Receptor
PDB id Resolution Class Description Source Keywords
1A2U 2 Å EC: 3.1.31.1 STAPHYLOCOCCAL NUCLEASE, V23C VARIANT, COMPLEX WITH 1-N- BUTANE THIOL AND 3',5'-THYMIDINE DIPHOSPHATE STAPHYLOCOCCUS AUREUS NUCLEASE UNNATURAL AMINO ACID HYDROLASE ENDONUCLEASE
Ref.: MOBILE UNNATURAL AMINO ACID SIDE CHAINS IN THE CORE OF STAPHYLOCOCCAL NUCLEASE. PROTEIN SCI. V. 5 1026 1996
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CA A:150;
Part of Protein;
none;
submit data
40.078 Ca [Ca+2...
THP A:151;
Valid;
none;
submit data
402.188 C10 H16 N2 O11 P2 CC1=C...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3MEH 1.5 Å EC: 3.1.31.1 CRYSTAL STRUCTURE OF STAPHYLOCOCCAL NUCLEASE VARIANT DELTA+P CRYOGENIC TEMPERATURE STAPHYLOCOCCUS AUREUS HYPERSTABLE VARIANT HYDROLASE PDTP CAVITY PRESSURE
Ref.: CAVITIES DETERMINE THE PRESSURE UNFOLDING OF PROTEI PROC.NATL.ACAD.SCI.USA V. 109 6945 2012
Members (43)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 5NUC - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
2 1A3U - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
3 4WOR - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
4 1STH - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
5 1ENC - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
6 3NQT - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
7 3MZ5 - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
8 1STA - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
9 3PMF - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
10 1STY - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
11 3MEH - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
12 1A3T - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
13 2SNM - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
14 3MHB - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
15 1STB - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
16 1SYF - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
17 1TR5 - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
18 3D8G - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
19 2ENB - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
20 1A2U - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
21 3R3O - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
22 1SNC - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
23 3BDC - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
24 1NUC - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
25 1TT2 - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
26 3MXP - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
27 3NUC - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
28 3NXW - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
29 1SNM - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
30 1A2T - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
31 1STG - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
32 1AEX - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
33 1SYB - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
34 3NP8 - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
35 2NUC - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
36 3D6C - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
37 2OXP - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
38 3DHQ - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
39 1SYD - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
40 3MVV - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
41 3NK9 - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
42 1A3V - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
43 3OSO - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
70% Homology Family (43)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 5NUC - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
2 1A3U - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
3 4WOR - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
4 1STH - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
5 1ENC - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
6 3NQT - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
7 3MZ5 - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
8 1STA - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
9 3PMF - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
10 1STY - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
11 3MEH - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
12 1A3T - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
13 2SNM - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
14 3MHB - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
15 1STB - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
