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
21.6 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.95, Jaccard 0.95, H-bond role recall 0.55
Reason: no major geometry red flags detected
1 protein-contact clashes
45% of hydrophobic surface appears solvent-exposed (9/20 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 (-1.246 kcal/mol/HA)
✓ Good fit quality (FQ -11.90)
✓ Strong H-bond network (8 bonds)
✓ Deep burial (81% SASA buried)
✓ Lipophilic contacts well-matched (68%)
✗ High strain energy (21.6 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (9)
Score
-36.140
kcal/mol
LE
-1.246
kcal/mol/HA
Fit Quality
-11.90
FQ (Leeson)
HAC
29
heavy atoms
MW
425
Da
LogP
4.23
cLogP
Interaction summary
HB 8
HY 14
PI 2
CLASH 1
⚠ Exposure 45%
Interaction summary
HB 8
HY 14
PI 2
CLASH 1
⚠ Exposure 45%
Partial hydrophobic solvent exposure
45% of hydrophobic surface appears solvent-exposed (9/20 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 20
Buried (contacted) 11
Exposed 9
LogP 4.23
H-bonds 8
Exposed fragments:
phenyl (6/6 atoms exposed)phenyl (3/5 atoms exposed)aliphatic chain/group (2 atoms exposed)
| Final rank | 2.453 | Score | -36.140 |
|---|---|---|---|
| Inter norm | -1.193 | Intra norm | -0.053 |
| Top1000 | no | Excluded | no |
| Contacts | 20 | H-bonds | 8 |
| Artifact reason | geometry warning; 9 clashes; 2 protein clashes; moderate strain Δ 21.6 | ||
| Residues |
ALA158
ALA24
ALA40
ASN126
ASN41
ASP129
GLN42
GLU73
GLY23
GLY25
LEU130
LEU39
LYS127
LYS159
LYS26
PHE38
SER157
SER22
SER27
SER28
| ||
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 | ||
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 | 20 | Native recall | 0.95 |
| Jaccard | 0.95 | RMSD | - |
| HB strict | 6 | Strict recall | 0.40 |
| HB same residue+role | 6 | HB role recall | 0.55 |
| HB same residue | 6 | HB residue recall | 0.55 |
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
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
-36.140kcal/mol
Ligand efficiency (LE)
-1.2462kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-11.896
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
29HA
Physicochemical properties
Molecular weight
424.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.23
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
21.58kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
80.69kcal/mol
Minimised FF energy
59.10kcal/mol
SASA & burial
✓ computed
SASA (unbound)
651.6Ų
Total solvent-accessible surface area of free ligand
BSA total
526.2Ų
Buried surface area upon binding
BSA apolar
358.2Ų
Hydrophobic contacts buried
BSA polar
168.0Ų
Polar contacts buried
Fraction buried
80.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
68.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1325.5Ų
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
1368.5Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
511.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)