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
26.5 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.95, Jaccard 0.91, H-bond role recall 0.36
Reason: no major geometry red flags detected
2 protein-contact clashes
38% of hydrophobic surface appears solvent-exposed (8/21 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 (-0.937 kcal/mol/HA)
✓ Good fit quality (FQ -9.04)
✓ Strong H-bond network (7 bonds)
✓ Deep burial (81% SASA buried)
✓ Lipophilic contacts well-matched (71%)
✗ High strain energy (26.5 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (10)
Score
-28.106
kcal/mol
LE
-0.937
kcal/mol/HA
Fit Quality
-9.04
FQ (Leeson)
HAC
30
heavy atoms
MW
438
Da
LogP
4.30
cLogP
Interaction summary
HB 7
HY 9
PI 1
CLASH 2
⚠ Exposure 38%
Interaction summary
HB 7
HY 9
PI 1
CLASH 2
⚠ Exposure 38%
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
Partial hydrophobic solvent exposure
38% of hydrophobic surface appears solvent-exposed (8/21 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 21
Buried (contacted) 13
Exposed 8
LogP 4.3
H-bonds 7
Exposed fragments:
phenyl (6/6 atoms exposed)aliphatic chain/group (2 atoms exposed)
| Final rank | 4.132 | Score | -28.106 |
|---|---|---|---|
| Inter norm | -1.202 | Intra norm | 0.265 |
| Top1000 | no | Excluded | no |
| Contacts | 21 | H-bonds | 7 |
| Artifact reason | geometry warning; 10 clashes; 3 protein clashes; moderate strain Δ 26.5 | ||
| Residues |
ALA158
ALA24
ALA40
ASN126
ASN41
ASP129
GLN42
GLU73
GLY23
GLY25
LEU130
LEU39
LYS127
LYS159
LYS26
PHE38
SER157
SER22
SER27
SER28
THR44
| ||
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 | 0.91 | RMSD | - |
| HB strict | 6 | Strict recall | 0.40 |
| 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
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 140 | 1.2028312903859626 | -0.957414 | -21.2812 | 6 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 151 | 2.739277308262385 | -0.745148 | -18.7035 | 7 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 144 | 2.882137024749568 | -0.650399 | -18.4118 | 4 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 132 | 2.9987766312849193 | -0.899344 | -21.0706 | 4 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 88 | 4.131968372363812 | -1.20215 | -28.1064 | 7 | 21 | 20 | 0.95 | 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
-28.106kcal/mol
Ligand efficiency (LE)
-0.9369kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.037
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
30HA
Physicochemical properties
Molecular weight
437.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.30
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
26.47kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-48.37kcal/mol
Minimised FF energy
-74.84kcal/mol
SASA & burial
✓ computed
SASA (unbound)
714.9Ų
Total solvent-accessible surface area of free ligand
BSA total
576.1Ų
Buried surface area upon binding
BSA apolar
409.8Ų
Hydrophobic contacts buried
BSA polar
166.3Ų
Polar contacts buried
Fraction buried
80.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
71.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1379.5Ų
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
532.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)