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
Promising but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA done
Strain ΔE
37.8 kcal/mol
Protein clashes
6
Internal clashes
6
Native overlap
contact recall 0.67, Jaccard 0.52, H-bond role recall 0.45
Reason: 6 internal clashes
6 protein-contact clashes
6 intramolecular clashes
55% of hydrophobic surface appears solvent-exposed (12/22 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 (-0.673 kcal/mol/HA)
✓ Good fit quality (FQ -6.62)
✓ Strong H-bond network (7 bonds)
✓ Deep burial (78% SASA buried)
✓ Lipophilic contacts well-matched (73%)
✗ Very high strain energy (37.8 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (11)
Score
-21.537
kcal/mol
LE
-0.673
kcal/mol/HA
Fit Quality
-6.62
FQ (Leeson)
HAC
32
heavy atoms
MW
467
Da
LogP
4.27
cLogP
Final rank
4.0168
rank score
Inter norm
-1.046
normalised
Contacts
20
H-bonds 9
Interaction summary
HBA 7
HY 3
PI 1
CLASH 6
Interaction summary
HBA 7
HY 3
PI 1
CLASH 6
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 6.
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 | 14 | Native recall | 0.67 |
| Jaccard | 0.52 | RMSD | - |
| HB strict | 6 | Strict recall | 0.40 |
| HB same residue+role | 5 | HB role recall | 0.45 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 141 | 0.9555486624199901 | -1.06796 | -27.3113 | 7 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 150 | 2.692334134189634 | -0.857115 | -24.5254 | 7 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 139 | 3.5857653823295363 | -0.813301 | -22.4093 | 5 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 87 | 4.016832404152804 | -1.04643 | -21.5366 | 9 | 20 | 14 | 0.67 | 0.45 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-21.537kcal/mol
Ligand efficiency (LE)
-0.6730kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.619
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
32HA
Physicochemical properties
Molecular weight
466.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.27
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
37.78kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
63.38kcal/mol
Minimised FF energy
25.59kcal/mol
SASA & burial
✓ computed
SASA (unbound)
765.0Ų
Total solvent-accessible surface area of free ligand
BSA total
595.3Ų
Buried surface area upon binding
BSA apolar
433.7Ų
Hydrophobic contacts buried
BSA polar
161.7Ų
Polar contacts buried
Fraction buried
77.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
72.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1392.7Ų
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
542.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)