Receptor
PDB id Resolution Class Description Source Keywords
3NBK 1.58 Å EC: 2.7.7.3 PHOSPHOPANTETHEINE ADENYLYLTRANSFERASE FROM MYCOBACTERIUM TU IN COMPLEX WITH 4'-PHOSPHOPANTETHEINE MYCOBACTERIUM TUBERCULOSIS PPAT PHP PANTETHEINE TUBERCULOSIS PHOSPHOPANTETHEINE ADENYLYLTRANSFERASE TRANSFERASE
Ref.: KINETIC, THERMODYNAMIC, AND STRUCTURAL INSIGHT INTO MECHANISM OF PHOSPHOPANTETHEINE ADENYLYLTRANSFERASE MYCOBACTERIUM TUBERCULOSIS. J.MOL.BIOL. V. 404 202 2010
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
NI A:162;
C:162;
Part of Protein;
Part of Protein;
none;
none;
submit data
58.693 Ni [Ni+2...
PNS A:200;
B:200;
C:200;
D:200;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
submit data
358.348 C11 H23 N2 O7 P S CC(C)...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3NBK 1.58 Å EC: 2.7.7.3 PHOSPHOPANTETHEINE ADENYLYLTRANSFERASE FROM MYCOBACTERIUM TU IN COMPLEX WITH 4'-PHOSPHOPANTETHEINE MYCOBACTERIUM TUBERCULOSIS PPAT PHP PANTETHEINE TUBERCULOSIS PHOSPHOPANTETHEINE ADENYLYLTRANSFERASE TRANSFERASE
Ref.: KINETIC, THERMODYNAMIC, AND STRUCTURAL INSIGHT INTO MECHANISM OF PHOSPHOPANTETHEINE ADENYLYLTRANSFERASE MYCOBACTERIUM TUBERCULOSIS. J.MOL.BIOL. V. 404 202 2010
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 11 families.
1 3PNB - COA C21 H36 N7 O16 P3 S CC(C)(CO[P....
2 3NBK - PNS C11 H23 N2 O7 P S CC(C)(COP(....
70% Homology Family (15)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 7 families.
1 3UC5 - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
2 3PNB - COA C21 H36 N7 O16 P3 S CC(C)(CO[P....
3 3NBK - PNS C11 H23 N2 O7 P S CC(C)(COP(....
4 1OD6 - PNS C11 H23 N2 O7 P S CC(C)(COP(....
5 5O0A Kd = 0.58 mM 9FH C11 H10 N2 O2 Cc1c(cnn1c....
6 5O0D - 9F5 C14 H12 O4 c1ccc(cc1)....
7 5O0F - IOP C11 H11 N O2 c1ccc2c(c1....
8 5O08 - COD C21 H35 N7 O13 P2 S CC(C)(CO[P....
9 5O0C - 9F8 C12 H13 N O2 Cc1cn(c2c1....
10 5O0B Kd = 66 uM 9FE C8 H5 Br N2 O2 c1cc2c(cc1....
11 5O0H - 9FN C14 H8 Cl N O5 c1ccc(c(c1....
12 1H1T - PNS C11 H23 N2 O7 P S CC(C)(COP(....
13 1GN8 - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
14 1QJC - PNS C11 H23 N2 O7 P S CC(C)(COP(....
15 3X1J Ki = 8.4 uM ACO C23 H38 N7 O17 P3 S CC(=O)SCCN....
50% Homology Family (28)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 3ND7 - PNY C11 H22 N2 O4 S CC(C)(CO)[....
2 3ND6 - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
3 3UC5 - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
4 3PNB - COA C21 H36 N7 O16 P3 S CC(C)(CO[P....
5 3NBK - PNS C11 H23 N2 O7 P S CC(C)(COP(....
6 1OD6 - PNS C11 H23 N2 O7 P S CC(C)(COP(....
7 5O0A Kd = 0.58 mM 9FH C11 H10 N2 O2 Cc1c(cnn1c....
8 5O0D - 9F5 C14 H12 O4 c1ccc(cc1)....
9 5O0F - IOP C11 H11 N O2 c1ccc2c(c1....
10 5O08 - COD C21 H35 N7 O13 P2 S CC(C)(CO[P....
11 5O0C - 9F8 C12 H13 N O2 Cc1cn(c2c1....
