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Receptor
PDB id Resolution Class Description Source Keywords
3UDG 2.4 Å NON-ENZYME: BINDING STRUCTURE OF DEINOCOCCUS RADIODURANS SSB BOUND TO SSDNA DEINOCOCCUS RADIODURANS SSB OB FOLD BETA-BARREL SINGLE-STRANDED DNA-BINDING DNA PROTEIN-DNA COMPLEX
Ref.: STRUCTURE AND CELLULAR DYNAMICS OF DEINOCOCCUS RADI SINGLE-STRANDED DNA (SSDNA)-BINDING PROTEIN (SSB)-D COMPLEXES. J.BIOL.CHEM. V. 287 22123 2012
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
TMP A:302;
B:302;
B:303;
C:302;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
submit data
322.208 C10 H15 N2 O8 P CC1=C...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3UDG 2.4 Å NON-ENZYME: BINDING STRUCTURE OF DEINOCOCCUS RADIODURANS SSB BOUND TO SSDNA DEINOCOCCUS RADIODURANS SSB OB FOLD BETA-BARREL SINGLE-STRANDED DNA-BINDING DNA PROTEIN-DNA COMPLEX
Ref.: STRUCTURE AND CELLULAR DYNAMICS OF DEINOCOCCUS RADI SINGLE-STRANDED DNA (SSDNA)-BINDING PROTEIN (SSB)-D COMPLEXES. J.BIOL.CHEM. V. 287 22123 2012
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 510 families.
1 3UDG - TMP C10 H15 N2 O8 P CC1=CN(C(=....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 391 families.
1 3UDG - TMP C10 H15 N2 O8 P CC1=CN(C(=....
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 298 families.
1 3UDG - TMP C10 H15 N2 O8 P CC1=CN(C(=....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: TMP; Similar ligands found: 90
No: Ligand ECFP6 Tc MDL keys Tc
1 TMP 1 1
2 TYD 0.80597 0.985714
3 TTP 0.760563 0.985714
4 UFP 0.716418 0.917808
5 TBD 0.708333 0.945205
6 BRU 0.705882 0.917808
7 5HU 0.705882 0.957747
8 5IU 0.695652 0.917808
9 THM 0.693548 0.859155
10 LLT 0.693548 0.859155
11 FDM 0.671429 0.931507
12 NYM 0.671429 0.971831
13 THP 0.661972 0.985507
14 TLO 0.654321 0.931507
15 0DN 0.646154 0.84507
16 ATM 0.64 0.906667
17 BVP 0.64 0.957747
18 DAU 0.635294 0.918919
19 DT DT DT 0.634146 0.930556
20 18T 0.623529 0.918919
21 TDX 0.623529 0.931507
22 TRH 0.623529 0.918919
23 3R2 0.623529 0.906667
24 1JB 0.623529 0.918919
25 3YN 0.609195 0.918919
26 T3F 0.609195 0.894737
27 T3Q 0.609195 0.894737
28 DWN 0.609195 0.894737
29 0N2 0.602273 0.883117
30 T46 0.602273 0.918919
31 T3P 0.6 0.957143
32 DT DT DT DT DT 0.597701 0.958333
33 MMF 0.595506 0.894737
34 0FX 0.595506 0.894737
35 AKM 0.593407 0.873418
36 DT DT PST 0.58427 0.881579
37 DU 0.583333 0.956522
38 UMP 0.583333 0.956522
39 QDM 0.582418 0.883117
40 1YF 0.576087 0.906667
41 JHZ 0.576087 0.871795
42 FNF 0.576087 0.906667
43 TXS 0.575342 0.8
44 4TG 0.569892 0.906667
45 T3S 0.56 0.8
46 2DT 0.555556 0.971429
47 ATY 0.548781 0.931507
48 DDN 0.547945 0.956522
49 AZD 0.535714 0.894737
50 FUH 0.53 0.894737
51 QUH 0.53 0.894737
52 T5A 0.524272 0.829268
53 DT ME6 DT 0.509804 0.881579
54 DC 0.506494 0.890411
55 DCM 0.506494 0.890411
56 AZZ 0.5 0.789474
57 4TA 0.495327 0.817073
58 ABT 0.483516 0.871795
