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
28.0 kcal/mol
Protein clashes
8
Internal clashes
8
Native overlap
contact recall 0.86, Jaccard 0.69, H-bond role recall 0.55
Reason: 8 internal clashes
8 protein-contact clashes
8 intramolecular clashes
61% of hydrophobic surface is solvent-exposed (11/18 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.185 kcal/mol/HA)
✓ Good fit quality (FQ -11.31)
✓ Strong H-bond network (10 bonds)
✓ Deep burial (91% SASA buried)
✓ Lipophilic contacts well-matched (76%)
✗ High strain energy (28.0 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (10)
Score
-34.356
kcal/mol
LE
-1.185
kcal/mol/HA
Fit Quality
-11.31
FQ (Leeson)
HAC
29
heavy atoms
MW
442
Da
LogP
2.15
cLogP
Final rank
4.4388
rank score
Inter norm
-1.119
normalised
Contacts
23
H-bonds 12
Interaction summary
HBD 1
HBA 9
HY 2
PI 1
CLASH 8
Interaction summary
HBD 1
HBA 9
HY 2
PI 1
CLASH 8
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 9.
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 | 18 | Native recall | 0.86 |
| Jaccard | 0.69 | RMSD | - |
| HB strict | 7 | Strict recall | 0.47 |
| HB same residue+role | 6 | HB role recall | 0.55 |
| HB same residue | 7 | HB residue recall | 0.64 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 577 | 1.8456609172943859 | -0.971588 | -30.9573 | 7 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 575 | 3.1434800879401728 | -0.673821 | -23.122 | 5 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 580 | 3.3205617867349813 | -0.862683 | -25.6873 | 9 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 553 | 3.6793675491034383 | -1.17348 | -34.8877 | 8 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 580 | 4.438807899427868 | -1.11879 | -34.3561 | 12 | 23 | 18 | 0.86 | 0.55 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-34.356kcal/mol
Ligand efficiency (LE)
-1.1847kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-11.309
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
29HA
Physicochemical properties
Molecular weight
441.9Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.15
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
27.99kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
77.23kcal/mol
Minimised FF energy
49.24kcal/mol
SASA & burial
✓ computed
SASA (unbound)
674.8Ų
Total solvent-accessible surface area of free ligand
BSA total
614.8Ų
Buried surface area upon binding
BSA apolar
466.6Ų
Hydrophobic contacts buried
BSA polar
148.1Ų
Polar contacts buried
Fraction buried
91.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
75.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1358.8Ų
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
521.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)