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 high
Native strong
SASA done
Strain ΔE
24.5 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.86, Jaccard 0.67, H-bond role recall 0.36
Reason: no major geometry red flags detected
1 protein-contact clashes
46% of hydrophobic surface appears solvent-exposed (13/28 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 (-0.934 kcal/mol/HA)
✓ Good fit quality (FQ -9.34)
✓ Good H-bonds (5 bonds)
✓ Deep burial (93% SASA buried)
✓ Lipophilic contacts well-matched (91%)
✗ High strain energy (24.5 kcal/mol)
✗ Geometry warnings
✗ Minor protein-contact clashes (4)
✗ Many internal clashes (14)
Score
-31.747
kcal/mol
LE
-0.934
kcal/mol/HA
Fit Quality
-9.34
FQ (Leeson)
HAC
34
heavy atoms
MW
449
Da
LogP
4.22
cLogP
Final rank
1.3545
rank score
Inter norm
-0.985
normalised
Contacts
24
H-bonds 6
Interaction summary
HBA 5
HY 5
PI 1
CLASH 1
Interaction summary
HBA 5
HY 5
PI 1
CLASH 1
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 4.
PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.
HY · Hydrophobic contacts
CLASH · Clashes
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | RAB5A | Contacts | 21 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ALA158
ALA24
ALA40
ASN126
ASN41
ASP129
GLN42
GLU21
GLU73
GLY23
GLY25
LEU130
LEU39
LYS127
LYS159
LYS26
PHE38
SER157
SER22
SER27
SER28
| ||
| Current overlap | 18 | Native recall | 0.86 |
| Jaccard | 0.67 | RMSD | - |
| HB strict | 5 | Strict recall | 0.33 |
| HB same residue+role | 4 | HB role recall | 0.36 |
| HB same residue | 4 | HB residue recall | 0.36 |
Protein summary
165 residues
| Protein target | T22 | Atoms | 2561 |
|---|---|---|---|
| Residues | 165 | Chains | 1 |
| Residue summary | LEU:363; LYS:242; ALA:231; ARG:214; ILE:190; GLU:180; VAL:144; SER:143; PHE:140; ASN:112; THR:112; TYR:105; GLN:102; ASP:96; GLY:77; TRP:48 | ||
All stored poses for this docking hit
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-31.747kcal/mol
Ligand efficiency (LE)
-0.9337kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.343
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
34HA
Physicochemical properties
Molecular weight
448.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.22
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
24.53kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
48.46kcal/mol
Minimised FF energy
23.93kcal/mol
SASA & burial
✓ computed
SASA (unbound)
735.5Ų
Total solvent-accessible surface area of free ligand
BSA total
681.1Ų
Buried surface area upon binding
BSA apolar
618.6Ų
Hydrophobic contacts buried
BSA polar
62.5Ų
Polar contacts buried
Fraction buried
92.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
90.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1530.8Ų
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
1368.5Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
496.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)