-->
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@...
View in 3D viewer
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 149 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: 12
No: Ligand ECFP6 Tc MDL keys Tc
1 RIP 1 1
2 XYS 1 1
3 ARB 1 1
4 HSY 1 1
5 ARA 1 1
6 XYP 1 1
7 LXC 1 1
8 0MK 1 1
9 XYP XYS 0.414634 0.84375
10 BXP 0.414634 0.84375
11 XYS XYP 0.414634 0.84375
12 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 with APoc: 131
This union binding pocket(no: 1) in the query (biounit: 3p13.bio1) has 9 residues
No: Leader PDB Ligand Sequence Similarity
1 1D01 ACE MET LEU SER VAL GLU GLU GLU GLY None
2 2ORV 4TA None
3 3NTY NAP 1.38889
4 3NTY 5P3 1.38889
5 2YGM GLA NAG GAL FUC 1.38889
6 2Q9U FMN 2.08333
7 1LBZ FBP 2.08333
8 1KZL CRM 2.08333
9 3A8T ATP 2.35988
10 5MBX SP5 2.77778
11 5MBX FAD 2.77778
12 4KFU ACP 2.77778
13 3ZNR NU9 2.77778
14 4INB 1F6 2.77778
15 6ASZ GLN THR ALA ARG M3L SER 2.77778
16 4X7R 3YW 2.77778
17 4X7R UDP 2.77778
18 2O4N TPV 3.0303
19 1OPK MYR 3.47222
20 1SC6 NAD 3.47222
21 1QXO FMN 3.47222
22 1QDS PGA 3.47222
23 4QC6 30N 3.47222
24 3QXG TLA 3.47222
25 2VK4 TPP 3.47222
26 3FSY SCA 3.47222
27 1RJD SAM 4.16667
28 4WEI GLC GAL 4.16667
29 5YS9 FAD 4.16667
30 2J9D ADP 4.20168
31 2PT9 2MH 4.6729
32 2PT9 S4M 4.6729
33 4YBN FAD 4.86111
34 5BUK FAD 4.86111
35 1PZ0 NAP 4.86111
36 4Z87 GDP 4.86111
37 1PZ1 NAP 4.86111
38 4URF NAD 4.86111
39 4RQU NAD 4.86111
40 5WRJ A3P 4.86111
41 3H7R NAP 4.86111
42 1CDO NAD 4.86111
43 2ZEJ GDP 4.86111
44 1Z4O GL1 4.86111
45 4PTZ FMN 4.86111
46 5WRI A3P 4.86111
47 2YI0 YI0 4.86111
48 2I7C AAT 5.30035
49 3E1T FAD 5.55556
50 3TN7 NJP 5.55556
51 2ZIF SAM 5.55556
52 5L3S GNP 5.55556
53 2VHW NAI 5.55556
54 5BN3 ADP 5.55556
55 2WCU FUC 6.25
56 3RUG DB6 6.25
57 3EUF BAU 6.25
58 1MVN PCO 6.25
59 1MVN FMN 6.25
60 5Z54 0HZ 6.25
61 1XG5 NAP 6.25
62 4P4M D3T 6.25
63 3A28 NAD 6.25
64 4ZLU ADP 6.4877
65 4ZLU 4PW 6.4877
66 2GRU NAD 6.94444
67 1UUO ORO 6.94444
68 1UUO BRF 6.94444
69 1UUO FMN 6.94444
70 2ZRU FMN 6.94444
71 6EOA FMN 6.94444
72 2VBF TPP 6.94444
73 3RC3 ANP 6.94444
74 1NZY BCA 6.94444
75 3G2O SAM 6.94444
76 4IDN GNP 6.94444
77 2CHG ANP 6.94444
78 2ZR9 DTP 6.94444
79 2CE7 ADP 7.63889
80 1P3D UMA 7.63889
81 1B4U DHB 7.63889
82 1G0H IPD 8.33333
83 3KLJ FAD 8.33333
84 4POO SAM 8.33333
85 3ZIA ADP 9.02778
86 3JQG NAP 9.72222
87 3JQB NAP 9.72222
88 3JQF NAP 9.72222
89 3BMO NAP 9.72222
90 3JQ7 NAP 9.72222
91 6F9Q NAD 9.72222
92 3JQ8 NAP 9.72222
93 5JDC NAP 9.72222
94 5TWB FAD 9.72222
95 3TLC 7MD 9.72222
96 4O33 3PG 10.4167
97 4O33 TZN 10.4167
98 1GP2 GDP 10.4167
99 2BIF ANP 10.4167
100 3MMH SME 10.4167
101 5N69 ADP 10.4167
102 5LEF GTP 10.4167
103 4YAG NAI 11.1111
104 1ZCB GDP 11.1111
105 3WDM ADN 11.1111
106 1ZPD DPX 11.1111
107 1VBI NAD 11.1111
108 4GBM A3P 11.8056
109 1YP4 ADP 11.8056
110 2WCV FUC 12.1429
111 5Y9D FAD 12.5
112 1QPB TPP 13.1944
113 1RRC ADP 13.1944
114 1QPB PYM 13.1944
115 4ZCC FAD 13.1944
116 2VVL FAD 13.8889
117 2VVM FAD 13.8889
118 2X7I CIT 13.8889
119 2VNO GAL GAL FUC 13.8889
120 1SQ5 ADP 13.8889
121 1G63 FMN 15.2778
122 4RKC PMP 15.9722
123 1IK4 PGH 16.6667
124 2QQ0 ADP 18.0556
