Receptor
PDB id Resolution Class Description Source Keywords
2PAR 2.1 Å EC: 3.1.3.5 CRYSTAL STRUCTURE OF THE 5'-DEOXYNUCLEOTIDASE YFBR MUTANT E7 COMPLEXED WITH CO(2+) AND TMP ESCHERICHIA COLI NUCLEOTIDASE 5-prime -DEOXYNUCLEOTIDASE YFBR HD DOMAIN PHOSPHOHHYDROLASE
Ref.: STRUCTURAL INSIGHT INTO THE MECHANISM OF SUBSTRATE SPECIFICITY AND CATALYTIC ACTIVITY OF AN HD-DOMAIN PHOSPHOHYDROLASE: THE 5'-DEOXYRIBONUCLEOTIDASE YFBR ESCHERICHIA COLI. J.MOL.BIOL. V. 378 215 2008
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CO A:201;
B:201;
Part of Protein;
Part of Protein;
none;
none;
submit data
58.933 Co [Co+2...
PEG A:401;
Invalid;
none;
submit data
106.12 C4 H10 O3 C(COC...
TMP A:301;
B:301;
Valid;
Valid;
none;
none;
submit data
322.208 C10 H15 N2 O8 P CC1=C...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2PAR 2.1 Å EC: 3.1.3.5 CRYSTAL STRUCTURE OF THE 5'-DEOXYNUCLEOTIDASE YFBR MUTANT E7 COMPLEXED WITH CO(2+) AND TMP ESCHERICHIA COLI NUCLEOTIDASE 5-prime -DEOXYNUCLEOTIDASE YFBR HD DOMAIN PHOSPHOHHYDROLASE
Ref.: STRUCTURAL INSIGHT INTO THE MECHANISM OF SUBSTRATE SPECIFICITY AND CATALYTIC ACTIVITY OF AN HD-DOMAIN PHOSPHOHYDROLASE: THE 5'-DEOXYRIBONUCLEOTIDASE YFBR ESCHERICHIA COLI. J.MOL.BIOL. V. 378 215 2008
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 9 families.
1 2PAU - D5M C10 H14 N5 O6 P c1nc(c2c(n....
2 2PAR - TMP C10 H15 N2 O8 P CC1=CN(C(=....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 9 families.
1 2PAU - D5M C10 H14 N5 O6 P c1nc(c2c(n....
2 2PAR - TMP C10 H15 N2 O8 P CC1=CN(C(=....
50% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 8 families.
1 2PAU - D5M C10 H14 N5 O6 P c1nc(c2c(n....
2 2PAR - TMP C10 H15 N2 O8 P CC1=CN(C(=....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: TMP; Similar ligands found: 92
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 5HU 0.705882 0.957747
7 BRU 0.705882 0.917808
8 5IU 0.695652 0.917808
9 THM 0.693548 0.859155
10 LLT 0.693548 0.859155
11 NYM 0.671429 0.971831
12 FDM 0.671429 0.931507
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 18T 0.623529 0.918919
20 1JB 0.623529 0.918919
21 TRH 0.623529 0.918919
22 3R2 0.623529 0.906667
23 TDX 0.623529 0.931507
24 DWN 0.609195 0.894737
25 T3Q 0.609195 0.894737
26 3YN 0.609195 0.918919
27 T3F 0.609195 0.894737
28 T46 0.602273 0.918919
29 0N2 0.602273 0.883117
30 T3P 0.6 0.957143
31 DT DT DT DT DT 0.597701 0.958333
32 MMF 0.595506 0.894737
33 0FX 0.595506 0.894737
34 AKM 0.593407 0.873418
35 UMP 0.583333 0.956522
36 DU 0.583333 0.956522
37 QDM 0.582418 0.883117
38 DT DT PST 0.577778 0.893333
39 FNF 0.576087 0.906667
40 JHZ 0.576087 0.871795
41 1YF 0.576087 0.906667
42 TXS 0.575342 0.8
43 4TG 0.569892 0.906667
44 T3S 0.56 0.8
45 2DT 0.555556 0.971429
46 ATY 0.548781 0.931507
47 DDN 0.547945 0.956522
48 AZD 0.535714 0.894737
49 FUH 0.53 0.894737
50 QUH 0.53 0.894737
51 T5A 0.524272 0.829268
52 DT DT DT 0.52381 0.890411
53 DT ME6 DT 0.509804 0.881579
54 DCM 0.506494 0.890411
55 DC 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 7SG 0.474138 0.851852
62 TQP 0.474138 0.851852
63 T4K 0.470085 0.841463
64 T5K 0.470085 0.841463