59 QBT 0.480519 0.915493
60 WMJ 0.477778 0.75
61 ADS THS THS THS 0.477477 0.767442
62 7SG 0.474138 0.851852
63 TQP 0.474138 0.851852
64 T4K 0.470085 0.841463
65 T5K 0.470085 0.841463
66 DUD 0.469136 0.942857
67 UMC 0.467532 0.901408
68 D3T 0.464286 0.957747
69 TPE 0.463158 0.881579
70 D4M 0.461538 0.927536
71 ID2 0.452055 0.786667
72 UC5 0.451219 0.929577
73 DUT 0.447059 0.942857
74 DUP 0.44186 0.916667
75 DUN 0.440476 0.916667
76 DT MA7 DT 0.42623 0.807229
77 8OG 0.425287 0.82716
78 BVD 0.423077 0.821918
79 74W 0.42 0.72093
80 74X 0.42 0.72093
81 5FU 0.4125 0.84
82 D4D 0.411765 0.914286
83 PAX 0.408333 0.839506
84 YYY 0.406977 0.878378
85 DA DT DA DA 0.404959 0.82716
86 BTD 0.404762 0.759494
87 DPB 0.404494 0.890411
88 5BU 0.402439 0.84
89 DUS 0.4 0.820513
90 3DT 0.4 0.821918
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3UDG; Ligand: TMP; Similar sites found with APoc: 64
This union binding pocket(no: 1) in the query (biounit: 3udg.bio2) has 7 residues
No: Leader PDB Ligand Sequence Similarity
1 1LR8 IHS None
2 6BSX E7S 1.1236
3 3FWN 6PG 1.66113
4 3FWN ATR 1.66113
5 2WK2 SN5 SN5 1.66113
6 2WK2 SN5 SN5 NGT 1.66113
7 1CTU ZEB 1.70068
8 4S28 AIR 1.99336
9 4S28 SAH 1.99336
10 3CQD ATP 1.99336
11 2X6T NAP 1.99336
12 3EPO MP5 2.32558
13 2GCG DGY 2.32558
14 1HKK NAA NAA AMI 2.65781
15 3G5N PB2 2.65781
16 2X3F APC 2.80702
17 1RYI GOA 2.87958
18 1RYI FAD 2.87958
19 1PGP 6PG 2.99003
20 2P4Q FLC 2.99003
21 3O84 HTJ 2.99003
22 4OOE FOM 2.99003
23 4OOE NDP 2.99003
24 3L6C MLI 2.99003
25 4MBY BGC SIA GAL 3.23741
26 1KQP ADJ 3.32103
27 2OZ5 7XY 3.37838
28 6CI9 NAP 3.4749
29 4XBA 5GP 3.5
30 4XDA ADP 3.65448
31 4XDA RIB 3.65448
32 2PEZ DAT 3.91061
33 2IZ1 ATR 3.98671
34 2IZ1 RES 3.98671
35 3OBT SLB 3.98671
36 3MKH FAD 4.31894
37 4A59 AMP 4.31894
38 1CSI OAA 4.31894
39 1CSI CMX 4.31894
40 1U8V FAD 4.65116
41 3FSM 2NC 4.92611
42 3K7S R52 5.02793
43 3NUG NAD 5.26316
44 1UMD TDP COI 5.31561
45 3ENV ABF 5.53191
46 4IPH 1FJ 5.69106
47 2JGV ADP 6.31229
48 3UKR CKH 6.31229
49 1V1A ADP 7.30897
50 4M1U MBG A2G 7.40741
51 4M1U A2G MBG 7.40741
52 4POS NAG SIA GAL 7.55396
53 5L4S NAP 8.30565
54 5L4S 6KX 8.30565
55 1W5F G2P 8.30565
56 5T2U NAP 8.87097
57 4X17 SIA 9.19118
58 4X17 SIA SIA 9.19118
59 2BES RES 9.30233
60 3CIP ATP 9.375
61 4CBX ATP 9.44882
62 3EVF SAH 10.1083
63 3EVF GTA 10.1083
64 3MEH THP 13.986
Pocket No.: 2; Query (leader) PDB : 3UDG; Ligand: TMP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 3udg.bio2) has 3 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 3UDG; Ligand: TMP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 3udg.bio2) has 3 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 3UDG; Ligand: TMP; Similar sites found with APoc: 126
This union binding pocket(no: 4) in the query (biounit: 3udg.bio1) has 9 residues
No: Leader PDB Ligand Sequence Similarity
1 3CR3 ADP None
2 2V1O COA 1.3245
3 1ADO 13P 1.3289