125 2QQ0 TMP 18.0556
126 2QQ0 ANP 18.0556
127 3NC9 TR3 20.1389
128 2UUU FAD 27.0833
129 2UUU PL3 27.0833
130 4NON GDP 30.5556
131 4A34 FUL 39.5833
Pocket No.: 2; Query (leader) PDB : 3P13; Ligand: RIP; Similar sites found with APoc: 59
This union binding pocket(no: 2) in the query (biounit: 3p13.bio1) has 9 residues
No: Leader PDB Ligand Sequence Similarity
1 1H5Q NAP None
2 4FN4 NAD None
3 4I42 1HA None
4 1W4R TTP None
5 3WSJ MK1 None
6 3T3C 017 None
7 5LW0 AR6 None
8 4NBW NAD None
9 4QJK COA 2.08333
10 3H2B SAH 2.77778
11 3H4V NAP 2.77778
12 2FFQ GSP 2.77778
13 1MXH NAP 3.47222
14 5XJ7 87O 3.47222
15 3D91 REM 4.16667
16 1F76 FMN 4.86111
17 3ZNN 4WL 4.86111
18 3ZNN FAD 4.86111
19 5I0H ADP BEF 4.86111
20 1C1X HFA 4.86111
21 6C4M NAP 4.86111
22 4IZC 1GZ 4.86111
23 3VKX T3 4.86111
24 1BW9 PPY 4.86111
25 1IY8 NAD 5.55556
26 2DVZ GLU 5.55556
27 5WGR FAD 5.55556
28 4MSG 2C6 6.25
29 5BYK OAQ 6.25
30 5BYK A3P 6.25
31 4YSW FAD 6.25
32 4YSW NAI 6.25
33 4WOP CTP 6.25
34 4IGH FMN 6.94444
35 4IGH ORO 6.94444
36 4IGH 1EA 6.94444
37 5FJN FAD 6.94444
38 4NJS G08 8.08081
39 1V97 FAD 8.33333
40 4ZG4 VO4 ADP 9.02778
41 1TV5 FMN 9.02778
42 1K6M AGS 9.02778
43 2R42 FPS 9.72222
44 4R98 GNH 10.4167
45 1GEG NAD 11.1111
46 2R5T ANP 11.8056
47 4QVH COA 11.8056
48 1WF3 GNP 12.5
49 3GEG NAD 13.8889
50 5EQY 5RA 14.5833
51 5M3E APR 15.9722
52 1QF9 C5P 15.9722
53 1QF9 ALF 15.9722
54 1QF9 ADP 15.9722
55 3OZV ECN 18.0556
56 3OZV FAD 18.0556
57 2Y7I ARG 19.4444
58 1U1W 3HA 20.1389
59 3AY6 NAI 22.2222
Pocket No.: 3; Query (leader) PDB : 3P13; Ligand: RIP; Similar sites found with APoc: 8
This union binding pocket(no: 3) in the query (biounit: 3p13.bio2) has 9 residues
No: Leader PDB Ligand Sequence Similarity
1 2JK0 ASP 2.08333
2 3NWQ 2NC 3.0303
3 2R5C C6P 3.47222
4 2PK3 A2R 4.16667
5 1JA9 NDP 4.86111
6 1YKF NAP 9.72222
7 1AFS NAP 12.5
8 1P9P SAH 15.9722
Pocket No.: 4; Query (leader) PDB : 3P13; Ligand: RIP; Similar sites found with APoc: 52
This union binding pocket(no: 4) in the query (biounit: 3p13.bio2) has 10 residues
No: Leader PDB Ligand Sequence Similarity
1 2XTN GTP None
2 1Z08 GNP None
3 5J60 FAD 1.38889
4 1ZD9 GDP 2.08333
5 1VGV UD1 2.08333
6 3KA2 2NC 2.08333
7 2GDZ NAD 2.08333
8 4GOX A3P 2.77778
9 1QX4 FAD 2.77778
10 4R2I ANP 2.77778
11 4RHE FMN 2.77778
12 4EIP FAD 3.47222
13 2GSD NAD 3.47222
14 4MKF AP5 4.16667
15 5U97 PIT 4.16667
16 1IOW PHY 4.16667
17 1IOW ADP 4.16667
18 3C3N FMN 4.86111
19 1ESW ACR 4.86111
20 5XFV FMN 4.86111
21 1OVD ORO 4.86111
22 3N7O N7O 4.86111
23 1OVD FMN 4.86111
24 6CZF G4P 5.55556
25 4B5P ACO 5.55556
26 2C9O ADP 6.25
27 5FSY AR6 6.25
28 2OHH FMN 6.94444
29 5LU5 M7P 6.94444
30 2FXD DR7 7.07071
31 2NAD NAD 7.63889
32 2FNU PMP UD1 8.33333
33 3OID NDP 8.33333
34 1S16 ANP 8.33333
35 5VW2 FDA 9.02778
36 5VW2 NAP 9.02778
37 2X65 M1P 9.02778
38 5KNK 11A 9.02778
39 4BUY F37 9.02778
40 3SM2 478 9.09091
41 4CM8 NAP 9.72222
42 4CLR NAP 9.72222
43 2X6T ADP BMA 9.72222
44 1Z8O DEB 9.72222
45 3MWS 017 10.101
46 2ZE7 DST 10.4167
47 2ZE7 AMP 10.4167
48 1HYH NAD 12.5
49 1F5N GNP 13.8889
50 5NWD 9C8 18.3673
51 1ZOA 140 28.4722
52 2ICY UPG 32.6389
APoc FAQ
Feedback