16 1SYF - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
17 1TR5 - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
18 3D8G - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
19 2ENB - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
20 1A2U - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
21 3R3O - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
22 1SNC - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
23 3BDC - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
24 1NUC - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
25 1TT2 - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
26 3MXP - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
27 3NUC - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
28 3NXW - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
29 1SNM - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
30 1A2T - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
31 1STG - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
32 1AEX - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
33 1SYB - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
34 3NP8 - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
35 2NUC - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
36 3D6C - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
37 2OXP - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
38 3DHQ - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
39 1SYD - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
40 3MVV - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
41 3NK9 - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
42 1A3V - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
43 3OSO - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
50% Homology Family (43)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 5NUC - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
2 1A3U - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
3 4WOR - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
4 1STH - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
5 1ENC - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
6 3NQT - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
7 3MZ5 - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
8 1STA - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
9 3PMF - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
10 1STY - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
11 3MEH - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
12 1A3T - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
13 2SNM - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
14 3MHB - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
15 1STB - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
16 1SYF - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
17 1TR5 - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
18 3D8G - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
19 2ENB - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
20 1A2U - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
21 3R3O - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
22 1SNC - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
23 3BDC - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
24 1NUC - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
25 1TT2 - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
26 3MXP - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
27 3NUC - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
28 3NXW - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
29 1SNM - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
30 1A2T - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
31 1STG - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
32 1AEX - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
33 1SYB - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
34 3NP8 - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
35 2NUC - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
36 3D6C - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
37 2OXP - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
38 3DHQ - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
39 1SYD - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
40 3MVV - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
41 3NK9 - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
42 1A3V - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
43 3OSO - THP C10 H16 N2 O11 P2 CC1=CN(C(=....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: THP; Similar ligands found: 56
No: Ligand ECFP6 Tc MDL keys Tc
1 THP 1 1
2 T3P 0.753846 0.971014
3 TMP 0.661972 0.985507
