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
21.2 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.71, Jaccard 0.60, H-bond role recall 0.36
Reason: no major geometry red flags detected
3 protein-contact clashes
3 intramolecular clashes
45% of hydrophobic surface appears solvent-exposed (10/22 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 (-1.012 kcal/mol/HA)
✓ Good fit quality (FQ -9.76)
✓ Strong H-bond network (6 bonds)
✓ Deep burial (83% SASA buried)
✓ Lipophilic contacts well-matched (80%)
✗ High strain energy (21.2 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (14)
Score
-30.348
kcal/mol
LE
-1.012
kcal/mol/HA
Fit Quality
-9.76
FQ (Leeson)
HAC
30
heavy atoms
MW
399
Da
LogP
2.84
cLogP
Final rank
3.5056
rank score
Inter norm
-1.069
normalised
Contacts
19
H-bonds 8
Interaction summary
HBD 1
HBA 5
HY 2
PI 1
CLASH 3
Interaction summary
HBD 1
HBA 5
HY 2
PI 1
CLASH 3
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. 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: permissive.
| 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 | 15 | Native recall | 0.71 |
| Jaccard | 0.60 | RMSD | - |
| HB strict | 5 | Strict recall | 0.33 |
| HB same residue+role | 4 | HB role recall | 0.36 |
| HB same residue | 5 | HB residue recall | 0.45 |
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
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 15 | 2.183193883230364 | -1.11694 | -33.1782 | 5 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 36 | 2.981557588522365 | -1.12397 | -31.1384 | 5 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 12 | 3.33297460468041 | -0.731541 | -21.4791 | 7 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 5 | 3.5055674267181955 | -1.06865 | -30.3475 | 8 | 19 | 15 | 0.71 | 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
-30.348kcal/mol
Ligand efficiency (LE)
-1.0116kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.758
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
30HA
Physicochemical properties
Molecular weight
399.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.84
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
21.16kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
58.36kcal/mol
Minimised FF energy
37.20kcal/mol
SASA & burial
✓ computed
SASA (unbound)
663.5Ų
Total solvent-accessible surface area of free ligand
BSA total
550.3Ų
Buried surface area upon binding
BSA apolar
442.3Ų
Hydrophobic contacts buried
BSA polar
108.0Ų
Polar contacts buried
Fraction buried
82.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
80.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1409.3Ų
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
505.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)