65 DUD 0.469136 0.942857
66 UMC 0.467532 0.901408
67 D3T 0.464286 0.957747
68 TPE 0.463158 0.881579
69 D4M 0.461538 0.927536
70 ID2 0.452055 0.786667
71 UC5 0.451219 0.929577
72 DUT 0.447059 0.942857
73 DUP 0.44186 0.916667
74 DUN 0.440476 0.916667
75 ADS THS THS THS 0.433628 0.776471
76 DT MA7 DT 0.42623 0.807229
77 8OG 0.425287 0.82716
78 BVD 0.423077 0.821918
79 74X 0.42 0.72093
80 74W 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 DUT MG 0.404494 0.876712
89 5BU 0.402439 0.84
90 3DT 0.4 0.821918
91 DUS 0.4 0.820513
92 UMP AF3 PO4 0.4 0.842105
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2PAR; Ligand: TMP; Similar sites found: 129
This union binding pocket(no: 1) in the query (biounit: 2par.bio2) has 24 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3S9K CIT 0.002368 0.5361 None
2 1SS4 GSH 0.004218 0.50816 None
3 4PNO U5P 0.00006353 0.50218 None
4 3GD8 BOG 0.001908 0.49003 None
5 1JOT GAL A2G 0.001039 0.46303 None
6 4Q3F TLA 0.004522 0.45694 None
7 5A2J ALA PRO ASP THR ARG PRO 0.01175 0.45223 None
8 1GXU 2HP 0.0002939 0.44713 None
9 3QDV A2G 0.01765 0.44619 None
10 1JAC AMG 0.04601 0.42978 None
11 3QDY A2G GAL 0.02747 0.42945 None
12 3QDX A2G GAL 0.02802 0.429 None
13 3QDW A2G 0.03689 0.42864 None
14 3WCS MAN NAG 0.01123 0.42743 None
15 4AF5 CIT 0.02627 0.41964 None
16 3CXQ GLP 0.02654 0.41467 None
17 1NF8 BOG 0.04701 0.4119 None
18 2CCV A2G 0.00224 0.4067 None
19 1Q3P GLU ALA GLN THR ARG LEU 0.03129 0.40297 None
20 2Q37 3AL 0.01396 0.4279 1.10497
21 1MJJ HAL 0.03472 0.4091 1.49254
22 1UFY MLI 0.04787 0.40676 1.63934
23 5T63 ALA ALA ALA ALA 0.00237 0.41529 1.99005
24 1F5F DHT 0.01012 0.40542 1.99005
25 4AP9 1PS 0.008721 0.40136 1.99005
26 1WKL ATP 0.01003 0.40225 2.18978
27 1DUC DUD 0.006949 0.40342 2.23881
28 5D6C 57S 0.005654 0.47721 2.48756
29 1IZC PYR 0.0003338 0.44519 2.48756
30 2QF7 COA 0.007389 0.41811 2.48756
31 1YXM ADE 0.04988 0.41129 2.48756
32 1T10 F6P 0.03424 0.40939 2.48756
33 1BTN I3P 0.0137 0.46965 2.83019
34 1C1L GAL BGC 0.01443 0.43801 2.91971
35 1W55 GPP 0.00001071 0.53362 2.98507
36 4N69 SER 0.007346 0.44669 2.98507
37 2YD6 FLC 0.049 0.43938 2.98507
38 3FN0 TRP ASN TRP PHE ASP ILE THR ASN LYS 0.01547 0.43091 2.98507
39 1FX8 BOG 0.004394 0.41946 2.98507
40 2QCX PF1 0.04535 0.40354 2.98507
41 1C3M MAN MAN 0.003527 0.4312 3.40136
42 1G0V NAG 0.004349 0.51019 3.48259
43 1LTH FBP 0.001271 0.48372 3.48259
44 1Y0L HAN 0.01043 0.46656 3.48259
45 3L24 GOA 0.0127 0.45397 3.48259
46 1XX4 BAM 0.00349 0.4534 3.48259
47 3VCA PRO 0.005706 0.4435 3.48259
48 2ZWS PLM 0.04302 0.43884 3.48259
49 4COQ SAN 0.0185 0.42711 3.48259
50 2NT8 ATP 0.0005639 0.4167 3.48259
51 2YP9 SIA CMO 0.008564 0.40997 3.48259
52 1TV5 ORO 0.009345 0.40848 3.48259
53 1YBH P22 0.02358 0.40458 3.48259
54 3I8T LBT 0.01649 0.41978 3.65854
55 3PHQ KDO 0.004056 0.50969 3.9801
56 4LO6 SIA GAL 0.00536 0.46309 3.9801
57 5DS8 GLY 5CT GLY ALA 0.00788 0.4579 3.9801
58 3MAG 3MA 0.01527 0.45716 3.9801
59 3IHB TRS 0.0103 0.45111 3.9801
60 1JN2 SFP 0.001264 0.44935 3.9801
61 1DXY COI 0.0001333 0.44694 3.9801
62 3IHB GLU 0.01433 0.43816 3.9801
63 5DTF 5CT 0.02326 0.43637 3.9801
