Receptor
PDB id Resolution Class Description Source Keywords
3P13 2.35 Å EC: 5.5.1.- COMPLEX STRUCTURE OF D-RIBOSE PYRANASE SA240 WITH D-RIBOSE STAPHYLOCOCCUS AUREUS RBSD D-RIBOSE PYRANASE SA240 CARBOHYDRATE METABOLISM ISO
Ref.: CRYSTAL STRUCTURE OF SA240: A RIBOSE PYRANASE HOMOL PARTIAL ACTIVE SITE FROM STAPHYLOCOCCUS AUREUS J.STRUCT.BIOL. V. 174 413 2011
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
RIP A:201;
B:201;
C:201;
D:201;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
submit data
150.13 C5 H10 O5 C1[C@...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3P13 2.35 Å EC: 5.5.1.- COMPLEX STRUCTURE OF D-RIBOSE PYRANASE SA240 WITH D-RIBOSE STAPHYLOCOCCUS AUREUS RBSD D-RIBOSE PYRANASE SA240 CARBOHYDRATE METABOLISM ISO
Ref.: CRYSTAL STRUCTURE OF SA240: A RIBOSE PYRANASE HOMOL PARTIAL ACTIVE SITE FROM STAPHYLOCOCCUS AUREUS J.STRUCT.BIOL. V. 174 413 2011
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 3P13 - RIP C5 H10 O5 C1[C@H]([C....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 3P13 - RIP C5 H10 O5 C1[C@H]([C....
50% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 141 families.
1 3P13 - RIP C5 H10 O5 C1[C@H]([C....
2 1OGE - RP5 C5 H11 O8 P C([C@@H]1[....
3 1OGD Kd = 0.93 mM RIP C5 H10 O5 C1[C@H]([C....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: RIP; Similar ligands found: 14
No: Ligand ECFP6 Tc MDL keys Tc
1 XYP 1 1
2 0MK 1 1
3 RIP 1 1
4 LXC 1 1
5 ARA 1 1
6 ARB 1 1
7 XYS 1 1
8 HSY 1 1
9 BXP 0.414634 0.84375
10 XYP XYP 0.414634 0.84375
11 XYS XYP 0.414634 0.84375
12 XYS XYS 0.414634 0.84375
13 XYP XYS 0.414634 0.84375
14 FU4 0.4 0.896552
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3P13; Ligand: RIP; Similar sites found: 96
This union binding pocket(no: 1) in the query (biounit: 3p13.bio1) has 9 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1D01 ACE MET LEU SER VAL GLU GLU GLU GLY 0.005234 0.43961 None
2 3NTY NAP 0.01143 0.44034 1.38889
3 3NTY 5P3 0.01183 0.44034 1.38889
4 2Q9U FMN 0.009981 0.42723 2.08333
5 1LBZ FBP 0.01895 0.41084 2.08333
6 1KZL CRM 0.01249 0.40004 2.08333
7 3A8T ATP 0.01587 0.40521 2.35988
8 5MBX FAD 0.04406 0.43409 2.77778
9 5MBX SP5 0.04406 0.43409 2.77778
10 1ZQ5 E04 0.03364 0.42301 2.77778
11 1ZQ5 NAP 0.03364 0.42301 2.77778
12 4KFU ACP 0.00748 0.42082 2.77778
13 3ZNR NU9 0.009976 0.4154 2.77778
14 4INB 1F6 0.01734 0.41049 2.77778
15 4X7R 3YW 0.01731 0.40096 2.77778
16 4X7R UDP 0.01731 0.40096 2.77778
17 2O4N TPV 0.01867 0.40733 3.0303
18 1OPK MYR 0.004749 0.41846 3.47222
19 5BR4 NAD 0.04073 0.40764 3.47222
20 1QDS PGA 0.0108 0.40521 3.47222
