Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Promising
SASA cached
Promising and worth follow-up
Binding strong
Geometry high
Native strong
SASA done
Strain ΔE
14.6 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.95, Jaccard 0.91, H-bond role recall 0.45
Reason: no major geometry red flags detected
1 protein-contact clashes
56% of hydrophobic surface appears solvent-exposed (9/16 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.452 kcal/mol/HA)
✓ Good fit quality (FQ -12.81)
✓ Strong H-bond network (10 bonds)
✓ Deep burial (88% SASA buried)
✓ Lipophilic contacts well-matched (75%)
✗ Moderate strain (14.6 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (6)
Score
-33.393
kcal/mol
LE
-1.452
kcal/mol/HA
Fit Quality
-12.81
FQ (Leeson)
HAC
23
heavy atoms
MW
353
Da
LogP
1.89
cLogP
Interaction summary
HB 10
HY 4
PI 1
CLASH 1
⚠ Exposure 56%
Interaction summary
HB 10
HY 4
PI 1
CLASH 1
⚠ Exposure 56%
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
56% of hydrophobic surface appears solvent-exposed (9/16 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 16
Buried (contacted) 7
Exposed 9
LogP 1.89
H-bonds 10
Exposed fragments:
phenyl (6/6 atoms exposed)aliphatic chain/group (3 atoms exposed)
| Final rank | 3.059 | Score | -33.393 |
|---|---|---|---|
| Inter norm | -1.489 | Intra norm | 0.037 |
| Top1000 | no | Excluded | no |
| Contacts | 21 | H-bonds | 10 |
| Artifact reason | geometry warning; 6 clashes; 3 protein clashes | ||
| 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 | 7 | Strict recall | 0.47 |
| HB same residue+role | 5 | HB role recall | 0.45 |
| HB same residue | 5 | HB residue recall | 0.45 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 554 | 0.2203022561644955 | -1.36019 | -30.3993 | 6 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 567 | 1.6542963930149828 | -1.18885 | -26.8787 | 5 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 573 | 2.71578287337706 | -1.10311 | -22.1924 | 4 | 19 | 1 | 0.05 | 0.00 | - | no | Open |
| 570 | 3.0587130104782503 | -1.48918 | -33.393 | 10 | 21 | 20 | 0.95 | 0.45 | - | no | Current |
| 552 | 3.4718491156602886 | -1.32651 | -28.7854 | 12 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 546 | 3.504691433720093 | -1.20709 | -25.4384 | 5 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 556 | 3.9343705953567754 | -1.06026 | -20.2148 | 13 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 582 | 4.168655656750893 | -1.04725 | -22.6406 | 14 | 17 | 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
-33.393kcal/mol
Ligand efficiency (LE)
-1.4519kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-12.814
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
23HA
Physicochemical properties
Molecular weight
352.8Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.89
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
14.60kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-60.26kcal/mol
Minimised FF energy
-74.86kcal/mol
SASA & burial
✓ computed
SASA (unbound)
584.0Ų
Total solvent-accessible surface area of free ligand
BSA total
517.0Ų
Buried surface area upon binding
BSA apolar
388.1Ų
Hydrophobic contacts buried
BSA polar
128.9Ų
Polar contacts buried
Fraction buried
88.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
75.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1310.8Ų
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
500.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)