Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Promising
SASA cached
Promising and worth follow-up
Binding strong
Geometry high
Native strong
SASA done
Strain ΔE
17.3 kcal/mol
Protein clashes
1
Internal clashes
2
Native overlap
contact recall 0.58, Jaccard 0.55, H-bond role recall 0.20
Reason: no major geometry red flags detected
1 protein-contact clashes
35% of hydrophobic surface appears solvent-exposed (7/20 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-0.715 kcal/mol/HA)
✓ Good fit quality (FQ -6.90)
✓ Deep burial (68% SASA buried)
✓ Lipophilic contacts well-matched (65%)
✗ Moderate strain (17.3 kcal/mol)
✗ Geometry warnings
✗ Minor protein-contact clashes (2)
✗ Internal clashes (7)
Score
-21.458
kcal/mol
LE
-0.715
kcal/mol/HA
Fit Quality
-6.90
FQ (Leeson)
HAC
30
heavy atoms
MW
458
Da
LogP
4.80
cLogP
Interaction summary
HB 1
HY 13
PI 1
CLASH 2
⚠ Exposure 35%
Interaction summary
HB 1
HY 13
PI 1
CLASH 2
⚠ Exposure 35%
Partial hydrophobic solvent exposure
35% of hydrophobic surface appears solvent-exposed (7/20 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 20
Buried (contacted) 13
Exposed 7
LogP 4.8
H-bonds 1
Exposed fragments:
phenyl (6/6 atoms exposed)aliphatic chain/group (1 atom exposed)
| Final rank | 0.343 | Score | -21.458 |
|---|---|---|---|
| Inter norm | -0.808 | Intra norm | 0.093 |
| Top1000 | no | Excluded | no |
| Contacts | 12 | H-bonds | 1 |
| Artifact reason | geometry warning; 7 clashes; 2 protein contact clashes; 2 cofactor-context clashes | ||
| Residues |
ARG17
ASP232
HIS241
LEU188
LEU226
LEU229
MET233
NDP302
PHE113
TYR191
TYR194
VAL230
| ||
Protein summary
308 residues
| Protein target | T04 | Atoms | 4210 |
|---|---|---|---|
| Residues | 308 | Chains | 3 |
| Residue summary | LEU:494; ALA:421; ARG:384; VAL:368; THR:295; TYR:231; SER:198; PRO:196; ILE:190; LYS:176; ASN:154; GLU:150; GLY:126; PHE:120; HIS:119; ASP:108 | ||
Receptor context
1 kept / 0 excluded
Receptor context filtering: interactions and SASA are computed against protein atoms plus allowed cofactors/ions. Native ligand-like HETATM partners are excluded from scoring.
Kept context 1
Excluded HETATM 0
Kept cofactors / ions
A:NDP302
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 7PXX | Contacts | 19 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ARG17
ASP181
GLY225
HIS241
LEU188
LEU226
LEU229
LYS198
MET233
NDP302
PHE113
PRO115
SER111
SER112
SER227
TYR191
TYR194
VAL230
ARG287
| ||
| Current overlap | 11 | Native recall | 0.58 |
| Jaccard | 0.55 | RMSD | - |
| HB strict | 1 | Strict recall | 0.17 |
| HB same residue+role | 1 | HB role recall | 0.20 |
| HB same residue | 1 | HB residue recall | 0.20 |
HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.
PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.
HY · Hydrophobic contacts
CLASH · Clashes
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 638 | 0.34325018158882725 | -0.807998 | -21.4581 | 1 | 12 | 11 | 0.58 | 0.20 | - | no | Current |
| 623 | 0.39759002964385937 | -0.907597 | -28.7047 | 4 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 626 | 1.1227923024226714 | -1.1074 | -32.2501 | 5 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 626 | 1.1240171034297752 | -0.831029 | -27.0616 | 5 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 630 | 1.7563715265578972 | -0.846368 | -25.076 | 4 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 646 | 2.8590489487856874 | -0.784314 | -23.0842 | 6 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 639 | 3.474974056717497 | -0.915663 | -28.6397 | 5 | 9 | 0 | 0.00 | 0.00 | - | no | Open |
| 649 | 3.8018158212879913 | -0.815353 | -24.1731 | 5 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-21.458kcal/mol
Ligand efficiency (LE)
-0.7153kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.900
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
30HA
Physicochemical properties
Molecular weight
457.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.80
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
17.32kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
9.77kcal/mol
Minimised FF energy
-7.55kcal/mol
SASA & burial
✓ computed
SASA (unbound)
720.4Ų
Total solvent-accessible surface area of free ligand
BSA total
486.6Ų
Buried surface area upon binding
BSA apolar
314.9Ų
Hydrophobic contacts buried
BSA polar
171.6Ų
Polar contacts buried
Fraction buried
67.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
64.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1614.2Ų
SASA_nonpolar(complex) − SASA_nonpolar(receptor) − SASA_nonpolar(ligand free). Negative = non-polar surface buried upon binding. Requires full polarity-decomposed SASA computation.
Receptor non-polar SASA
2179.4Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
1064.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)