4 FDM 0.652778 0.944444
5 NYM 0.652778 0.957747
6 DT DT DT 0.64557 0.902778
7 ATM 0.602564 0.918919
8 ATY 0.592593 0.944444
9 TYD 0.556962 0.971429
10 DT DT DT DT DT 0.549451 0.944444
11 2DT 0.540541 0.985507
12 DT DT PST 0.531915 0.88
13 TTP 0.53012 0.971429
14 THM 0.528571 0.84507
15 LLT 0.528571 0.84507
16 TBD 0.506024 0.931507
17 AZD 0.505747 0.906667
18 DC DC DT DG 0.505155 0.864865
19 TPE 0.5 0.893333
20 PAX 0.5 0.85
21 0DN 0.493151 0.830986
22 TRH 0.473684 0.905405
23 1JB 0.473684 0.905405
24 18T 0.473684 0.905405
25 ABT 0.473118 0.883117
26 DT ME6 DT 0.471698 0.868421
27 DAU 0.46875 0.905405
28 AZZ 0.468354 0.8
29 T3F 0.463918 0.881579
30 T3Q 0.463918 0.881579
31 UFP 0.4625 0.90411
32 TLO 0.462366 0.917808
33 0N2 0.459184 0.87013
34 TDX 0.458333 0.917808
35 5HU 0.45679 0.943662
36 BRU 0.45679 0.90411
37 MMF 0.454545 0.881579
38 5IU 0.451219 0.90411
39 D4M 0.45 0.941176
40 DWN 0.44898 0.881579
41 QDM 0.445545 0.87013
42 T46 0.444444 0.905405
43 TXS 0.444444 0.786667
44 DT DC 0.443396 0.855263
45 AKM 0.441176 0.860759
46 1YF 0.441176 0.893333
47 FNF 0.441176 0.893333
48 0FX 0.44 0.881579
49 D3T 0.436782 0.971429
50 T3S 0.433735 0.786667
51 DA DT DA DA 0.433333 0.814815
52 UM3 0.43038 0.927536
53 JHZ 0.427184 0.858974
54 DG DT DC 0.425 0.77907
55 4TG 0.423077 0.893333
56 BVP 0.420455 0.943662
Similar Binding Sites
Pocket no: 1; Query (leader) PDB : 3MEH; Ligand: THP; Similar sites found: 111
This union binding pocket (no: 1) in the query (biounit: 3meh.bio1) has 15 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc)
1 3MEH THP 5.218e-15 1
2 2BW7 APC 0.007377 0.45983
3 3ZW2 GLA 0.013 0.4325
4 4CSD MFU 0.03445 0.43063
5 3LQ8 88Z 0.02208 0.42997
6 3ZW2 GAL 0.0229 0.41927
7 4NW6 2NS 0.01924 0.4185
8 4HP0 NOJ 0.04798 0.41785
9 3BZF VAL 0.02639 0.41704
10 1H0H MGD 0.02297 0.41688
11 3PDQ KC6 0.03599 0.41465
12 3SXF BK5 0.0262 0.41261
13 3W6C NAG 0.02655 0.41105
14 3FPF MTA 0.03866 0.41104
15 4JZU GCP 0.01741 0.4086
16 3NXD BGC 0.003468 0.40789
17 4PJT 2YQ 0.03209 0.40666
18 4B7X NAP 0.0335 0.40439
19 4AG8 AXI 0.04702 0.4001
20 4H1M 0YJ 0.04841 0.39826
21 1N71 COA 0.03061 0.3977
22 3QKD HI0 0.04478 0.39765
23 4NJH 2K8 0.04814 0.3972
24 2BRY FAD 0.04569 0.39718
25 2TPS TPS 0.0423 0.39634
26 3IGO ANP 0.031 0.39573
27 4JQE ANP 0.02011 0.39521
28 4DRX GTP 0.03491 0.39474
29 1E5Q NDP 0.04751 0.39366
30 4IPH 1FJ 0.04046 0.393
31 2HKJ RDC 0.04055 0.39294
32 3FEI CTM 0.03562 0.39261
33 3Q60 ATP 0.02335 0.39199
34 4FG8 ATP 0.03678 0.39189
35 4GAH 0ET 0.03516 0.39115
36 3A8W ATP 0.03031 0.39062
37 2OYL IDC 0.04327 0.38989
38 4FL3 ANP 0.04343 0.38815
39 3KYG 5GP 0.04356 0.38808
40 4K4D HFQ 0.04235 0.38699
41 2ZQO NGA 0.03685 0.38632
42 4MJ0 BGC 0.003655 0.38577
43 4K39 SAM 0.04208 0.3853
44 1QPR PPC 0.04588 0.38519
45 2NSX IFM 0.04321 0.38471
46 4MJ0 SIA 0.004133 0.38381
47 4K37 SAM 0.04148 0.3837
48 1UOZ GLC 0.04754 0.38258
49 3D1R FBP 0.02061 0.38231
50 4L4J NAG 0.01471 0.38052
51 4MJ0 SIA 0.005496 0.37934
52 1Y2F WAI 0.03409 0.37896
53 3UKR CKH 0.03475 0.37855
54 1WOQ BGC 0.02756 0.37597
55 3PHZ NAG 0.01953 0.37528
56 3NBC LAT 0.01933 0.37521
57 1VPD TLA 0.003611 0.37521
58 4J6W C 0.02118 0.37323
59 4CC5 L5V 0.04851 0.37138
60 4BS0 6NT 0.02442 0.371
61 4JKV 1KS 0.0417 0.36913
62 3ZW0 FUC 0.01003 0.36905
63 3DGY 2GP 0.04093 0.36828
64 1SZ2 BGC 0.04189 0.36764
65 1Y7P RIP 0.01231 0.36658
66 1I1E DM2 0.03162 0.36607
67 4C6H HE2 0.003551 0.36498
68 4LO2 GAL 0.004501 0.36195
69 1NJJ GET 0.004786 0.36158
70 1Z0N BCD 0.00973 0.36136
71 4LH7 1X8 0.02659 0.36061
72 2OEM 1AE 0.0444 0.35997
73 1ONI BEZ 0.04382 0.35952
74 4BBE 3O4 0.0471 0.35887
75 2O2U 738 0.03166 0.35762
76 2R5A MLZ 0.006896 0.35688
77 1UNQ 4IP 0.0354 0.35677
78 4OUJ LBT 0.01279 0.35665
79 3HUN ZZ7 0.03908 0.35439
80 1D6Z HY1 0.02581 0.35378
81 1JC9 NAG 0.0162 0.3537
82 1NA0 IPT 0.009452 0.35281
83 4DSU BZI 0.04276 0.35262
84 4GLW 0XT 0.02995 0.35153
85 4L80 OXL 0.03213 0.35084
86 4CQK PIO 0.03177 0.35048
87 3KV4 OGA 0.03694 0.34905
88 3UPY FOM 0.0353 0.34895
89 3KV5 OGA 0.01326 0.3486
90 3AJ4 SEP 0.01425 0.3483
91 2RHI THR 0.007304 0.34797
92 1B09 PC 0.02687 0.34633
93 1ULM NAG 0.008251 0.34628
94 1WB4 SXX 0.04331 0.34538
95 2ORZ LYS 0.04589 0.34491
96 1WMZ NGA 0.03133 0.34427
97 1WMZ A2G 0.03327 0.34347
98 4CZ1 VNJ 0.006917 0.34125
99 1NX9 AIC 0.02494 0.34011
100 2J5B TYE 0.02943 0.33915
101 4CCW VKC 0.02789 0.33891
102 1JPA ANP 0.01613 0.33866
103 1P7T PYR 0.04412 0.33833
104 4N2R AHR 0.04491 0.33823
105 4JYM KKN 0.0483 0.3377
106 1A78 TDG 0.0313 0.33737
107 4FMJ SIA 0.02173 0.33615
108 2ZL7 FUC 0.03884 0.33482
109 4FMJ SIA 0.02511 0.33459
110 3F70 MLZ 0.02883 0.33261
111 3I7S PYR 0.04944 0.32683
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