4 4EIL NDP 1.3289
5 5JPH COA 1.38889
6 1IYK MIM 1.66113
7 3FV3 IVA VAL VAL STA ALA STA 1.66113
8 4GLW NMN 1.66113
9 5AHS FAD 1.66113
10 2XVD AS6 1.66113
11 3CGB FAD 1.66113
12 2YNE YNE 1.99336
13 2YNE NHW 1.99336
14 3PP0 03Q 1.99336
15 1IZE IVA VAL VAL STA ALA STA 1.99336
16 1XV5 UDP 1.99336
17 2WSA MYA 2.32558
18 2WSA 646 2.32558
19 3EYA FAD 2.32558
20 5X8G S0N 2.32558
21 4P5Z Q7M 2.32558
22 5YIC 8VO 2.32558
23 1LLU NAD 2.32558
24 3F7Z 34O 2.32558
25 1O9J NAD 2.32558
26 3IHG FAD 2.32558
27 2QRK AMP 2.32558
28 1OVD FMN 2.32558
29 1OVD ORO 2.32558
30 3E7O 35F 2.65781
31 4UXL 5P8 2.65781
32 4ZUL UN1 2.65781
33 5KJW 53C 2.65781
34 4FG8 ATP 2.65781
35 2R09 4IP 2.65781
36 5DMZ ADP 2.65781
37 2R0D 4IP 2.65781
38 3OKP GDD 2.65781
39 1LTH NAD 2.99003
40 1UMP SQA 2.99003
41 3C3N FMN 2.99003
42 5N5S NAP 2.99003
43 6BII NAP 2.99003
44 5DBX ANP 2.99003
45 2YVK MRU 2.99003
46 1H74 ADP 3.04054
47 5LPG 71V 3.04878
48 1GS5 NLG 3.10078
49 1GS5 ANP 3.10078
50 3OII SAH 3.16206
51 1QPR PPC 3.16901
52 1T9D FAD 3.32226
53 1KGZ PRP 3.32226
54 6C1S EFV 3.32226
55 5KMS FAD 3.32226
56 3ZRM ZRM 3.32226
57 3CV3 UDP 3.32226
58 1LK7 DER 3.49345
59 2IYF UDP 3.61446
60 2YIC TPP 3.65448
61 3MJY IJZ 3.65448
62 3MJY FMN 3.65448
63 6FYV 3NG 3.65448
64 4MCC 21X 3.65854
65 2HW1 ANP 3.69128
66 4CUB GAL NAG 3.82514
67 4XXH T6P 3.92157
68 2QZX IVA VAL VAL STA ALA STA 3.98671
69 2C0U FAD NBT 3.98671
70 6C5B SAH 3.98671
71 5JFL NAD 3.98671
72 5KVM THR TYR PHE ALA VAL LEU MET VAL SER 4.21053
73 3RWP ABQ 4.31894
74 5F7R GLC GLC 4.31894
75 3ETH ATP 4.65116
76 3EBL GA4 4.65753
77 5OJL TXP 4.69799
78 3AHC TPP 4.98339
79 4REP FAD 4.98339
80 4WZH FMN 4.98339
81 5DEY 59T 5.05051
82 2BEK ATP 5.05837
83 1TU3 GNP 5.26316
84 5W4W 9WG 5.31561
85 4KBA 1QM 5.31561
86 3D9F FAD 5.31561
87 1JQ5 NAD 5.31561
88 3B82 NAD 5.64784
89 5U3B 7TD 5.68562
90 1KY8 NAP 5.98007
91 4I53 1C1 5.98007
92 6DEF GCP 5.98007
93 4ONA UW1 6.31229
94 2H6T IVA VAL VAL STA ALA STA 6.31229
95 1UKW FAD 6.31229
96 4ASE AV9 6.31229
97 4K26 SFF 6.52174
98 4JE7 BB2 6.59898
99 1FL2 FAD 6.64452
100 4HJY NAG NAG NAG 6.79612
101 1T90 NAD 6.97674
102 3AI7 TPP 6.97674
103 3EMY IVA VAL VAL STA ALA STA 6.97674
104 4YEE 4CQ 7.77778
105 2WQN ADP 7.97342
106 3PFD FDA 7.97342
107 5Y80 IRE 7.97342
108 4LRZ ADP 8.53081
109 4LFL TG6 8.72093
110 1UJ5 5RP 8.81057
111 3PE2 E1B 8.90208
112 1ZMT RNO 9.05512
113 4O1P ANP 9.30233
114 6C7Y ADP 9.40171
115 4CBU ATP 9.44882
116 4BCM T7Z 9.54198
117 5EW9 5VC 9.63455
118 4GIM PSU 9.85075
119 3AIA SAM 9.95261
120 2ZSH GA3 10
121 4CQE CQE 10.0719
122 2YFO GAL 10.6312
123 2YFO GLA 10.6312
124 4Y8D 49J 12.6246
125 1FAO 4IP 15.873
126 1S8F GDP 25.4237
Pocket No.: 5; Query (leader) PDB : 3UDG; Ligand: TMP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 5) in the query (biounit: 3udg.bio1) has 9 residues
No: Leader PDB Ligand Sequence Similarity
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