPG 5GP 0.002293 0.454 5.23256
50 1LVL FAD 0.009376 0.41823 5.23256
51 1YWQ FMN 0.001268 0.41739 5.23256
52 1V8K ANP 0.006105 0.41318 5.23256
53 1KOL NAD 0.01109 0.40841 5.23256
54 3S9K CIT 0.000519 0.51685 5.81395
55 4G1V FAD 0.002358 0.42553 5.81395
56 3LZW FAD 0.006363 0.42044 5.81395
57 2XVE FAD 0.02895 0.40889 5.81395
58 3LZW NAP 0.02737 0.40808 5.81395
59 1H65 GDP 0.004959 0.40327 5.81395
60 1H2B NAJ 0.001873 0.43637 6.39535
61 2BLE 5GP 0.01303 0.42285 6.39535
62 1GAD NAD 0.009294 0.40059 6.39535
63 1TDF FAD 0.01 0.41963 6.97674
64 1TDF NAP 0.0211 0.41963 6.97674
65 3MPI GRA 0.02073 0.41066 6.97674
66 1XLI GLT 0.01316 0.40211 6.97674
67 3QV9 QV7 0.008487 0.40089 6.97674
68 1C1L GAL BGC 0.001313 0.44879 7.29927
69 2NVK FAD 0.0005423 0.46794 7.55814
70 1FL2 FAD 0.002542 0.439 7.55814
71 3AHC TPP 0.00159 0.43521 7.55814
72 4IVG ANP 0.001936 0.42247 7.55814
73 4KQI RBZ 0.01083 0.40318 7.55814
74 4KQI NIO 0.01083 0.40318 7.55814
75 1LO8 4CA 0.02833 0.4093 7.80142
76 3VHZ SOG 0.01465 0.42193 8.39695
77 3FS8 TDR 0.007682 0.4398 8.72093
78 1UKW FAD 0.005824 0.42097 8.72093
79 3OND ADN 0.01422 0.41395 8.72093
80 3OND NAD 0.01422 0.41395 8.72093
81 1I0Z NAI 0.01025 0.4029 8.72093
82 3C1O NAP 0.007967 0.40028 8.72093
83 1BUC FAD 0.002366 0.43472 9.30233
84 2YVF FAD 0.02094 0.41447 9.30233
85 3BW2 FMN 0.01153 0.40085 9.30233
86 9LDT NAD 0.01268 0.40041 9.30233
87 3UEC ALA ARG TPO LYS 0.002858 0.43365 9.58904
88 3E5H GNP 0.0009605 0.436 10.4651
89 1XHL NDP 0.003696 0.4232 10.4651
90 1T0S BML 0.008258 0.41956 10.4651
91 1M7Y PPG 0.005469 0.4138 10.4651
92 1V5F TPP 0.004892 0.47256 11.0465
93 1V5F FAD 0.004892 0.47256 11.0465
94 3RF4 FUN 0.006489 0.40047 11.2069
95 2C7G FAD 0.01583 0.41714 11.6279
96 2C7G ODP 0.01525 0.41714 11.6279
97 4E13 NAD 0.0027 0.41336 11.6279
98 3O03 NAP 0.02042 0.41301 11.6279
99 1ITZ TPP 0.003668 0.41175 12.2093
100 2GSD NAD 0.008975 0.4111 12.2093
101 1OLS TDP 0.01464 0.41095 12.2093
102 1O51 ADP 0.00522 0.40897 12.2807
103 2F01 BTQ 0.01176 0.42801 12.5984
104 1SS4 GSH 0.005453 0.46065 13.0719
105 1IYE PGU 0.00763 0.40929 13.3721
106 4BJZ FAD 0.04798 0.40354 13.3721
107 4BJZ P3A 0.04798 0.40354 13.3721
108 1O9U ADZ 0.01879 0.40936 13.9535
109 1B9I PXG 0.007059 0.40075 13.9535
110 2J07 HDF 0.01584 0.41274 14.5349
111 2J07 FAD 0.01584 0.41274 14.5349
112 1MDZ DCS 0.0004061 0.46318 15.6977
113 1MDZ PLP 0.0005874 0.45533 15.6977
114 1YBH CIE 0.01088 0.41179 16.8605
Pocket No.: 4; Query (leader) PDB : 2BES; Ligand: RES; Similar sites found: 23
This union binding pocket(no: 4) in the query (biounit: 2bes.bio2) has 17 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1DR1 HBI 0.03968 0.40051 2.32558
2 1DR1 NAP 0.03968 0.40051 2.32558
3 3A4T SFG 0.01835 0.40033 2.32558
4 5MPT SAH 0.01257 0.40307 3.48837
5 5IXJ THR 0.009559 0.42401 4.06977
6 2HQM FAD 0.04036 0.40454 4.65116
7 4MZU COA 0.01645 0.40416 4.65116
8 1VPE ANP 0.0152 0.40582 5.23256
9 5A3B APR 0.02188 0.40237 5.23256
10 1KYQ NAD 0.01319 0.40208 5.23256
11 1LLU NAD 0.03357 0.40127 5.23256
12 5M67 NAD 0.04858 0.40493 5.81395
13 1D6S PLP MET 0.01628 0.40282 5.81395
14 2C6Q NDP 0.04833 0.40045 5.81395
15 2KCE D16 0.04713 0.40019 6.39535
16 2WPF FAD 0.03411 0.43337 6.97674
17 4YNU FAD 0.04507 0.40364 6.97674
18 2Z48 A2G 0.01017 0.40615 7.55814
19 1W62 PYC 0.01426 0.40494 7.55814
20 5FJN FAD 0.01917 0.42131 8.13953
21 2OGA PGU 0.01313 0.40568 9.30233
22 1IWE IMP 0.0478 0.42633 9.88372
23 2Y88 2ER 0.02826 0.40609 15.6977
Pocket No.: 5; Query (leader) PDB : 2BES; Ligand: RES; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 5) in the query (biounit: 2bes.bio2) has 17 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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