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
18.6 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.81, Jaccard 0.65, H-bond role recall 0.09
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.962 kcal/mol/HA)
✓ Good fit quality (FQ -9.46)
✓ Good H-bonds (5 bonds)
✓ Deep burial (81% SASA buried)
✓ Lipophilic contacts well-matched (99%)
✗ Moderate strain (18.6 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (16)
Score
-30.795
kcal/mol
LE
-0.962
kcal/mol/HA
Fit Quality
-9.46
FQ (Leeson)
HAC
32
heavy atoms
MW
427
Da
LogP
4.18
cLogP
Final rank
2.4078
rank score
Inter norm
-1.096
normalised
Contacts
22
H-bonds 5
Interaction summary
HBD 4
HBA 1
HY 3
PI 1
CLASH 1
Interaction summary
HBD 4
HBA 1
HY 3
PI 1
CLASH 1
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 5.
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 | 17 | Native recall | 0.81 |
| Jaccard | 0.65 | RMSD | - |
| HB strict | 1 | Strict recall | 0.07 |
| HB same residue+role | 1 | HB role recall | 0.09 |
| HB same residue | 2 | HB residue recall | 0.18 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 160 | 2.4078393581606727 | -1.09573 | -30.7953 | 5 | 22 | 17 | 0.81 | 0.09 | - | no | Current |
| 219 | 3.7484771026539887 | -0.732981 | -19.9757 | 6 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-30.795kcal/mol
Ligand efficiency (LE)
-0.9624kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.464
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
32HA
Physicochemical properties
Molecular weight
426.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.18
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
18.64kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
86.43kcal/mol
Minimised FF energy
67.79kcal/mol
SASA & burial
✓ computed
SASA (unbound)
741.7Ų
Total solvent-accessible surface area of free ligand
BSA total
599.3Ų
Buried surface area upon binding
BSA apolar
593.8Ų
Hydrophobic contacts buried
BSA polar
5.5Ų
Polar contacts buried
Fraction buried
80.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
99.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1577.3Ų
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
527.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)