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
37.3 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.76, Jaccard 0.73, H-bond role recall 0.45
Reason: no major geometry red flags detected
1 protein-contact clashes
57% of hydrophobic surface appears solvent-exposed (12/21 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 (-0.878 kcal/mol/HA)
✓ Good fit quality (FQ -8.63)
✓ Strong H-bond network (12 bonds)
✓ Good burial (65% SASA buried)
✓ Lipophilic contacts well-matched (65%)
✗ Very high strain energy (37.3 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (10)
Score
-28.091
kcal/mol
LE
-0.878
kcal/mol/HA
Fit Quality
-8.63
FQ (Leeson)
HAC
32
heavy atoms
MW
491
Da
LogP
2.90
cLogP
Interaction summary
HB 12
HY 8
PI 0
CLASH 1
⚠ Exposure 57%
Interaction summary
HB 12
HY 8
PI 0
CLASH 1
⚠ Exposure 57%
HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.
PI · π–π interactions
No pi · π–π interactions detected for this pose.
HY · Hydrophobic contacts
CLASH · Clashes
Partial hydrophobic solvent exposure
57% of hydrophobic surface appears solvent-exposed (12/21 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 21
Buried (contacted) 9
Exposed 12
LogP 2.9
H-bonds 12
Exposed fragments:
phenyl (4/6 atoms exposed)phenyl (4/5 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (2 atoms exposed)
| Final rank | 5.248 | Score | -28.091 |
|---|---|---|---|
| Inter norm | -0.984 | Intra norm | 0.107 |
| Top1000 | no | Excluded | no |
| Contacts | 17 | H-bonds | 12 |
| Artifact reason | geometry warning; 10 clashes; 4 protein clashes; high strain Δ 37.2 | ||
| Residues |
ALA24
ALA40
ASN41
GLN42
GLU21
GLU73
GLY23
GLY25
LEU130
LEU39
LYS127
LYS26
PHE38
SER22
SER27
SER28
THR69
| ||
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 | 16 | Native recall | 0.76 |
| Jaccard | 0.73 | RMSD | - |
| HB strict | 6 | Strict recall | 0.40 |
| HB same residue+role | 5 | HB role recall | 0.45 |
| HB same residue | 6 | HB residue recall | 0.55 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 388 | 1.6739574789448688 | -0.785498 | -20.7679 | 3 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 470 | 2.14944625408721 | -0.848107 | -27.8128 | 4 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 410 | 3.2339066525278364 | -0.799953 | -23.8187 | 9 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 419 | 3.676646703013552 | -0.584824 | -21.5311 | 5 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 403 | 5.248144074796463 | -0.984439 | -28.0906 | 12 | 17 | 16 | 0.76 | 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
-28.091kcal/mol
Ligand efficiency (LE)
-0.8778kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.633
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
32HA
Physicochemical properties
Molecular weight
490.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.90
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
37.26kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-113.93kcal/mol
Minimised FF energy
-151.19kcal/mol
SASA & burial
✓ computed
SASA (unbound)
733.1Ų
Total solvent-accessible surface area of free ligand
BSA total
475.3Ų
Buried surface area upon binding
BSA apolar
307.7Ų
Hydrophobic contacts buried
BSA polar
167.6Ų
Polar contacts buried
Fraction buried
64.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
64.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1371.2Ų
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
528.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)