Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
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Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Promising
SASA cached
Promising and worth follow-up
Binding strong
Geometry medium
Native strong
SASA done
Strain ΔE
11.6 kcal/mol
Protein clashes
1
Internal clashes
5
Native overlap
contact recall 0.53, Jaccard 0.53, H-bond role recall 0.60
Reason: no major geometry red flags detected
1 protein-contact clashes
5 intramolecular clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.969 kcal/mol/HA)
✓ Good fit quality (FQ -13.57)
✓ Good H-bonds (4 bonds)
✓ Deep burial (89% SASA buried)
✓ Lipophilic contacts well-matched (74%)
✗ Moderate strain (11.6 kcal/mol)
✗ Geometry warnings
Score
-25.593
kcal/mol
LE
-1.969
kcal/mol/HA
Fit Quality
-13.57
FQ (Leeson)
HAC
13
heavy atoms
MW
329
Da
LogP
1.60
cLogP
Interaction summary
HB 4
HY 11
PI 1
CLASH 5
Interaction summary
HB 4
HY 11
PI 1
CLASH 5
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
| Final rank | 0.164 | Score | -25.593 |
|---|---|---|---|
| Inter norm | -1.944 | Intra norm | -0.025 |
| Top1000 | no | Excluded | no |
| Contacts | 10 | H-bonds | 4 |
| Artifact reason | geometry warning; 4 clashes; 1 protein clash; 6 cofactor-context clashes | ||
| Residues |
ARG17
HIS241
LEU226
LEU229
MET233
NDP302
PHE113
SER111
TYR194
VAL230
| ||
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 | 10 | Native recall | 0.53 |
| Jaccard | 0.53 | RMSD | - |
| HB strict | 3 | Strict recall | 0.50 |
| HB same residue+role | 3 | HB role recall | 0.60 |
| HB same residue | 3 | HB residue recall | 0.60 |
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
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 268 | 0.1641627853983935 | -1.94408 | -25.5933 | 4 | 10 | 10 | 0.53 | 0.60 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-25.593kcal/mol
Ligand efficiency (LE)
-1.9687kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-13.570
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
13HA
Physicochemical properties
Molecular weight
329.0Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.60
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
11.57kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-72.14kcal/mol
Minimised FF energy
-83.71kcal/mol
SASA & burial
✓ computed
SASA (unbound)
420.4Ų
Total solvent-accessible surface area of free ligand
BSA total
373.5Ų
Buried surface area upon binding
BSA apolar
274.7Ų
Hydrophobic contacts buried
BSA polar
98.8Ų
Polar contacts buried
Fraction buried
88.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
73.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1453.0Ų
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
1043.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)