64 2W8Q SIN 0.01651 0.43505 3.9801
65 3CBG FER 0.02931 0.43413 3.9801
66 5DUB GLY 5GG GLY ALA 0.03096 0.42969 3.9801
67 2VMD MBG 0.04232 0.42535 3.9801
68 2X0K PPV 0.04424 0.40199 3.9801
69 3PAK MAN 0.006255 0.41533 4.05405
70 3NOJ PYR 0.004049 0.45041 4.47761
71 4M5P MLA 0.02195 0.4482 4.47761
72 2V9M CIT 0.002309 0.44812 4.47761
73 2PNZ 5GP 0.004042 0.44251 4.47761
74 2EFJ 37T 0.01566 0.42081 4.47761
75 3M6W SAM 0.0114 0.40681 4.47761
76 2V5E SCR 0.007923 0.47331 4.5
77 2NVK NAP 0.02241 0.41366 4.97512
78 1QO0 BMD 0.01656 0.42946 5.10204
79 1NU4 MLA 0.02974 0.40396 5.15464
80 1GPJ CIT 0.03019 0.41667 5.44554
81 4ODV GP1 Z9M 0.0007666 0.54248 5.47264
82 3VPD BUA 0.03247 0.44842 5.47264
83 3VPD CIT 0.03758 0.43485 5.47264
84 1Q72 COC 0.01328 0.42409 5.47264
85 1RYD GLC 0.03069 0.41632 5.47264
86 4GCS 1RG 0.00433 0.40156 5.47264
87 3EYK EYK 0.0003564 0.51051 5.81395
88 2HVK TBA 0.0000543 0.55016 5.97015
89 1LDM OXM 0.005001 0.43368 5.97015
90 5DRN 5CT 0.00129 0.51268 6.46766
91 2FGQ MLT 0.004791 0.45572 6.46766
92 5DSC GLY 5CT GLY SER GLY 0.01811 0.43022 6.46766
93 2DWU DGL 0.03468 0.40096 6.46766
94 2XI7 XI7 0.0003243 0.56451 6.52174
95 4EXO PYR 0.04149 0.41997 6.84932
96 2NZ2 ASP 0.0005863 0.48592 6.96517
97 1O9U ADZ 0.01347 0.45258 6.96517
98 2V5K OXM 0.002953 0.44113 6.96517
99 4M7F BM3 0.01169 0.42662 6.96517
100 1NPL MAN 0.0007674 0.43249 7.33945
101 3OAZ 2M5 0.005382 0.48751 7.46269
102 1H6H PIB 0.008947 0.45606 7.69231
103 3K3G MMU 0.03268 0.40819 7.9602
104 2GN2 C5P 0.0095 0.40648 8.18713
105 2WMO GTP 0.01906 0.40126 8.42105
106 3B9Z CO2 0.03474 0.41366 8.45771
107 3JQ3 ADP 0.0175 0.4102 8.45771
108 1U5V ATP 0.003853 0.51177 8.95522
109 1Z6K OAA 0.009043 0.42048 8.95522
110 1V5F FAD 0.002743 0.41081 8.95522
111 1V5F TPP 0.002743 0.41081 8.95522
112 2OFD NGA 0.02526 0.42047 9.85915
113 4DN8 BMA 0.001046 0.48783 10.2564
114 1NXJ TLA 0.002391 0.4317 10.3825
115 1NXJ GLV 0.015 0.41724 10.3825
116 4JCA CIT 0.04061 0.4329 10.7784
117 3IB9 BTN 0.0004097 0.5202 10.9453
118 4RJK PYR 0.005554 0.49173 10.9453
119 1RYI GOA 0.0396 0.4458 10.9453
120 3LTW HLZ 0.03503 0.41348 10.9453
121 3EJ0 11X 0.001781 0.40997 11.7347
122 1OGZ EQU 0.02127 0.40281 12
123 4CIB 7UZ 0.003003 0.45936 12.4378
124 4NTX AMR 0.04439 0.40191 13.4454
125 1NME 159 0.01081 0.41136 14.1304
126 4K7O EKZ 0.004169 0.46519 14.2857
127 1Q11 TYE 0.02544 0.41111 14.9254
128 1UUY PPI 0.001885 0.49891 15.5689
129 3KPE TM3 0.009822 0.44054 28.2051
Pocket No.: 2; Query (leader) PDB : 2PAR; Ligand: TMP; 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: 2par.bio2) has 16 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 2PAR; Ligand: TMP; Similar sites found: 3
This union binding pocket(no: 3) in the query (biounit: 2par.bio1) has 24 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1HFA PIO 0.02606 0.44336 4.97512
2 1YOA FMN 0.01758 0.42057 5.03145
3 5URY PAM 0.0266 0.42108 13.0137
Pocket No.: 4; Query (leader) PDB : 2PAR; Ligand: TMP; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 2par.bio1) has 16 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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