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
Weak
SASA cached
Weak or marginal quality
Binding strong
Geometry medium
Native strong
SASA done
Strain ΔE
18.2 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 0.76, Jaccard 0.65, H-bond role recall 0.36
Reason: no major geometry red flags detected
4 protein-contact clashes
4 intramolecular clashes
54% of hydrophobic surface appears solvent-exposed (15/28 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.732 kcal/mol/HA)
✓ Good fit quality (FQ -7.38)
✓ Strong H-bond network (7 bonds)
✓ Deep burial (68% SASA buried)
✓ Lipophilic contacts well-matched (90%)
✗ Moderate strain (18.2 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (20)
Score
-25.606
kcal/mol
LE
-0.732
kcal/mol/HA
Fit Quality
-7.38
FQ (Leeson)
HAC
35
heavy atoms
MW
465
Da
LogP
4.61
cLogP
Interaction summary
HB 7
HY 12
PI 2
CLASH 4
⚠ Exposure 53%
Interaction summary
HB 7
HY 12
PI 2
CLASH 4
⚠ Exposure 53%
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
Partial hydrophobic solvent exposure
54% of hydrophobic surface appears solvent-exposed (15/28 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 28
Buried (contacted) 13
Exposed 15
LogP 4.61
H-bonds 7
Exposed fragments:
phenyl (4/6 atoms exposed)phenyl (6/6 atoms exposed)phenyl (5/6 atoms exposed)aliphatic chain/group (2 atoms exposed)
| Final rank | 4.790 | Score | -25.606 |
|---|---|---|---|
| Inter norm | -0.725 | Intra norm | -0.007 |
| Top1000 | no | Excluded | no |
| Contacts | 16 | H-bonds | 7 |
| Artifact reason | geometry warning; 20 clashes; 2 protein clashes | ||
| Residues |
ALA15
ARG116
ARG140
ARG144
ASP13
CYS72
GLY73
HIS105
HIS14
HIS141
LEU101
SER46
THR117
THR74
TYR49
VAL97
| ||
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 6FXW | Contacts | 17 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ALA15
ARG116
ARG140
ARG144
ASN106
ASP13
CYS72
GLY73
GLY75
GLY77
HIS105
HIS14
HIS141
ILE76
LEU101
THR74
TYR49
| ||
| Current overlap | 13 | Native recall | 0.76 |
| Jaccard | 0.65 | RMSD | - |
| HB strict | 5 | Strict recall | 0.38 |
| HB same residue+role | 4 | HB role recall | 0.36 |
| HB same residue | 4 | HB residue recall | 0.36 |
Protein summary
155 residues
| Protein target | T10 | Atoms | 4590 |
|---|---|---|---|
| Residues | 155 | Chains | 1 |
| Residue summary | ILE:494; ARG:384; ALA:360; VAL:352; LEU:304; GLU:300; THR:280; MET:272; LYS:220; ASP:216; TYR:210; HIS:204; GLY:182; SER:176; GLN:170; ASN:140 | ||
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 646 | 1.3657698551883037 | -0.768602 | -26.4431 | 0 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 673 | 4.789953759320182 | -0.724768 | -25.6062 | 7 | 16 | 13 | 0.76 | 0.36 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-25.606kcal/mol
Ligand efficiency (LE)
-0.7316kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.379
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
35HA
Physicochemical properties
Molecular weight
464.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.61
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
18.18kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
102.66kcal/mol
Minimised FF energy
84.48kcal/mol
SASA & burial
✓ computed
SASA (unbound)
722.3Ų
Total solvent-accessible surface area of free ligand
BSA total
489.9Ų
Buried surface area upon binding
BSA apolar
443.4Ų
Hydrophobic contacts buried
BSA polar
46.5Ų
Polar contacts buried
Fraction buried
67.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
90.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2393.5Ų
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
2417.4Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
666.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)