21 2VK4 TPP 0.01739 0.40407 3.47222
22 3QXG TLA 0.01554 0.40398 3.47222
23 3FSY SCA 0.04407 0.40373 3.47222
24 1RJD SAM 0.011 0.41754 4.16667
25 4WEI GLC GAL 0.005894 0.41544 4.16667
26 2J9D ADP 0.02066 0.40905 4.20168
27 2PT9 2MH 0.02757 0.41562 4.6729
28 2PT9 S4M 0.01931 0.41562 4.6729
29 4YBN FAD 0.008125 0.45841 4.86111
30 5BUK FAD 0.00889 0.45493 4.86111
31 1PZ0 NAP 0.01084 0.42266 4.86111
32 1PZ1 NAP 0.02437 0.41588 4.86111
33 4RQU NAD 0.01826 0.41466 4.86111
34 3H7R NAP 0.02247 0.41106 4.86111
35 2ZEJ GDP 0.04867 0.41005 4.86111
36 1Z4O GL1 0.01166 0.40974 4.86111
37 5WRI A3P 0.03488 0.4047 4.86111
38 2I7C AAT 0.04482 0.40004 5.30035
39 3E1T FAD 0.01258 0.44091 5.55556
40 3TN7 NJP 0.01665 0.43597 5.55556
41 2ZIF SAM 0.008053 0.41435 5.55556
42 2VHW NAI 0.04867 0.40423 5.55556
43 2WCU FUC 0.0000001893 0.64626 6.25
44 3RUG DB6 0.002434 0.48834 6.25
45 3EUF BAU 0.002149 0.45033 6.25
46 1MVN FMN 0.008883 0.43612 6.25
47 1MVN PCO 0.01479 0.43612 6.25
48 3FMI KAP 0.007308 0.41571 6.25
49 3WE0 FAD 0.02654 0.41171 6.25
50 1XG5 NAP 0.04638 0.40842 6.25
51 4P4M D3T 0.01307 0.4032 6.25
52 2GRU NAD 0.004519 0.45913 6.94444
53 1UUO FMN 0.0201 0.42549 6.94444
54 1UUO BRF 0.02111 0.42549 6.94444
55 1UUO ORO 0.0201 0.42549 6.94444
56 1W7J ADP BEF 0.02005 0.41145 6.94444
57 2VBF TPP 0.01644 0.41077 6.94444
58 3RC3 ANP 0.01393 0.40862 6.94444
59 2CHG ANP 0.01619 0.40109 6.94444
60 2ZR9 DTP 0.02846 0.40069 6.94444
61 1P3D UMA 0.03059 0.40209 7.63889
62 1B4U DHB 0.02267 0.40171 7.63889
63 1G0H IPD 0.007641 0.43515 8.33333
64 3KLJ FAD 0.02963 0.4053 8.33333
65 4POO SAM 0.02702 0.40369 8.33333
66 3ZIA ADP 0.008315 0.42823 9.02778
67 3TLC 7MD 0.02475 0.40025 9.72222
68 4O33 3PG 0.02459 0.42346 10.4167
69 4O33 TZN 0.02459 0.42346 10.4167
70 1GP2 GDP 0.0342 0.41292 10.4167
71 2BIF ANP 0.04907 0.41257 10.4167
72 3MMH SME 0.01992 0.4099 10.4167
73 1ZCB GDP 0.01999 0.42599 11.1111
74 5ITV NAI 0.02805 0.42125 11.1111
75 1ZPD DPX 0.0147 0.41304 11.1111
76 1VBI NAD 0.03026 0.40253 11.1111
77 1YP4 ADP 0.005315 0.42699 11.8056
78 4GBM A3P 0.02142 0.42601 11.8056
79 2WCV FUC 0.000009473 0.57322 12.1429
80 1JWY ADP 0.01768 0.41017 13.1944
81 1RRC ADP 0.01466 0.40575 13.1944
82 1QPB PYM 0.02065 0.40198 13.1944
83 1QPB TPP 0.02065 0.40198 13.1944
84 2VVL FAD 0.009008 0.44898 13.8889
85 2VVM FAD 0.01108 0.44128 13.8889
86 2X7I CIT 0.01318 0.4174 13.8889
87 2VNO GAL GAL FUC 0.007147 0.41192 13.8889
88 1SQ5 ADP 0.01317 0.40686 13.8889
89 1G63 FMN 0.01514 0.42088 15.2778
90 2QQ0 TMP 0.0201 0.42474 18.0556
91 2QQ0 ANP 0.02231 0.42228 18.0556
92 3NC9 TR3 0.0327 0.40187 20.1389