12 5O0B Kd = 66 uM 9FE C8 H5 Br N2 O2 c1cc2c(cc1....
13 5O0H - 9FN C14 H8 Cl N O5 c1ccc(c(c1....
14 3K9W - ADE C5 H5 N5 c1[nH]c2c(....
15 3PXU - COD C21 H35 N7 O13 P2 S CC(C)(CO[P....
16 1O6B - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
17 1H1T - PNS C11 H23 N2 O7 P S CC(C)(COP(....
18 1GN8 - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
19 1B6T - COD C21 H35 N7 O13 P2 S CC(C)(CO[P....
20 1QJC - PNS C11 H23 N2 O7 P S CC(C)(COP(....
21 4NAU - 2W3 C25 H26 Cl2 N6 O4 CCc1cc(nc(....
22 4NAH - 2VJ C24 H25 Cl2 N5 O3 S CCc1cc(nc(....
23 3F3M - PPS C10 H15 N5 O13 P2 S c1nc(c2c(n....
24 4NAT - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
25 4RUK - COA C21 H36 N7 O16 P3 S CC(C)(CO[P....
26 3X1J Ki = 8.4 uM ACO C23 H38 N7 O17 P3 S CC(=O)SCCN....
27 3X1M Ki = 6.5 uM COA C21 H36 N7 O16 P3 S CC(C)(CO[P....
28 1VLH - PNS C11 H23 N2 O7 P S CC(C)(COP(....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: PNS; Similar ligands found: 17
No: Ligand ECFP6 Tc MDL keys Tc
1 PNS 1 1
2 4PS 0.783333 1
3 PAZ 0.666667 0.881356
4 H2V 0.656716 0.966667
5 N7E 0.656716 0.904762
6 PSR 0.647059 0.966667
7 PNY 0.631579 0.827586
8 SH3 0.576923 0.791667
9 OPI 0.492537 0.8
10 3B2 0.463158 0.783784
11 168 0.452055 0.786885
12 S2N 0.433333 0.890625
13 COD 0.429907 0.670588
14 PN4 0.426471 0.770492
15 COA 0.419643 0.682353
16 ENW 0.410959 0.786885
17 ENV 0.402778 0.783333
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3NBK; Ligand: PNS; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 3nbk.bio2) has 20 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 3NBK; Ligand: PNS; Similar sites found: 94
This union binding pocket(no: 2) in the query (biounit: 3nbk.bio2) has 21 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1UO4 PIH 0.001833 0.49519 None
2 2BZ1 TAU 0.007629 0.47071 None
3 1XX4 BAM 0.001259 0.45956 None
4 1NU4 MLA 0.01171 0.45118 None
5 1H8G CHT 0.01713 0.45053 None
6 1UO5 PIH 0.02641 0.43969 None
7 3KO0 TFP 0.01447 0.41992 None
8 4DN8 BMA 0.01567 0.41835 None
9 1UUY PPI 0.02037 0.41054 None
10 1RL4 BL5 0.03478 0.41664 1.12994
11 1JN2 SFP 0.009243 0.44492 1.69492
12 1E4E ADP 0.004803 0.40111 1.69492
13 1QZZ SAM 0.005203 0.41114 2.25989
14 1RZM E4P 0.04165 0.4031 2.25989
15 3CXQ GLP 0.0031 0.44511 2.71739
16 3QDT A2G GAL 0.01552 0.43021 2.7972
17 3QDY A2G GAL 0.01664 0.42867 2.7972
18 3QDY CBS 0.04069 0.4036 2.7972
19 2YP9 SIA CMO 0.00416 0.40891 2.82486
20 1YHM AHD 0.02215 0.4064 2.82486
21 2F2U M77 0.003409 0.42732 3.38983
22 1LTH NAD 0.0008092 0.42062 3.38983
23 3H86 AP5 0.001236 0.4104 3.38983
24 1A5Z OXM 0.03883 0.40996 3.38983
25 3FSY SCA 0.0005066 0.40668 3.38983
26 2ZO9 MLI 0.0124 0.40217 3.38983