93 2UUU PL3 0.01019 0.44231 27.0833
94 2UUU FAD 0.01019 0.44231 27.0833
95 4NON GDP 0.03255 0.4192 30.5556
96 4A34 FUL 0.0000001765 0.66428 39.5833
Pocket No.: 2; Query (leader) PDB : 3P13; Ligand: RIP; 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: 3p13.bio1) has 9 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 3P13; Ligand: RIP; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 3p13.bio2) has 9 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 3P13; Ligand: RIP; Similar sites found: 53
This union binding pocket(no: 4) in the query (biounit: 3p13.bio2) has 10 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2XTN GTP 0.005353 0.43783 None
2 1Z08 GNP 0.01133 0.42887 None
3 1H5Q NAP 0.0363 0.41166 None
4 3T3C 017 0.03645 0.40827 None
5 4I42 1HA 0.04591 0.40452 None
6 1ZD9 GDP 0.00942 0.42481 2.08333
7 1VGV UD1 0.01205 0.42315 2.08333
8 2GDZ NAD 0.04525 0.40794 2.08333
9 4QJK COA 0.03573 0.40088 2.08333
10 1QX4 FAD 0.02179 0.41394 2.77778
11 4GOX A3P 0.02276 0.41245 2.77778
12 4R2I ANP 0.01495 0.4046 2.77778
13 3NWQ 2NC 0.04595 0.40353 3.0303
14 2GSD NAD 0.0495 0.40025 3.47222
15 4MKF AP5 0.04717 0.40783 4.16667
16 3D91 REM 0.04754 0.40742 4.16667
17 1IOW ADP 0.0314 0.40495 4.16667
18 1IOW PHY 0.0314 0.40495 4.16667
19 1F76 FMN 0.0142 0.4244 4.86111
20 3C3N FMN 0.01848 0.42344 4.86111
21 2B4G ORO 0.009557 0.4048 4.86111
22 1OVD FMN 0.04346 0.40228 4.86111
23 1OVD ORO 0.04346 0.40228 4.86111
24 4B5P ACO 0.03772 0.40159 5.55556
25 2C9O ADP 0.01296 0.4225 6.25
26 4MSG 2C6 0.03643 0.40568 6.25
27 5FSY AR6 0.01835 0.40197 6.25
28 4IGH 1EA 0.03308 0.43546 6.94444
29 4IGH FMN 0.03308 0.43546 6.94444
30 4IGH ORO 0.03308 0.43546 6.94444
31 2OHH FMN 0.02557 0.40237 6.94444
32 2FXD DR7 0.04566 0.40405 7.07071
33 1W07 FAD 0.03026 0.41712 7.63889
34 2FNU PMP UD1 0.03754 0.4106 8.33333
35 1S16 ANP 0.04235 0.40334 8.33333
36 5VW2 FDA 0.02079 0.42769 9.02778
37 5VW2 NAP 0.02079 0.42769 9.02778
38 4BUY F37 0.03434 0.40309 9.02778
39 1K6M AGS 0.04282 0.40179 9.02778
40 3SM2 478 0.04922 0.40364 9.09091
41 1YKF NAP 0.03302 0.40852 9.72222
42 4CM8 NAP 0.03464 0.40677 9.72222
43 2X6T ADP BMA 0.01629 0.40496 9.72222
44 1Z8O DEB 0.04083 0.40181 9.72222
45 3MWS 017 0.04445 0.41065 10.101
46 2ZE7 DST 0.03044 0.40764 10.4167
47 2ZE7 AMP 0.03097 0.40631 10.4167
48 4R98 GNH 0.02353 0.40509 10.4167
49 1WF3 GNP 0.01658 0.4164 12.5
50 1G0N PHH 0.04368 0.41882 13.1944
51 4UI8 IY5 0.02375 0.41484 18.75
52 1ZOA 140 0.03458 0.40344 28.4722
53 2ICY UPG 0.006151 0.44249 32.6389
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