27 3BY8 MLT 0.02385 0.415 3.52113
28 3MAG 3MA 0.005461 0.46931 3.9548
29 1X1T NAD 0.002411 0.41248 3.9548
30 1TV5 N8E 0.0002117 0.44973 4.51977
31 3BHO B4P 0.02488 0.43319 4.51977
32 5DRN 5CT 0.0288 0.42612 4.51977
33 1MVN PCO 0.001869 0.40725 4.51977
34 1MVN FMN 0.000671 0.40494 4.51977
35 4F8L GAL 0.02283 0.44334 4.82759
36 2W3L DRO 0.03478 0.41841 4.86111
37 3VHZ L2P GLC MAN SGA 0.004642 0.40107 5.08475
38 2WGC SIA GAL BGC 0.03712 0.43111 5.26316
39 4LKK SIA GAL 0.0005142 0.43591 5.64972
40 3AQT RCO 0.01723 0.41666 5.64972
41 2Q1A 2KT 0.01743 0.41618 5.64972
42 3O2K DST 0.02212 0.4019 5.64972
43 4QGE 35O 0.000001724 0.50473 6.21469
44 2Q8H TF4 0.01066 0.44551 6.21469
45 1H16 PYR 0.008775 0.4427 6.21469
46 1H0C AOA 0.01462 0.42537 6.21469
47 3FS8 ACO 0.001907 0.42173 6.21469
48 2NZ2 ASP 0.009866 0.41734 6.21469
49 1YOA FMN 0.01441 0.45486 6.28931
50 3NOJ PYR 0.001229 0.46002 6.30252
51 2OFE NAG 0.03476 0.40201 6.33803
52 4IAE 1DX 0.0005968 0.41746 6.34921
53 4WBD CIT 0.00969 0.44053 6.77966
54 3EYK EYK 0.02488 0.42545 6.77966
55 1A8S PPI 0.00376 0.42323 6.77966
56 1F8F NAD 0.0005752 0.42198 6.77966
57 2BO4 FLC 0.01743 0.42165 6.77966
58 1Z44 NPO 0.03202 0.43484 7.10059
59 1RYI GOA 0.01749 0.45088 7.34463
60 3ZPG 5GP 0.02206 0.42888 7.34463
61 1T0S BML 0.01943 0.42526 7.34463
62 1JH7 UVC 0.02354 0.40519 7.34463
63 1M48 FRG 0.02525 0.40031 7.5188
64 1TFZ 869 0.0006239 0.42867 8.47458
65 3N7S 3N7 0.005991 0.44496 9.375
66 4RJK PYR 0.006038 0.47652 9.60452
67 3O01 DXC 0.00001612 0.59425 10.1695
68 3F8C HT1 0.01071 0.42075 10.3175
69 1ULE GLA GAL NAG 0.0367 0.41121 10.6667
70 1WVC CTP 0.003524 0.41287 10.7345
71 2VWA PTY 0.02219 0.41327 10.8911
72 1ECM TSA 0.01898 0.40055 11.0092
73 1O9U ADZ 0.003835 0.46877 11.2994
74 1V5F TPP 0.001965 0.44136 11.2994
75 1V5F FAD 0.001965 0.44136 11.2994
76 1Y7P RIP 0.03891 0.40991 11.2994
77 2YIV YIV 0.0176 0.42744 11.8644
78 2HVK TBA 0.01663 0.41714 11.8644
79 1H6W SER LEU ASN TYR ILE ILE LYS VAL LYS GLU 0.001004 0.41054 11.8644
80 3P3N AKG 0.009185 0.42924 12.4294
81 3KPE TM3 0.003218 0.45056 12.8205
82 4M51 BEZ 0.01722 0.42792 12.9944
83 1SS4 GSH 0.0131 0.46016 14.3791
84 3K3G MMU 0.00458 0.43465 15.8192
85 4OZJ ADP 0.0005527 0.40198 16.0839
86 3VCA PRO 0.0001014 0.50813 16.3842
87 2PP3 LGT 0.0005392 0.40702 16.3842
88 1SQ5 PAU 0.02384 0.40047 16.3842
89 2WCI GSH 0.007151 0.42869 17.037
90 4CO3 ATP 0.0008194 0.40578 18.75
91 1KQN NAD 0.001567 0.44791 19.774
92 4OYA 1VE 0.01102 0.40194 20.339
93 4M5P MLA 0.04207 0.42055 22.5989
94 4M5P 23W 0.04171 0.40837 22.5989
Pocket No.: 3; Query (leader) PDB : 3NBK; Ligand: PNS; Similar sites found: 63
This union binding pocket(no: 3) in the query (biounit: 3nbk.bio1) has 22 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1BTN I3P 0.01837 0.45347 None
2 2QLX RM4 0.02986 0.41191 None
3 3NGU ADP 0.005371 0.4125 1.98676
4 1RZM PEP 0.00838 0.4223 2.25989
5 4CCO OGA 0.01693 0.4088 2.25989
6 1ZZ7 S0H 0.02648 0.40017 2.25989
7 4EXO PYR 0.04293 0.40937 2.73973
8 2GJ3 FAD 0.003219 0.40722 2.82486
9 2C5S AMP 0.01978 0.40153 2.82486
10 4COQ SAN 0.04011 0.40071 2.82486
11 1FX8 BOG 0.002998 0.41421 3.38983
12 2R5T ANP 0.001811 0.41087 3.38983
13 4C2G ALA ALA ALA ALA 0.01694 0.40442 3.38983
14 2Y6P CTP 0.01436 0.40334 3.38983
15 2NLI LAC 0.001365 0.40298 3.38983
16 2NLI FMN 0.001365 0.40298 3.38983
17 4B9E FAH 0.0469 0.4022 3.38983
18 4FR3 0V4 0.003744 0.40212 3.38983
19 1RP0 AHZ 0.003789 0.40133 3.38983
20 2ZJ5 ADP 0.004977 0.43772 3.9548
21 4WVH ASP HIS ASP ALA HIS ALA 0.008495 0.41727 3.9548
22 1EDO NAP 0.002486 0.40708 3.9548
23 4K10 NI9 0.02576 0.40155 3.9548
24 2NVK NAP 0.01359 0.41302 4.51977
25 1PEA ACM 0.03747 0.41242 4.51977
26 1WTC ACP 0.01578 0.4078 4.51977
27 1TV5 A26 0.002342 0.40363 4.51977
28 4NAO AKG 0.04709 0.40211 4.51977
29 3TFC PEP 0.02568 0.40076 4.51977
30 1TV5 ORO 0.007847 0.40046 4.51977
31 3OIG NAD 0.001185 0.41142 5.08475
32 1D09 PAL 0.007313 0.40734 5.08475
33 2VVM PRO 0.02019 0.40513 5.08475
34 3EJ0 11X 0.02261 0.40543 5.64972
35 1T26 GBD 0.003239 0.4146 5.90062
36 1T26 NAI 0.003239 0.4146 5.90062
37 1Y75 NAG 0.005302 0.42602 5.9322
38 4WBD ADP 0.02712 0.41398 6.77966
39 3CEV ARG 0.01664 0.40475 6.77966
40 1TH8 ADP 0.01208 0.40646 6.89655
41 3I0O SMI 0.004595 0.4393 9.03955
42 4B1X LAB 0.0188 0.40434 9.03955
43 1RM4 NDP 0.001462 0.40862 9.49555
44 2XBP ATP 0.0002226 0.42288 9.73451
45 1Q11 TYE 0.006955 0.42587 10.7345
46 3U1T MLI 0.01789 0.42286 11.2994
47 1EXB NDP 0.001754 0.41313 11.6505
48 4NTX AMR 0.02136 0.40654 11.8644
49 2YIV NBN 0.04693 0.40218 11.8644
50 4GO7 THR 0.01359 0.40433 12.4294
51 4G4S LDZ 0.00227 0.4187 13.1707
52 1SS4 CIT 0.01273 0.44646 14.3791
53 1Y1A GSH 0.04171 0.433 16.3842
54 1I2B USQ 0.002292 0.42931 16.9492
55 1I2B NAD 0.002292 0.42931 16.9492
56 1I2B UPG 0.002292 0.42931 16.9492
57 1KTC NGA 0.007444 0.42457 17.5141
58 1U5R ATP 0.008118 0.40171 18.0791
59 1C1L GAL BGC 0.04872 0.40137 20.438
60 2JBH 5GP 0.01415 0.40778 20.904
61 2JC9 ADN 0.01211 0.41523 23.1638
62 3F81 STT 0.03503 0.41993 23.7288
63 2V5E SCR 0.004831 0.47413 28.7129
Pocket No.: 4; Query (leader) PDB : 3NBK; Ligand: PNS; 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: 3nbk.bio1) has 21 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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